Starting phenix.real_space_refine
on Fri Aug 22 18:45:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uby_42109/08_2025/8uby_42109_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uby_42109/08_2025/8uby_42109.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uby_42109/08_2025/8uby_42109.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uby_42109/08_2025/8uby_42109.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uby_42109/08_2025/8uby_42109_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uby_42109/08_2025/8uby_42109_trim.cif"
  }
  resolution = 2.67
  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=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2262      2.51       5
     N     503      2.21       5
     O     628      1.98       5
     H    3345      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6756
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 6598
          Classifications: {'peptide': 419}
          Link IDs: {'PTRANS': 17, 'TRANS': 401}
          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
    Chain: "A"
      Number of atoms: 158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 158
          Unusual residues: {'CHT': 1, 'Y01': 3}
          Classifications: {'undetermined': 4, 'water': 46}
          Link IDs: {None: 49}
  Time building chain proxies: 1.50, per 1000 atoms: 0.22
  Number of scatterers: 6756
  At special positions: 0
  Unit cell: (81.2, 56.55, 65.975, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     O     628      8.00
     N     503      7.00
     C    2262      6.00
     H    3345      1.00
    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: 0.43
  Conformation dependent library (CDL) restraints added in 217.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 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:
      17 helices and 0 sheets defined
      89.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 105 through 131
      removed outlier: 3.661A  pdb=" N   VAL A 109 " --> pdb=" O   PRO A 105 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASN A 121 " --> pdb=" O   TYR A 117 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   TYR A 128 " --> pdb=" O   GLN A 124 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   SER A 129 " --> pdb=" O   TRP A 125 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 140
    Processing helix  chain 'A' and resid 142 through 172
      removed outlier: 3.557A  pdb=" N   ILE A 146 " --> pdb=" O   THR A 142 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   TYR A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   MET A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   VAL A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
      removed outlier: 5.056A  pdb=" N   PHE A 162 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      Proline residue:  A 163  - end of helix
    Processing helix  chain 'A' and resid 172 through 193
      removed outlier: 3.779A  pdb=" N   THR A 176 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 216
      removed outlier: 3.547A  pdb=" N   THR A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   PHE A 216 " --> pdb=" O   VAL A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 4.079A  pdb=" N   ARG A 223 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 260
      removed outlier: 3.575A  pdb=" N   ASN A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
      Proline residue:  A 256  - end of helix
    Processing helix  chain 'A' and resid 266 through 296
    Processing helix  chain 'A' and resid 305 through 314
    Processing helix  chain 'A' and resid 320 through 331
      removed outlier: 3.682A  pdb=" N   ASN A 331 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 363
      removed outlier: 5.114A  pdb=" N   ASN A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   GLN A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   TYR A 362 " --> pdb=" O   MET A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 396
    Processing helix  chain 'A' and resid 398 through 418
    Processing helix  chain 'A' and resid 419 through 423
      removed outlier: 3.827A  pdb=" N   LEU A 422 " --> pdb=" O   THR A 419 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ARG A 423 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 419 through 423'
    Processing helix  chain 'A' and resid 424 through 454
      Proline residue:  A 444  - end of helix
    Processing helix  chain 'A' and resid 458 through 488
      removed outlier: 3.506A  pdb=" N   SER A 462 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 511
      removed outlier: 3.804A  pdb=" N   GLY A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)

    272 hydrogen bonds defined for protein.
    816 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.59

