Starting phenix.real_space_refine
on Wed Sep 17 05:17:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fnd_50590/09_2025/9fnd_50590.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fnd_50590/09_2025/9fnd_50590.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fnd_50590/09_2025/9fnd_50590.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fnd_50590/09_2025/9fnd_50590.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fnd_50590/09_2025/9fnd_50590.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fnd_50590/09_2025/9fnd_50590.map"
  }
  resolution = 4.0
  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=   0.001
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      12      5.16       5
     C    3057      2.51       5
     N     889      2.21       5
     O     956      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4914
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "X"
      Number of atoms: 2531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2531
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314}
    Chain: "Y"
      Number of atoms: 2383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2383
          Classifications: {'peptide': 317}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 296}
  Time building chain proxies: 1.65, per 1000 atoms: 0.34
  Number of scatterers: 4914
  At special positions: 0
  Unit cell: (97.65, 81.9, 108.675, 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      12     16.00
     O     956      8.00
     N     889      7.00
     C    3057      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: 0.41
  Conformation dependent library (CDL) restraints added in 182.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1206

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 6 sheets defined
      43.0% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'X' and resid 4 through 18
    Processing helix  chain 'X' and resid 24 through 32
    Processing helix  chain 'X' and resid 40 through 58
    Processing helix  chain 'X' and resid 79 through 84
      removed outlier: 3.565A  pdb=" N   ALA X  84 " --> pdb=" O   ARG X  80 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 91 through 102
    Processing helix  chain 'X' and resid 107 through 125
      removed outlier: 3.840A  pdb=" N   GLY X 125 " --> pdb=" O   LEU X 121 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 150 through 163
    Processing helix  chain 'X' and resid 235 through 245
      removed outlier: 3.554A  pdb=" N   ALA X 245 " --> pdb=" O   ARG X 241 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 262 through 268
      removed outlier: 3.508A  pdb=" N   GLN X 268 " --> pdb=" O   ALA X 264 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 291 through 303
      removed outlier: 3.821A  pdb=" N   TYR X 302 " --> pdb=" O   GLU X 298 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY X 303 " --> pdb=" O   ILE X 299 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 311 through 327
    Processing helix  chain 'Y' and resid 3 through 21
      removed outlier: 4.588A  pdb=" N   VAL Y  15 " --> pdb=" O   LEU Y  11 " (cutoff:3.500A)
      Proline residue:  Y  16  - end of helix
    Processing helix  chain 'Y' and resid 26 through 34
    Processing helix  chain 'Y' and resid 36 through 49
      removed outlier: 3.554A  pdb=" N   MET Y  49 " --> pdb=" O   ASP Y  45 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 85 through 100
    Processing helix  chain 'Y' and resid 107 through 123
    Processing helix  chain 'Y' and resid 141 through 153
    Processing helix  chain 'Y' and resid 217 through 223
      removed outlier: 4.090A  pdb=" N   ALA Y 221 " --> pdb=" O   PRO Y 217 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 250 through 255
      removed outlier: 3.924A  pdb=" N   TYR Y 254 " --> pdb=" O   TRP Y 250 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR Y 255 " --> pdb=" O   MET Y 251 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Y' and resid 250 through 255'
    Processing helix  chain 'Y' and resid 276 through 288
      removed outlier: 3.832A  pdb=" N   PHE Y 287 " --> pdb=" O   PHE Y 283 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLY Y 288 " --> pdb=" O   ILE Y 284 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 296 through 317
    Processing sheet with id=AA1, first strand: chain 'X' and resid 62 through 66
    Processing sheet with id=AA2, first strand: chain 'X' and resid 207 through 211
      removed outlier: 6.051A  pdb=" N   ARG X 194 " --> pdb=" O   THR X 190 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   THR X 190 " --> pdb=" O   ARG X 194 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   TYR X 196 " --> pdb=" O   VAL X 188 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   VAL X 188 " --> pdb=" O   TYR X 196 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   VAL X 198 " --> pdb=" O   TRP X 186 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'X' and resid 271 through 277
      removed outlier: 6.633A  pdb=" N   ARG X 254 " --> pdb=" O   LEU X 309 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Y' and resid 24 through 25
      removed outlier: 3.968A  pdb=" N   VAL Y  24 " --> pdb=" O   ILE Y  70 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 196 through 201
      removed outlier: 7.151A  pdb=" N   ASN Y 184 " --> pdb=" O   LEU Y 180 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   LEU Y 180 " --> pdb=" O   ASN Y 184 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   TYR Y 186 " --> pdb=" O   VAL Y 178 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   VAL Y 178 " --> pdb=" O   TYR Y 186 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   GLU Y 188 " --> pdb=" O   ILE Y 176 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLU Y 159 " --> pdb=" O   ASP Y 207 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   ASP Y 207 " --> pdb=" O   GLU Y 159 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   TYR Y 161 " --> pdb=" O   ILE Y 205 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE Y 205 " --> pdb=" O   TYR Y 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'Y' and resid 270 through 273
      removed outlier: 6.798A  pdb=" N   THR Y 241 " --> pdb=" O   LEU Y 294 " (cutoff:3.500A)

    243 hydrogen bonds defined for protein.
