Starting phenix.real_space_refine
on Tue Feb  3 13:03:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uap_63988/02_2026/9uap_63988_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uap_63988/02_2026/9uap_63988.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uap_63988/02_2026/9uap_63988.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uap_63988/02_2026/9uap_63988.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uap_63988/02_2026/9uap_63988_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uap_63988/02_2026/9uap_63988_neut.cif"
  }
  resolution = 3.62
  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=   0.047
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    1759      2.51       5
     N     461      2.21       5
     O     486      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2718
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2502
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2502
          Classifications: {'peptide': 372}
          Incomplete info: {'truncation_to_alanine': 130}
          Link IDs: {'PTRANS': 13, 'TRANS': 358}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 475
          Unresolved non-hydrogen angles: 600
          Unresolved non-hydrogen dihedrals: 388
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'PHE:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4, 'TRP:plan': 1, 'ARG:plan': 10, 'GLN:plan1': 5, 'GLU:plan': 16, 'TYR:plan': 3}
          Unresolved non-hydrogen planarities: 236
    Chain: "B"
      Number of atoms: 216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 216
          Classifications: {'peptide': 27}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 0.83, per 1000 atoms: 0.31
  Number of scatterers: 2718
  At special positions: 0
  Unit cell: (58.1887, 61.4824, 97.7131, 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     486      8.00
     N     461      7.00
     C    1759      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  98 " - pdb=" SG  CYS A 178 " distance=2.03

  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: 0.25
  Conformation dependent library (CDL) restraints added in 122.4 milliseconds
  

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      88.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 50
      removed outlier: 3.798A  pdb=" N   LEU A  34 " --> pdb=" O   ILE A  30 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   LEU A  35 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 60
      No H-bonds generated for 'chain 'A' and resid 58 through 60'
    Processing helix  chain 'A' and resid 61 through 78
    Processing helix  chain 'A' and resid 78 through 88
    Processing helix  chain 'A' and resid 93 through 129
      removed outlier: 4.174A  pdb=" N   ALA A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASP A  99 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 127 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
    Processing helix  chain 'A' and resid 139 through 168
      Proline residue:  A 159  - end of helix
      removed outlier: 3.879A  pdb=" N   LEU A 162 " --> pdb=" O   ALA A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 184
      removed outlier: 3.504A  pdb=" N   LEU A 183 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 197
    Processing helix  chain 'A' and resid 199 through 232
      removed outlier: 4.214A  pdb=" N   CYS A 205 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 247
    Processing helix  chain 'A' and resid 251 through 273
      Proline residue:  A 264  - end of helix
      removed outlier: 3.889A  pdb=" N   GLU A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LYS A 272 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 288
      removed outlier: 3.614A  pdb=" N   LEU A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 311
      removed outlier: 3.592A  pdb=" N   THR A 305 " --> pdb=" O   SER A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 338
      removed outlier: 3.785A  pdb=" N   ARG A 318 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   PHE A 334 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 349
      removed outlier: 4.089A  pdb=" N   ASN A 342 " --> pdb=" O   TRP A 338 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE A 343 " --> pdb=" O   THR A 339 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   MET A 344 " --> pdb=" O   PRO A 340 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 379
      removed outlier: 3.961A  pdb=" N   GLU A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LEU A 362 " --> pdb=" O   THR A 358 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 363 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TYR A 368 " --> pdb=" O   TYR A 364 " (cutoff:3.500A)
      Proline residue:  A 375  - end of helix
    Processing helix  chain 'A' and resid 380 through 382
      No H-bonds generated for 'chain 'A' and resid 380 through 382'
    Processing helix  chain 'A' and resid 383 through 395
      removed outlier: 4.136A  pdb=" N   ASP A 387 " --> pdb=" O   LYS A 383 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ARG A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 356

    240 hydrogen bonds defined for protein.