    699 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: 0.78

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1720
        1.34 -     1.46: 1006
        1.46 -     1.58: 2256
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 5002
  Sorted by residual:
  bond pdb=" C   PRO Y 218 "
       pdb=" N   PRO Y 219 "
    ideal  model  delta    sigma   weight residual
    1.329  1.341 -0.011 1.18e-02 7.18e+03 9.42e-01
  bond pdb=" CA  ASP Y 135 "
       pdb=" C   ASP Y 135 "
    ideal  model  delta    sigma   weight residual
    1.522  1.533 -0.011 1.14e-02 7.69e+03 9.22e-01
  bond pdb=" CA  ASP Y 135 "
       pdb=" CB  ASP Y 135 "
    ideal  model  delta    sigma   weight residual
    1.529  1.515  0.014 1.54e-02 4.22e+03 8.66e-01
  bond pdb=" N   PRO Y 219 "
       pdb=" CA  PRO Y 219 "
    ideal  model  delta    sigma   weight residual
    1.465  1.482 -0.017 2.03e-02 2.43e+03 7.35e-01
  bond pdb=" CB  PRO X 221 "
       pdb=" CG  PRO X 221 "
    ideal  model  delta    sigma   weight residual
    1.492  1.527 -0.035 5.00e-02 4.00e+02 4.85e-01
  ... (remaining 4997 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 6613
        0.98 -     1.95: 151
        1.95 -     2.93: 36
        2.93 -     3.91: 15
        3.91 -     4.88: 5
  Bond angle restraints: 6820
  Sorted by residual:
  angle pdb=" N   PRO Y 218 "
        pdb=" CA  PRO Y 218 "
        pdb=" C   PRO Y 218 "
      ideal   model   delta    sigma   weight residual
     110.70  113.82   -3.12 1.22e+00 6.72e-01 6.53e+00
  angle pdb=" CA  PRO Y 218 "
        pdb=" C   PRO Y 218 "
        pdb=" N   PRO Y 219 "
      ideal   model   delta    sigma   weight residual
     117.93  120.45   -2.52 1.20e+00 6.94e-01 4.40e+00
  angle pdb=" N   PRO Y 219 "
        pdb=" CA  PRO Y 219 "
        pdb=" C   PRO Y 219 "
      ideal   model   delta    sigma   weight residual
     110.70  113.24   -2.54 1.22e+00 6.72e-01 4.35e+00
  angle pdb=" N   GLU Y 269 "
        pdb=" CA  GLU Y 269 "
        pdb=" C   GLU Y 269 "
      ideal   model   delta    sigma   weight residual
     109.65  112.79   -3.14 1.56e+00 4.11e-01 4.06e+00
  angle pdb=" CA  PRO Y 219 "
        pdb=" C   PRO Y 219 "
        pdb=" N   PRO Y 220 "
      ideal   model   delta    sigma   weight residual
     117.93  120.08   -2.15 1.20e+00 6.94e-01 3.22e+00
  ... (remaining 6815 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.44: 2829
       11.44 -    22.88: 158
       22.88 -    34.33: 36
       34.33 -    45.77: 15
       45.77 -    57.21: 2
  Dihedral angle restraints: 3040
    sinusoidal: 1173
      harmonic: 1867
  Sorted by residual:
  dihedral pdb=" CA  CYS Y 268 "
           pdb=" C   CYS Y 268 "
           pdb=" N   GLU Y 269 "
           pdb=" CA  GLU Y 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.40  -15.60     0      5.00e+00 4.00e-02 9.73e+00
  dihedral pdb=" CA  GLU X  63 "
           pdb=" CB  GLU X  63 "
           pdb=" CG  GLU X  63 "
           pdb=" CD  GLU X  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.79  -57.21     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" CA  LEU Y  11 "
           pdb=" CB  LEU Y  11 "
           pdb=" CG  LEU Y  11 "
           pdb=" CD1 LEU Y  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.58   45.42     3      1.50e+01 4.44e-03 8.17e+00
  ... (remaining 3037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 491
       0.026 -    0.052: 177
       0.052 -    0.078: 64
       0.078 -    0.104: 42
       0.104 -    0.130: 16
  Chirality restraints: 790
  Sorted by residual:
  chirality pdb=" CA  ILE X 255 "
            pdb=" N   ILE X 255 "
            pdb=" C   ILE X 255 "
            pdb=" CB  ILE X 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  PRO Y  22 "
            pdb=" N   PRO Y  22 "
            pdb=" C   PRO Y  22 "
            pdb=" CB  PRO Y  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.53e-01
  chirality pdb=" CA  ILE Y  70 "
            pdb=" N   ILE Y  70 "
            pdb=" C   ILE Y  70 "
            pdb=" CB  ILE Y  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.40e-01
  ... (remaining 787 not shown)

  Planarity restraints: 904
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO Y 219 "    0.031 5.00e-02 4.00e+02   4.68e-02 3.50e+00
        pdb=" N   PRO Y 220 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 220 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 220 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO Y 217 "    0.025 5.00e-02 4.00e+02   3.83e-02 2.35e+00
        pdb=" N   PRO Y 218 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 218 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 218 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO Y 218 "   -0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO Y 219 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 219 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 219 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 901 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1285
        2.81 -     3.33: 4554
        3.33 -     3.86: 7777
        3.86 -     4.38: 8083
        4.38 -     4.90: 14578
  Nonbonded interactions: 36277
  Sorted by model distance:
  nonbonded pdb=" OG  SER X 272 "
            pdb=" OE1 GLU X 283 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OD1 ASN X  11 "
            pdb=" OH  TYR Y  55 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   SER Y   2 "
            pdb=" OG  SER Y   5 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" N   SER X 107 "
            pdb=" OE2 GLU X 150 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" O   VAL Y  66 "
            pdb=" OG1 THR Y  69 "
     model   vdw
     2.396 3.040
  ... (remaining 36272 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.190
  Find NCS groups from input model:        0.030
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
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      :  0.002   0.035   5002  Z= 0.091
  Angle     :  0.423   4.884   6820  Z= 0.229
  Chirality :  0.038   0.130    790
  Planarity :  0.004   0.047    904
  Dihedral  :  8.173  57.210   1834
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  4.34 %
    Favored  : 95.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.35), residues: 643
  helix:  2.84 (0.32), residues: 274
  sheet:  0.00 (0.47), residues: 111
  loop : -0.48 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X 122 
 TYR   0.006   0.001   TYR Y 186 
 PHE   0.007   0.001   PHE Y 231 
 TRP   0.004   0.001   TRP Y 250 
 HIS   0.001   0.000   HIS X 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 ( 5002)
  covalent geometry    : angle       0.42341 ( 6820)
  hydrogen bonds       : bond        0.11312 (  243)
  hydrogen bonds       : angle       4.70224 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.6563 (tpt) cc_final: 0.6105 (tpp)
REVERT: X   37 ASP cc_start: 0.6998 (m-30) cc_final: 0.6544 (t0)
REVERT: X   76 TYR cc_start: 0.7424 (m-10) cc_final: 0.7040 (m-10)
REVERT: X  106 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8001 (mm110)
REVERT: X  120 LYS cc_start: 0.8308 (mttp) cc_final: 0.8062 (mttt)
REVERT: X  168 PHE cc_start: 0.8517 (p90) cc_final: 0.8063 (p90)
REVERT: X  274 PRO cc_start: 0.6789 (Cg_exo) cc_final: 0.5881 (Cg_endo)
REVERT: X  298 GLU cc_start: 0.9194 (tt0) cc_final: 0.8957 (mt-10)
REVERT: X  321 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.7679 (mtt90)
REVERT: Y   46 GLN cc_start: 0.8826 (tp40) cc_final: 0.8319 (tm-30)
REVERT: Y  117 LYS cc_start: 0.8239 (mttp) cc_final: 0.7696 (mptt)
REVERT: Y  161 TYR cc_start: 0.8211 (t80) cc_final: 0.6904 (t80)
REVERT: Y  254 TYR cc_start: 0.6264 (m-80) cc_final: 0.5016 (t80)
REVERT: Y  287 PHE cc_start: 0.7724 (m-80) cc_final: 0.6744 (m-80)
REVERT: Y  305 GLN cc_start: 0.8308 (mt0) cc_final: 0.8013 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1126
  time to fit residues: 19.7128
Evaluate side-chains
  86 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0270
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0470
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0010
   overall best weight:    0.3342

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

Flipped N/Q/H residues before XYZ refinement:
X 191 HIS
Y  19 GLN
Y  46 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.184226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.144041 restraints weight = 8261.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.142207 restraints weight = 13024.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.143880 restraints weight = 10903.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.144164 restraints weight = 7296.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.144820 restraints weight = 7150.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5002  Z= 0.126
  Angle     :  0.547   5.738   6820  Z= 0.285
  Chirality :  0.042   0.203    790
  Planarity :  0.005   0.053    904
  Dihedral  :  3.553  17.747    725
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 11.24 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.34), residues: 643
  helix:  2.43 (0.31), residues: 277
  sheet: -0.03 (0.48), residues: 109
  loop : -0.42 (0.39), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG Y 302 
 TYR   0.022   0.002   TYR X 302 
 PHE   0.023   0.002   PHE Y 252 
 TRP   0.005   0.001   TRP Y 250 
 HIS   0.002   0.001   HIS X 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5002)
  covalent geometry    : angle       0.54729 ( 6820)
  hydrogen bonds       : bond        0.03371 (  243)
  hydrogen bonds       : angle       4.19111 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.6900 (tpt) cc_final: 0.6216 (tpp)
REVERT: X   12 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7875 (tt)
REVERT: X   37 ASP cc_start: 0.7498 (m-30) cc_final: 0.6937 (t0)
REVERT: X   76 TYR cc_start: 0.7619 (m-10) cc_final: 0.7041 (m-80)
REVERT: X  120 LYS cc_start: 0.8518 (mttp) cc_final: 0.8251 (mttt)