    717 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: 0.41

  Time building geometry restraints manager: 0.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 881
        1.34 -     1.47: 678
        1.47 -     1.59: 1191
        1.59 -     1.71: 0
        1.71 -     1.83: 17
  Bond restraints: 2767
  Sorted by residual:
  bond pdb=" CA  TYR A 341 "
       pdb=" C   TYR A 341 "
    ideal  model  delta    sigma   weight residual
    1.519  1.538 -0.018 1.01e-02 9.80e+03 3.34e+00
  bond pdb=" N   THR B 333 "
       pdb=" CA  THR B 333 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  bond pdb=" N   GLN A 185 "
       pdb=" CA  GLN A 185 "
    ideal  model  delta    sigma   weight residual
    1.463  1.452  0.011 8.80e-03 1.29e+04 1.43e+00
  bond pdb=" N   TYR A  82 "
       pdb=" CA  TYR A  82 "
    ideal  model  delta    sigma   weight residual
    1.459  1.469 -0.010 1.23e-02 6.61e+03 7.12e-01
  bond pdb=" C   GLY A 191 "
       pdb=" N   THR A 192 "
    ideal  model  delta    sigma   weight residual
    1.334  1.324  0.011 1.27e-02 6.20e+03 7.09e-01
  ... (remaining 2762 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 3498
        1.02 -     2.05: 246
        2.05 -     3.07: 45
        3.07 -     4.09: 13
        4.09 -     5.12: 5
  Bond angle restraints: 3807
  Sorted by residual:
  angle pdb=" N   VAL A  52 "
        pdb=" CA  VAL A  52 "
        pdb=" C   VAL A  52 "
      ideal   model   delta    sigma   weight residual
     113.42  109.53    3.89 1.17e+00 7.31e-01 1.10e+01
  angle pdb=" C   ILE A 343 "
        pdb=" CA  ILE A 343 "
        pdb=" CB  ILE A 343 "
      ideal   model   delta    sigma   weight residual
     112.22  107.75    4.47 1.38e+00 5.25e-01 1.05e+01
  angle pdb=" N   TYR A  82 "
        pdb=" CA  TYR A  82 "
        pdb=" C   TYR A  82 "
      ideal   model   delta    sigma   weight residual
     111.36  107.88    3.48 1.09e+00 8.42e-01 1.02e+01
  angle pdb=" N   ASN A 342 "
        pdb=" CA  ASN A 342 "
        pdb=" C   ASN A 342 "
      ideal   model   delta    sigma   weight residual
     111.11  114.27   -3.16 1.20e+00 6.94e-01 6.94e+00
  angle pdb=" N   TYR A 364 "
        pdb=" CA  TYR A 364 "
        pdb=" C   TYR A 364 "
      ideal   model   delta    sigma   weight residual
     111.28  108.58    2.70 1.09e+00 8.42e-01 6.12e+00
  ... (remaining 3802 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.85: 1412
       14.85 -    29.69: 134
       29.69 -    44.54: 49
       44.54 -    59.38: 18
       59.38 -    74.23: 2
  Dihedral angle restraints: 1615
    sinusoidal: 435
      harmonic: 1180
  Sorted by residual:
  dihedral pdb=" CB  CYS A  98 "
           pdb=" SG  CYS A  98 "
           pdb=" SG  CYS A 178 "
           pdb=" CB  CYS A 178 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.02  -41.02     1      1.00e+01 1.00e-02 2.36e+01
  dihedral pdb=" CA  ASN A 115 "
           pdb=" CB  ASN A 115 "
           pdb=" CG  ASN A 115 "
           pdb=" OD1 ASN A 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -164.23   74.23     2      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  ASN A 110 "
           pdb=" CB  ASN A 110 "
           pdb=" CG  ASN A 110 "
           pdb=" OD1 ASN A 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -158.69   68.69     2      2.00e+01 2.50e-03 1.04e+01
  ... (remaining 1612 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 320
       0.027 -    0.053: 95
       0.053 -    0.079: 52
       0.079 -    0.106: 13
       0.106 -    0.132: 3
  Chirality restraints: 483
  Sorted by residual:
  chirality pdb=" CB  VAL A 347 "
            pdb=" CA  VAL A 347 "
            pdb=" CG1 VAL A 347 "
            pdb=" CG2 VAL A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CA  PRO A 292 "
            pdb=" N   PRO A 292 "
            pdb=" C   PRO A 292 "
            pdb=" CB  PRO A 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.11 2.00e-01 2.50e+01 3.29e-01
  chirality pdb=" CA  VAL A 173 "
            pdb=" N   VAL A 173 "
            pdb=" C   VAL A 173 "
            pdb=" CB  VAL A 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 2.83e-01
  ... (remaining 480 not shown)

  Planarity restraints: 477
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 263 "    0.023 5.00e-02 4.00e+02   3.54e-02 2.01e+00
        pdb=" N   PRO A 264 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 264 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 264 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 262 "    0.006 2.00e-02 2.50e+03   1.26e-02 1.59e+00
        pdb=" C   ASN A 262 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   ASN A 262 "    0.008 2.00e-02 2.50e+03
        pdb=" N   PHE A 263 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 197 "   -0.007 2.00e-02 2.50e+03   7.86e-03 1.08e+00
        pdb=" CG  PHE A 197 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 197 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 197 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 197 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 197 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 197 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 474 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 359
        2.74 -     3.28: 2890
        3.28 -     3.82: 4640
        3.82 -     4.36: 4504
        4.36 -     4.90: 8029
  Nonbonded interactions: 20422
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 221 "
            pdb=" OD1 ASP B 346 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   ASN A 262 "
            pdb=" OD1 ASN A 262 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" N   GLU A 235 "
            pdb=" OE1 GLU A 235 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" O   ALA A 384 "
            pdb=" OG1 THR A 388 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" O   TRP A 338 "
            pdb=" ND2 ASN A 342 "
     model   vdw
     2.354 3.120