REVERT: X  167 GLN cc_start: 0.7708 (pm20) cc_final: 0.7500 (pm20)
REVERT: X  295 LEU cc_start: 0.8698 (tt) cc_final: 0.8339 (tt)
REVERT: Y   62 ASP cc_start: 0.7184 (t0) cc_final: 0.6970 (t0)
REVERT: Y  147 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7425 (mtm-85)
REVERT: Y  161 TYR cc_start: 0.8214 (t80) cc_final: 0.7164 (t80)
REVERT: Y  203 ASP cc_start: 0.7584 (p0) cc_final: 0.7370 (p0)
REVERT: Y  220 PRO cc_start: 0.7990 (Cg_exo) cc_final: 0.7737 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6547 (m-80) cc_final: 0.5028 (t80)
REVERT: Y  283 PHE cc_start: 0.7379 (t80) cc_final: 0.6505 (t80)
REVERT: Y  302 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (ptm160)
  outliers start: 20
  outliers final: 10
  residues processed: 102
  average time/residue: 0.1013
  time to fit residues: 12.6160
Evaluate side-chains
  85 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   12 LEU
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  265 LEU
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   12 LEU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  302 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
X 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.178329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.138646 restraints weight = 8307.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.132486 restraints weight = 11207.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.134221 restraints weight = 11220.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.135273 restraints weight = 7265.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.135742 restraints weight = 6744.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5002  Z= 0.196
  Angle     :  0.605   7.454   6820  Z= 0.319
  Chirality :  0.043   0.215    790
  Planarity :  0.006   0.057    904
  Dihedral  :  3.953  17.297    725
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 13.21 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.33), residues: 643
  helix:  1.70 (0.31), residues: 277
  sheet: -0.22 (0.47), residues: 114
  loop : -0.77 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG X 171 
 TYR   0.018   0.002   TYR X 178 
 PHE   0.030   0.003   PHE Y 252 
 TRP   0.006   0.001   TRP Y 250 
 HIS   0.002   0.001   HIS X 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 5002)
  covalent geometry    : angle       0.60465 ( 6820)
  hydrogen bonds       : bond        0.03705 (  243)
  hydrogen bonds       : angle       4.41730 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7372 (tpt) cc_final: 0.6925 (tpp)
REVERT: X   37 ASP cc_start: 0.7583 (m-30) cc_final: 0.6846 (t0)
REVERT: X  120 LYS cc_start: 0.8404 (mttp) cc_final: 0.8134 (mttt)
REVERT: X  167 GLN cc_start: 0.7622 (pm20) cc_final: 0.7277 (pm20)
REVERT: Y   71 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6965 (tm-30)
REVERT: Y  161 TYR cc_start: 0.8418 (t80) cc_final: 0.7562 (t80)
REVERT: Y  197 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.7925 (p)
REVERT: Y  220 PRO cc_start: 0.8061 (Cg_exo) cc_final: 0.7826 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6997 (m-80) cc_final: 0.5293 (t80)
REVERT: Y  272 MET cc_start: 0.6824 (mmm) cc_final: 0.6621 (tpt)
REVERT: Y  302 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7877 (ptm-80)
  outliers start: 25
  outliers final: 15
  residues processed: 90
  average time/residue: 0.1012
  time to fit residues: 11.1903
Evaluate side-chains
  84 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  166 VAL
Chi-restraints excluded: chain X residue  198 VAL
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   12 LEU
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  302 ARG
Chi-restraints excluded: chain Y residue  305 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 46 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0170
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6618

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.178796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.138482 restraints weight = 8148.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.135116 restraints weight = 13788.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.136798 restraints weight = 10960.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.136971 restraints weight = 7661.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.137263 restraints weight = 8821.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5002  Z= 0.155
  Angle     :  0.575   8.625   6820  Z= 0.297
  Chirality :  0.042   0.128    790
  Planarity :  0.005   0.051    904
  Dihedral  :  4.021  18.970    725
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.38 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.33), residues: 643
  helix:  1.59 (0.32), residues: 276
  sheet: -0.31 (0.45), residues: 119
  loop : -0.79 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG X 171 
 TYR   0.017   0.001   TYR Y  17 
 PHE   0.022   0.002   PHE Y 252 
 TRP   0.004   0.001   TRP X 195 
 HIS   0.001   0.000   HIS X 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5002)
  covalent geometry    : angle       0.57506 ( 6820)
  hydrogen bonds       : bond        0.03276 (  243)
  hydrogen bonds       : angle       4.27447 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7232 (tpt) cc_final: 0.6908 (tpp)
REVERT: X   37 ASP cc_start: 0.7688 (m-30) cc_final: 0.7095 (t0)
REVERT: X  120 LYS cc_start: 0.8475 (mttp) cc_final: 0.8226 (mttt)
REVERT: X  167 GLN cc_start: 0.7558 (pm20) cc_final: 0.7287 (pm20)
REVERT: Y  161 TYR cc_start: 0.8473 (t80) cc_final: 0.7777 (t80)
REVERT: Y  197 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7882 (p)
REVERT: Y  220 PRO cc_start: 0.8080 (Cg_exo) cc_final: 0.7855 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6871 (m-80) cc_final: 0.5182 (t80)
REVERT: Y  283 PHE cc_start: 0.7744 (t80) cc_final: 0.6950 (t80)
REVERT: Y  302 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7866 (ptm-80)
  outliers start: 18
  outliers final: 14
  residues processed: 87
  average time/residue: 0.1056
  time to fit residues: 11.2442
Evaluate side-chains
  85 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   12 LEU
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  122 VAL
Chi-restraints excluded: chain Y residue  157 THR
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  302 ARG
Chi-restraints excluded: chain Y residue  305 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0970
   chunk 10 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0170
   chunk 7 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.4616

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.179262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.140300 restraints weight = 8458.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.138071 restraints weight = 13322.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.140108 restraints weight = 12202.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.141875 restraints weight = 7391.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.142479 restraints weight = 6586.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5002  Z= 0.128
  Angle     :  0.552   6.200   6820  Z= 0.287
  Chirality :  0.041   0.126    790
  Planarity :  0.005   0.051    904
  Dihedral  :  4.017  18.063    725
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.98 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.33), residues: 643
  helix:  1.64 (0.32), residues: 277
  sheet: -0.28 (0.45), residues: 117
  loop : -0.87 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG X 252 
 TYR   0.012   0.001   TYR Y  17 
 PHE   0.014   0.002   PHE Y 252 
 TRP   0.003   0.000   TRP X 186 
 HIS   0.002   0.001   HIS X 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5002)
  covalent geometry    : angle       0.55153 ( 6820)
  hydrogen bonds       : bond        0.03138 (  243)
  hydrogen bonds       : angle       4.20456 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7346 (tpt) cc_final: 0.6974 (tpp)
REVERT: X   37 ASP cc_start: 0.7600 (m-30) cc_final: 0.7021 (t0)
REVERT: X  120 LYS cc_start: 0.8509 (mttp) cc_final: 0.8272 (mttt)
REVERT: X  167 GLN cc_start: 0.7615 (pm20) cc_final: 0.7362 (pm20)
REVERT: Y  161 TYR cc_start: 0.8464 (t80) cc_final: 0.7762 (t80)
REVERT: Y  197 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7869 (p)
REVERT: Y  220 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7876 (Cg_endo)
REVERT: Y  254 TYR cc_start: 0.6873 (m-80) cc_final: 0.5219 (t80)
REVERT: Y  287 PHE cc_start: 0.7453 (m-80) cc_final: 0.6607 (m-80)
REVERT: Y  302 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7887 (ptm-80)
  outliers start: 17
  outliers final: 13
  residues processed: 84
  average time/residue: 0.1033
  time to fit residues: 10.6873
Evaluate side-chains
  82 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  122 VAL
Chi-restraints excluded: chain Y residue  132 ILE
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  302 ARG
Chi-restraints excluded: chain Y residue  305 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0770
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** Y  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.177853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.139063 restraints weight = 8451.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.132992 restraints weight = 12056.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.134611 restraints weight = 12805.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.137095 restraints weight = 8069.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.137365 restraints weight = 6416.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5002  Z= 0.152
  Angle     :  0.569   6.146   6820  Z= 0.296
  Chirality :  0.042   0.201    790
  Planarity :  0.005   0.050    904
  Dihedral  :  4.177  19.473    725