  ... (remaining 20417 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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.900
  Find NCS groups from input model:        0.010
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
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      :  0.003   0.032   2768  Z= 0.165
  Angle     :  0.617   5.117   3809  Z= 0.385
  Chirality :  0.034   0.132    483
  Planarity :  0.003   0.035    477
  Dihedral  : 15.128  74.227    844
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.05 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 28.91 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.92 (0.45), residues: 395
  helix:  1.31 (0.31), residues: 308
  sheet:  None (None), residues: 0
  loop : -1.88 (0.73), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 213 
 TYR   0.008   0.001   TYR A 133 
 PHE   0.018   0.001   PHE A 197 
 TRP   0.009   0.001   TRP A 338 
 HIS   0.001   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 2767)
  covalent geometry    : angle       0.61581 ( 3807)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       2.05053 (    2)
  hydrogen bonds       : bond        0.15556 (  240)
  hydrogen bonds       : angle       6.03084 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  325 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7875 (mtm180)
REVERT: A  338 TRP cc_start: 0.8426 (OUTLIER) cc_final: 0.6023 (t60)
REVERT: A  342 ASN cc_start: 0.7972 (m-40) cc_final: 0.7220 (m110)
REVERT: A  364 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7148 (m-80)
  outliers start: 3
  outliers final: 1
  residues processed: 79
  average time/residue: 0.0733
  time to fit residues: 6.8002
Evaluate side-chains
  71 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 TRP
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain B residue  357 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0870
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 ASN
A 342 ASN
B 350 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.118786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.100758 restraints weight = 5566.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.103753 restraints weight = 2843.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.105897 restraints weight = 1769.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.106801 restraints weight = 1272.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.107875 restraints weight = 1065.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2768  Z= 0.140
  Angle     :  0.566   7.144   3809  Z= 0.293
  Chirality :  0.038   0.128    483
  Planarity :  0.004   0.040    477
  Dihedral  :  5.765  53.563    427
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.80 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 26.07 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.37 (0.45), residues: 395
  helix:  1.60 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -2.23 (0.80), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 221 
 TYR   0.008   0.001   TYR A 341 
 PHE   0.005   0.001   PHE A 154 
 TRP   0.010   0.001   TRP A 365 
 HIS   0.001   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 2767)
  covalent geometry    : angle       0.56589 ( 3807)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.89959 (    2)
  hydrogen bonds       : bond        0.04233 (  240)
  hydrogen bonds       : angle       4.39405 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A  325 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7831 (mtm180)
REVERT: A  364 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7072 (m-80)
  outliers start: 13
  outliers final: 9
  residues processed: 81
  average time/residue: 0.0562
  time to fit residues: 5.3946
Evaluate side-chains
  80 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  360 TRP
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain B residue  357 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 15 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.117682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.099660 restraints weight = 5713.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.102590 restraints weight = 2914.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.104423 restraints weight = 1826.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.106030 restraints weight = 1340.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.106469 restraints weight = 1063.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2768  Z= 0.143
  Angle     :  0.555   8.008   3809  Z= 0.287
  Chirality :  0.039   0.202    483
  Planarity :  0.004   0.039    477
  Dihedral  :  5.269  53.596    425
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.04 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 26.07 %
    Favored  : 66.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.48 (0.44), residues: 395
  helix:  1.69 (0.30), residues: 325
  sheet:  None (None), residues: 0
  loop : -2.47 (0.75), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 221 
 TYR   0.007   0.001   TYR A 309 
 PHE   0.005   0.001   PHE A 154 
 TRP   0.012   0.001   TRP A 101 
 HIS   0.000   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2767)
  covalent geometry    : angle       0.55512 ( 3807)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.87180 (    2)
  hydrogen bonds       : bond        0.04306 (  240)
  hydrogen bonds       : angle       4.21465 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.063 
Fit side-chains
REVERT: A  180 ILE cc_start: 0.8565 (tp) cc_final: 0.8203 (pt)
REVERT: A  325 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7821 (mtm180)
REVERT: A  364 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7220 (m-80)
  outliers start: 16
  outliers final: 10
  residues processed: 80
  average time/residue: 0.0653
  time to fit residues: 6.1477
Evaluate side-chains
  81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  338 TRP