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.38 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.33), residues: 643
  helix:  1.54 (0.32), residues: 276
  sheet: -0.44 (0.45), residues: 118
  loop : -0.96 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG X 171 
 TYR   0.014   0.001   TYR Y  17 
 PHE   0.013   0.002   PHE X  44 
 TRP   0.003   0.001   TRP X 195 
 HIS   0.002   0.000   HIS X 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 5002)
  covalent geometry    : angle       0.56921 ( 6820)
  hydrogen bonds       : bond        0.03190 (  243)
  hydrogen bonds       : angle       4.35593 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7426 (tpt) cc_final: 0.7088 (tpp)
REVERT: X   37 ASP cc_start: 0.7561 (m-30) cc_final: 0.6984 (t0)
REVERT: X  120 LYS cc_start: 0.8522 (mttp) cc_final: 0.8275 (mttt)
REVERT: X  167 GLN cc_start: 0.7629 (pm20) cc_final: 0.7281 (pm20)
REVERT: Y   78 VAL cc_start: 0.7936 (OUTLIER) cc_final: 0.7530 (m)
REVERT: Y   92 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8218 (tp)
REVERT: Y  161 TYR cc_start: 0.8531 (t80) cc_final: 0.7754 (t80)
REVERT: Y  197 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.7934 (p)
REVERT: Y  254 TYR cc_start: 0.6927 (m-80) cc_final: 0.5250 (t80)
REVERT: Y  283 PHE cc_start: 0.7634 (t80) cc_final: 0.7151 (t80)
REVERT: Y  287 PHE cc_start: 0.7363 (m-80) cc_final: 0.7089 (m-80)
REVERT: Y  302 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7928 (ptm-80)
  outliers start: 22
  outliers final: 15
  residues processed: 87
  average time/residue: 0.0938
  time to fit residues: 10.2599
Evaluate side-chains
  84 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   78 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   92 ILE
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  122 VAL
Chi-restraints excluded: chain Y residue  132 ILE
Chi-restraints excluded: chain Y residue  157 THR
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  302 ARG
Chi-restraints excluded: chain Y residue  305 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0980
   chunk 60 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0000
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
** Y  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.178257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.138397 restraints weight = 8380.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.131916 restraints weight = 9081.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.133526 restraints weight = 10618.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.134385 restraints weight = 7201.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.134457 restraints weight = 6410.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5002  Z= 0.137
  Angle     :  0.566   6.424   6820  Z= 0.294
  Chirality :  0.041   0.135    790
  Planarity :  0.004   0.043    904
  Dihedral  :  4.157  18.787    725
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 15.58 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.33), residues: 643
  helix:  1.51 (0.32), residues: 276
  sheet: -0.31 (0.45), residues: 115
  loop : -1.04 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG X 280 
 TYR   0.012   0.001   TYR Y  17 
 PHE   0.013   0.002   PHE X  44 
 TRP   0.002   0.000   TRP X 186 
 HIS   0.002   0.000   HIS X 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5002)
  covalent geometry    : angle       0.56567 ( 6820)
  hydrogen bonds       : bond        0.03121 (  243)
  hydrogen bonds       : angle       4.28335 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7288 (tpt) cc_final: 0.6887 (tpp)
REVERT: X   37 ASP cc_start: 0.7589 (m-30) cc_final: 0.6981 (t0)
REVERT: X  120 LYS cc_start: 0.8481 (mttp) cc_final: 0.8247 (mttt)
REVERT: X  167 GLN cc_start: 0.7681 (pm20) cc_final: 0.7148 (pm20)
REVERT: Y   78 VAL cc_start: 0.7929 (OUTLIER) cc_final: 0.7494 (m)
REVERT: Y  161 TYR cc_start: 0.8590 (t80) cc_final: 0.7721 (t80)
REVERT: Y  197 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.7968 (p)
REVERT: Y  254 TYR cc_start: 0.6939 (m-80) cc_final: 0.5251 (t80)
REVERT: Y  283 PHE cc_start: 0.7823 (t80) cc_final: 0.7363 (t80)
REVERT: Y  287 PHE cc_start: 0.7528 (m-80) cc_final: 0.7198 (m-80)
  outliers start: 23
  outliers final: 15
  residues processed: 85
  average time/residue: 0.1000
  time to fit residues: 10.3948
Evaluate side-chains
  81 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  190 THR
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   78 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  122 VAL
Chi-restraints excluded: chain Y residue  132 ILE
Chi-restraints excluded: chain Y residue  157 THR
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0040
   chunk 35 optimal weight:    0.4980
   chunk 51 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