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain B residue  357 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0870
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0570
   overall best weight:    0.5476

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 342 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.119524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.101639 restraints weight = 5612.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.104610 restraints weight = 2842.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.106413 restraints weight = 1761.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.108034 restraints weight = 1298.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.108566 restraints weight = 1028.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2768  Z= 0.129
  Angle     :  0.548   8.300   3809  Z= 0.279
  Chirality :  0.038   0.127    483
  Planarity :  0.004   0.042    477
  Dihedral  :  5.209  54.524    425
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.29 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 28.44 %
    Favored  : 64.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.73 (0.45), residues: 395
  helix:  1.83 (0.30), residues: 326
  sheet:  None (None), residues: 0
  loop : -2.26 (0.77), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 217 
 TYR   0.007   0.001   TYR A 368 
 PHE   0.005   0.001   PHE A 263 
 TRP   0.006   0.001   TRP A 157 
 HIS   0.000   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 2767)
  covalent geometry    : angle       0.54744 ( 3807)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.83039 (    2)
  hydrogen bonds       : bond        0.03985 (  240)
  hydrogen bonds       : angle       4.08126 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  180 ILE cc_start: 0.8642 (tp) cc_final: 0.8403 (pt)
REVERT: A  325 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7778 (mtm180)
REVERT: A  364 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7290 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 79
  average time/residue: 0.0573
  time to fit residues: 5.3668
Evaluate side-chains
  77 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  338 TRP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain B residue  357 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0980
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 342 ASN
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.118873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.101032 restraints weight = 5590.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.103905 restraints weight = 2830.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.105654 restraints weight = 1774.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.107324 restraints weight = 1311.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.108057 restraints weight = 1036.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2768  Z= 0.131
  Angle     :  0.546   7.323   3809  Z= 0.281
  Chirality :  0.038   0.127    483
  Planarity :  0.004   0.043    477
  Dihedral  :  5.196  55.517    425
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.78 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  8.06 %
    Allowed  : 27.96 %
    Favored  : 63.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.89 (0.44), residues: 395
  helix:  1.94 (0.29), residues: 324
  sheet:  None (None), residues: 0
  loop : -2.10 (0.77), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 217 
 TYR   0.007   0.001   TYR A 309 
 PHE   0.005   0.001   PHE A 263 
 TRP   0.005   0.001   TRP A 157 
 HIS   0.000   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 2767)
  covalent geometry    : angle       0.54555 ( 3807)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.81761 (    2)
  hydrogen bonds       : bond        0.04043 (  240)
  hydrogen bonds       : angle       4.05755 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   90 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.5997 (p90)
REVERT: A  187 ILE cc_start: 0.7244 (mt) cc_final: 0.7003 (mm)
REVERT: A  227 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8112 (tm-30)
REVERT: A  325 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7777 (mtm180)
REVERT: A  364 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7215 (m-80)
  outliers start: 17
  outliers final: 13
  residues processed: 79
  average time/residue: 0.0717
  time to fit residues: 6.7102
Evaluate side-chains
  83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  338 TRP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain B residue  357 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.115242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.097055 restraints weight = 5773.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.099889 restraints weight = 2974.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.101845 restraints weight = 1878.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.102848 restraints weight = 1378.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.103940 restraints weight = 1153.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2768  Z= 0.196
  Angle     :  0.643   8.565   3809  Z= 0.324
  Chirality :  0.040   0.128    483
  Planarity :  0.004   0.044    477
  Dihedral  :  5.416  58.937    425
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.54 %
    Favored  : 96.20 %
  Rotamer:
    Outliers : 11.37 %
    Allowed  : 27.01 %
    Favored  : 61.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.45 (0.43), residues: 395
  helix:  1.64 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -2.40 (0.76), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 221 
 TYR   0.010   0.002   TYR A 133 
 PHE   0.007   0.001   PHE A 263 
 TRP   0.009   0.001   TRP A 338 
 HIS   0.001   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 2767)
  covalent geometry    : angle       0.64233 ( 3807)
  SS BOND              : bond        0.00032 (    1)
  SS BOND              : angle       1.18323 (    2)
  hydrogen bonds       : bond        0.04613 (  240)
  hydrogen bonds       : angle       4.33054 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A   90 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6182 (p90)
REVERT: A  227 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8412 (tm-30)
REVERT: A  325 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7838 (mtm180)
REVERT: A  364 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.6989 (m-80)
  outliers start: 24
  outliers final: 17
  residues processed: 82
  average time/residue: 0.0414
  time to fit residues: 4.0844
Evaluate side-chains
  81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  338 TRP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain A residue  365 TRP
Chi-restraints excluded: chain B residue  357 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.122012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.103611 restraints weight = 5639.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.106314 restraints weight = 2883.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.108287 restraints weight = 1858.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.109287 restraints weight = 1377.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.110230 restraints weight = 1163.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2768  Z= 0.151
  Angle     :  0.609   8.812   3809  Z= 0.308
  Chirality :  0.039   0.129    483
  Planarity :  0.004   0.046    477
  Dihedral  :  5.360  59.042    425
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.78 %
    Favored  : 96.96 %
  Rotamer:
    Outliers : 10.90 %
    Allowed  : 29.86 %
    Favored  : 59.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.57 (0.44), residues: 395
  helix:  1.74 (0.29), residues: 325
  sheet:  None (None), residues: 0
  loop : -2.41 (0.73), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 217 
 TYR   0.007   0.001   TYR A 133 
 PHE   0.021   0.001   PHE B 339 
 TRP   0.006   0.001   TRP A 338 
 HIS   0.000   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 2767)
  covalent geometry    : angle       0.60823 ( 3807)
  SS BOND              : bond        0.00027 (    1)
  SS BOND              : angle       1.03767 (    2)
  hydrogen bonds       : bond        0.04251 (  240)
  hydrogen bonds       : angle       4.18150 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   90 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.6214 (p90)
REVERT: A  187 ILE cc_start: 0.7154 (mt) cc_final: 0.6910 (mm)
REVERT: A  227 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: A  325 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7763 (mtm180)
REVERT: A  364 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.6875 (m-80)
REVERT: B  359 VAL cc_start: 0.7002 (OUTLIER) cc_final: 0.6467 (p)
  outliers start: 23
  outliers final: 19
  residues processed: 81
  average time/residue: 0.0681
  time to fit residues: 6.5769
Evaluate side-chains
  90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  338 TRP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain A residue  365 TRP
Chi-restraints excluded: chain B residue  357 ASN
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 18 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    0.2980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.123412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.105321 restraints weight = 5633.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.108209 restraints weight = 2851.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.110201 restraints weight = 1803.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.111042 restraints weight = 1326.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.112067 restraints weight = 1135.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2768  Z= 0.133
  Angle     :  0.593   8.989   3809  Z= 0.298
  Chirality :  0.038   0.128    483
  Planarity :  0.004   0.047    477
  Dihedral  :  5.257  57.298    425
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.78 %
    Favored  : 96.96 %
  Rotamer:
    Outliers : 11.85 %
    Allowed  : 29.86 %
    Favored  : 58.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.74 (0.44), residues: 395
  helix:  1.83 (0.29), residues: 325
  sheet:  None (None), residues: 0
  loop : -2.15 (0.76), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 217 
 TYR   0.009   0.001   TYR A 309 
 PHE   0.005   0.001   PHE B 339 
 TRP   0.006   0.001   TRP A 157 
 HIS   0.000   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 2767)
  covalent geometry    : angle       0.59237 ( 3807)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       0.89806 (    2)
  hydrogen bonds       : bond        0.03997 (  240)
  hydrogen bonds       : angle       4.09296 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   90 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.5975 (p90)
REVERT: A  187 ILE cc_start: 0.7135 (mt) cc_final: 0.6904 (mm)
REVERT: A  325 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7755 (mtm180)
REVERT: A  364 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.6859 (m-80)
  outliers start: 25
  outliers final: 17
  residues processed: 85
  average time/residue: 0.0774
  time to fit residues: 7.6850
Evaluate side-chains
  86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  338 TRP
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain B residue  357 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.122669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.104517 restraints weight = 5771.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.107385 restraints weight = 2919.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.109391 restraints weight = 1832.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.110412 restraints weight = 1336.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.111444 restraints weight = 1115.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2768  Z= 0.156