** Y  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.176976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.138105 restraints weight = 8381.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.132484 restraints weight = 11746.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134087 restraints weight = 12323.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.134602 restraints weight = 8023.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.135163 restraints weight = 7422.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5002  Z= 0.166
  Angle     :  0.599   6.258   6820  Z= 0.312
  Chirality :  0.043   0.217    790
  Planarity :  0.005   0.045    904
  Dihedral  :  4.223  17.319    725
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 16.17 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.33), residues: 643
  helix:  1.32 (0.31), residues: 276
  sheet: -0.30 (0.45), residues: 115
  loop : -1.12 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG X  20 
 TYR   0.014   0.001   TYR Y  17 
 PHE   0.014   0.002   PHE X  44 
 TRP   0.003   0.001   TRP X 186 
 HIS   0.001   0.000   HIS X 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 5002)
  covalent geometry    : angle       0.59858 ( 6820)
  hydrogen bonds       : bond        0.03546 (  243)
  hydrogen bonds       : angle       4.49249 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7499 (tpt) cc_final: 0.7175 (tpp)
REVERT: X   37 ASP cc_start: 0.7518 (m-30) cc_final: 0.7038 (t0)
REVERT: X  120 LYS cc_start: 0.8434 (mttp) cc_final: 0.8171 (mttt)
REVERT: X  167 GLN cc_start: 0.7623 (pm20) cc_final: 0.7291 (pm20)
REVERT: Y   78 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7639 (m)
REVERT: Y   92 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8249 (tp)
REVERT: Y  161 TYR cc_start: 0.8551 (t80) cc_final: 0.7726 (t80)
REVERT: Y  197 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.7933 (p)
REVERT: Y  254 TYR cc_start: 0.6920 (m-80) cc_final: 0.5260 (t80)
REVERT: Y  283 PHE cc_start: 0.7625 (t80) cc_final: 0.7092 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 83
  average time/residue: 0.0941
  time to fit residues: 9.7926
Evaluate side-chains
  85 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  153 LEU
Chi-restraints excluded: chain X residue  190 THR
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   12 LEU
Chi-restraints excluded: chain Y residue   78 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   92 ILE
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  105 MET
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  122 VAL
Chi-restraints excluded: chain Y residue  132 ILE
Chi-restraints excluded: chain Y residue  157 THR
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 14 optimal weight:    0.3980
   chunk 23 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 42 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0870
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.3558

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

Flipped N/Q/H residues before XYZ refinement:
** X 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  19 GLN
** Y 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.178466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.139269 restraints weight = 8386.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.134604 restraints weight = 10982.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.136444 restraints weight = 10048.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.136432 restraints weight = 7019.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.137189 restraints weight = 6378.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5002  Z= 0.124
  Angle     :  0.576   6.153   6820  Z= 0.303
  Chirality :  0.042   0.186    790
  Planarity :  0.004   0.050    904
  Dihedral  :  4.096  16.638    725
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.55 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.33), residues: 643
  helix:  1.45 (0.31), residues: 276
  sheet: -0.24 (0.45), residues: 115
  loop : -1.02 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG X  20 
 TYR   0.010   0.001   TYR Y  17 
 PHE   0.013   0.002   PHE X  44 
 TRP   0.002   0.000   TRP Y  48 
 HIS   0.003   0.001   HIS X 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5002)
  covalent geometry    : angle       0.57634 ( 6820)
  hydrogen bonds       : bond        0.03272 (  243)
  hydrogen bonds       : angle       4.36941 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7015 (tpt) cc_final: 0.6398 (tpt)
REVERT: X   37 ASP cc_start: 0.7283 (m-30) cc_final: 0.6915 (t0)
REVERT: X  120 LYS cc_start: 0.8489 (mttp) cc_final: 0.8232 (mttt)
REVERT: X  167 GLN cc_start: 0.7607 (pm20) cc_final: 0.7315 (pm20)
REVERT: Y  161 TYR cc_start: 0.8458 (t80) cc_final: 0.7600 (t80)
REVERT: Y  197 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7855 (p)
REVERT: Y  254 TYR cc_start: 0.6866 (m-80) cc_final: 0.5235 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 78
  average time/residue: 0.1181
  time to fit residues: 11.0622
Evaluate side-chains
  75 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   78 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  132 ILE
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Chi-restraints excluded: chain Y residue  251 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0370
   chunk 12 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 52 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
X 325 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.177343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.137274 restraints weight = 8093.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.133667 restraints weight = 11191.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.135186 restraints weight = 11804.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.136343 restraints weight = 6913.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.136939 restraints weight = 6139.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5002  Z= 0.150
  Angle     :  0.639  14.775   6820  Z= 0.325
  Chirality :  0.043   0.185    790
  Planarity :  0.005   0.049    904
  Dihedral  :  4.188  16.403    725
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.74 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.33), residues: 643
  helix:  1.21 (0.31), residues: 276
  sheet: -0.28 (0.46), residues: 115
  loop : -1.08 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG X  20 
 TYR   0.012   0.001   TYR Y  17 
 PHE   0.018   0.002   PHE Y 283 
 TRP   0.017   0.001   TRP Y 279 
 HIS   0.001   0.000   HIS X 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5002)
  covalent geometry    : angle       0.63937 ( 6820)
  hydrogen bonds       : bond        0.03445 (  243)
  hydrogen bonds       : angle       4.43584 (  699)

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

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

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1286 Ramachandran restraints generated.
    643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: X   10 MET cc_start: 0.7262 (tpt) cc_final: 0.6925 (tpp)
REVERT: X   37 ASP cc_start: 0.7482 (m-30) cc_final: 0.7058 (t0)
REVERT: X  120 LYS cc_start: 0.8447 (mttp) cc_final: 0.8217 (mttt)
REVERT: X  167 GLN cc_start: 0.7658 (pm20) cc_final: 0.7135 (pm20)
REVERT: X  168 PHE cc_start: 0.8559 (p90) cc_final: 0.8288 (p90)
REVERT: X  251 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6599 (tm-30)
REVERT: Y   78 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7486 (m)
REVERT: Y  161 TYR cc_start: 0.8508 (t80) cc_final: 0.7557 (t80)
REVERT: Y  197 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7907 (p)
REVERT: Y  254 TYR cc_start: 0.6901 (m-80) cc_final: 0.5261 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 74
  average time/residue: 0.1016
  time to fit residues: 9.2787
Evaluate side-chains
  76 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   88 ILE
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  200 HIS
Chi-restraints excluded: chain X residue  209 THR
Chi-restraints excluded: chain Y residue    9 VAL
Chi-restraints excluded: chain Y residue   78 VAL
Chi-restraints excluded: chain Y residue   88 GLU
Chi-restraints excluded: chain Y residue   93 LEU
Chi-restraints excluded: chain Y residue  113 SER
Chi-restraints excluded: chain Y residue  132 ILE
Chi-restraints excluded: chain Y residue  184 ASN
Chi-restraints excluded: chain Y residue  197 VAL
Chi-restraints excluded: chain Y residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0770
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** X 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.177531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.137229 restraints weight = 8456.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.133178 restraints weight = 11303.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.134754 restraints weight = 10687.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.135573 restraints weight = 6836.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.136019 restraints weight = 6236.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5002  Z= 0.152
  Angle     :  0.626  12.733   6820  Z= 0.323
  Chirality :  0.043   0.162    790
  Planarity :  0.005   0.047    904
  Dihedral  :  4.263  16.857    725
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.15 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.33), residues: 643
  helix:  1.17 (0.31), residues: 276
  sheet: -0.30 (0.46), residues: 115
  loop : -1.10 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG X  20 
 TYR   0.012   0.001   TYR Y  17 
 PHE   0.014   0.002   PHE Y 283 
 TRP   0.009   0.001   TRP Y 279 
 HIS   0.014   0.002   HIS X 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 5002)
  covalent geometry    : angle       0.62621 ( 6820)
  hydrogen bonds       : bond        0.03505 (  243)
  hydrogen bonds       : angle       4.57877 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1073.14 seconds
wall clock time: 19 minutes 11.81 seconds (1151.81 seconds total)