  Angle     :  0.654   8.714   3809  Z= 0.329
  Chirality :  0.039   0.128    483
  Planarity :  0.004   0.046    477
  Dihedral  :  5.236  55.882    425
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.29 %
    Favored  : 96.46 %
  Rotamer:
    Outliers : 10.90 %
    Allowed  : 31.28 %
    Favored  : 57.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.73 (0.44), residues: 395
  helix:  1.89 (0.29), residues: 324
  sheet:  None (None), residues: 0
  loop : -2.50 (0.74), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 217 
 TYR   0.014   0.001   TYR A 309 
 PHE   0.008   0.001   PHE B 339 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.001   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 2767)
  covalent geometry    : angle       0.65396 ( 3807)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.91970 (    2)
  hydrogen bonds       : bond        0.04220 (  240)
  hydrogen bonds       : angle       4.14626 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   90 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.6131 (p90)
REVERT: A  187 ILE cc_start: 0.7103 (mt) cc_final: 0.6894 (mm)
REVERT: A  325 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7766 (mtm180)
REVERT: A  364 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.6925 (m-80)
REVERT: B  359 VAL cc_start: 0.6929 (OUTLIER) cc_final: 0.6398 (p)
  outliers start: 23
  outliers final: 19
  residues processed: 83
  average time/residue: 0.0721
  time to fit residues: 7.0702
Evaluate side-chains
  88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  338 TRP
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain A residue  365 TRP
Chi-restraints excluded: chain B residue  357 ASN
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0970
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0050
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.125002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.106471 restraints weight = 5668.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.109441 restraints weight = 2871.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.111373 restraints weight = 1810.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.112769 restraints weight = 1345.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.113571 restraints weight = 1095.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2768  Z= 0.133
  Angle     :  0.628   8.570   3809  Z= 0.314
  Chirality :  0.038   0.128    483
  Planarity :  0.004   0.046    477
  Dihedral  :  5.099  52.996    425
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.04 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  9.95 %
    Allowed  : 31.28 %
    Favored  : 58.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.90 (0.44), residues: 395
  helix:  1.99 (0.29), residues: 324
  sheet:  None (None), residues: 0
  loop : -2.32 (0.74), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 221 
 TYR   0.013   0.001   TYR A 309 
 PHE   0.005   0.001   PHE B 339 
 TRP   0.008   0.001   TRP A 157 
 HIS   0.000   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 2767)
  covalent geometry    : angle       0.62814 ( 3807)
  SS BOND              : bond        0.00053 (    1)
  SS BOND              : angle       0.82302 (    2)
  hydrogen bonds       : bond        0.03901 (  240)
  hydrogen bonds       : angle       4.04892 (  717)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   90 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.5982 (p90)
REVERT: A  325 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7755 (mtm180)
REVERT: A  364 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.6901 (m-80)
REVERT: B  359 VAL cc_start: 0.6960 (OUTLIER) cc_final: 0.6348 (p)
  outliers start: 21
  outliers final: 18
  residues processed: 83
  average time/residue: 0.0673
  time to fit residues: 6.6062
Evaluate side-chains
  88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 SER
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  261 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  338 TRP
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  364 TYR
Chi-restraints excluded: chain A residue  365 TRP
Chi-restraints excluded: chain B residue  357 ASN
Chi-restraints excluded: chain B residue  359 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.123051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.104865 restraints weight = 5611.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.107628 restraints weight = 2853.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.109641 restraints weight = 1823.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.110453 restraints weight = 1337.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.111576 restraints weight = 1145.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   2768  Z= 0.155
  Angle     :  0.653   9.234   3809  Z= 0.326
  Chirality :  0.039   0.128    483
  Planarity :  0.004   0.046    477
  Dihedral  :  5.081  50.369    425
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.80 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  9.95 %
    Allowed  : 31.75 %
    Favored  : 58.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.81 (0.44), residues: 395
  helix:  1.91 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -2.40 (0.76), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 221 
 TYR   0.013   0.001   TYR A 309 
 PHE   0.008   0.001   PHE B 339 
 TRP   0.010   0.001   TRP A 164 
 HIS   0.000   0.000   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2767)
  covalent geometry    : angle       0.65247 ( 3807)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.87462 (    2)
  hydrogen bonds       : bond        0.04154 (  240)
  hydrogen bonds       : angle       4.13270 (  717)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 645.05 seconds
wall clock time: 11 minutes 44.12 seconds (704.12 seconds total)