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3337
        1.03 -     1.23: 11
        1.23 -     1.42: 1396
        1.42 -     1.61: 2029
        1.61 -     1.81: 28
  Bond restraints: 6801
  Sorted by residual:
  bond pdb=" N   PRO A 303 "
       pdb=" CA  PRO A 303 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.31e-02 5.83e+03 1.08e+00
  bond pdb=" CA  ILE A 332 "
       pdb=" CB  ILE A 332 "
    ideal  model  delta    sigma   weight residual
    1.539  1.534  0.005 5.40e-03 3.43e+04 9.61e-01
  bond pdb=" N   VAL A 195 "
       pdb=" CA  VAL A 195 "
    ideal  model  delta    sigma   weight residual
    1.474  1.461  0.014 1.57e-02 4.06e+03 7.77e-01
  bond pdb=" CB  PRO A 304 "
       pdb=" CG  PRO A 304 "
    ideal  model  delta    sigma   weight residual
    1.492  1.529 -0.037 5.00e-02 4.00e+02 5.60e-01
  bond pdb=" N   PRO A 221 "
       pdb=" CA  PRO A 221 "
    ideal  model  delta    sigma   weight residual
    1.469  1.478 -0.009 1.28e-02 6.10e+03 4.81e-01
  ... (remaining 6796 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 11430
        1.02 -     2.04: 794
        2.04 -     3.06: 38
        3.06 -     4.08: 16
        4.08 -     5.10: 4
  Bond angle restraints: 12282
  Sorted by residual:
  angle pdb=" N   VAL A 195 "
        pdb=" CA  VAL A 195 "
        pdb=" C   VAL A 195 "
      ideal   model   delta    sigma   weight residual
     106.21  109.71   -3.50 1.07e+00 8.73e-01 1.07e+01
  angle pdb=" N   LEU A 220 "
        pdb=" CA  LEU A 220 "
        pdb=" C   LEU A 220 "
      ideal   model   delta    sigma   weight residual
     109.81  114.91   -5.10 2.21e+00 2.05e-01 5.34e+00
  angle pdb=" C   VAL A 195 "
        pdb=" CA  VAL A 195 "
        pdb=" CB  VAL A 195 "
      ideal   model   delta    sigma   weight residual
     113.22  110.76    2.46 1.12e+00 7.97e-01 4.82e+00
  angle pdb=" N   TYR A 117 "
        pdb=" CA  TYR A 117 "
        pdb=" C   TYR A 117 "
      ideal   model   delta    sigma   weight residual
     113.18  110.57    2.61 1.21e+00 6.83e-01 4.65e+00
  angle pdb=" CA  LEU A 220 "
        pdb=" C   LEU A 220 "
        pdb=" N   PRO A 221 "
      ideal   model   delta    sigma   weight residual
     118.44  121.85   -3.41 1.59e+00 3.96e-01 4.61e+00
  ... (remaining 12277 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.87: 2963
       15.87 -    31.73: 258
       31.73 -    47.60: 64
       47.60 -    63.46: 80
       63.46 -    79.33: 4
  Dihedral angle restraints: 3369
    sinusoidal: 1889
      harmonic: 1480
  Sorted by residual:
  dihedral pdb=" CA  TYR A 117 "
           pdb=" C   TYR A 117 "
           pdb=" N   SER A 118 "
           pdb=" CA  SER A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.48   18.52     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CG  ARG A 423 "
           pdb=" CD  ARG A 423 "
           pdb=" NE  ARG A 423 "
           pdb=" CZ  ARG A 423 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -42.14  -47.86     2      1.50e+01 4.44e-03 1.17e+01
  dihedral pdb=" N   LYS A 330 "
           pdb=" CA  LYS A 330 "
           pdb=" CB  LYS A 330 "
           pdb=" CG  LYS A 330 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.78  -59.22     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3366 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.021: 358
       0.021 -    0.042: 117
       0.042 -    0.063: 33
       0.063 -    0.084: 50
       0.084 -    0.104: 11
  Chirality restraints: 569
  Sorted by residual:
  chirality pdb=" CA  PRO A 221 "
            pdb=" N   PRO A 221 "
            pdb=" C   PRO A 221 "
            pdb=" CB  PRO A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.10 2.00e-01 2.50e+01 2.73e-01
  chirality pdb=" CA  ILE A 131 "
            pdb=" N   ILE A 131 "
            pdb=" C   ILE A 131 "
            pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.45e-01
  chirality pdb=" CA  PRO A 304 "
            pdb=" N   PRO A 304 "
            pdb=" C   PRO A 304 "
            pdb=" CB  PRO A 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.62    0.10 2.00e-01 2.50e+01 2.34e-01
  ... (remaining 566 not shown)

  Planarity restraints: 959
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 256 "   -0.049 5.00e-02 4.00e+02   7.33e-02 8.60e+00
        pdb=" N   PRO A 257 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 257 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 257 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 423 "   -0.163 9.50e-02 1.11e+02   5.47e-02 3.48e+00
        pdb=" NE  ARG A 423 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 423 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 423 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 423 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A 423 "    0.006 2.00e-02 2.50e+03
        pdb="HH12 ARG A 423 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A 423 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 423 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 114 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.58e+00
        pdb=" C   PHE A 114 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   PHE A 114 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER A 115 "    0.009 2.00e-02 2.50e+03
  ... (remaining 956 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.34: 1996
        2.34 -     2.90: 15817
        2.90 -     3.47: 19065
        3.47 -     4.03: 25376
        4.03 -     4.60: 38501
  Nonbonded interactions: 100755
  Sorted by model distance:
  nonbonded pdb="HD21 ASN A 356 "
            pdb=" O   HOH A 705 "
     model   vdw
     1.772 2.450
  nonbonded pdb=" O   MET A 382 "
            pdb=" HG  SER A 385 "
     model   vdw
     1.786 2.450
  nonbonded pdb=" O   SER A 104 "
            pdb=" HE  ARG A 107 "
     model   vdw
     1.799 2.450
  nonbonded pdb=" HG2 ARG A 423 "
            pdb="HH11 ARG A 423 "
     model   vdw
     1.810 2.270
  nonbonded pdb=" O   GLY A 474 "
            pdb=" HG1 THR A 478 "
     model   vdw
     1.814 2.450
  ... (remaining 100750 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             4.990
  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:             0.040
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.900
  Find NCS groups from input model:        0.020
  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:8.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
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   0.037   3456  Z= 0.115
  Angle     :  0.474   5.105   4731  Z= 0.270
  Chirality :  0.032   0.104    569
  Planarity :  0.006   0.073    558
  Dihedral  : 14.527  79.329   1370
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 13.28 %
    Favored  : 86.16 %
  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 aren not related in a simple way.
  whole:  3.72 (0.42), residues: 417
  helix:  3.06 (0.27), residues: 347
  sheet:  None (None), residues: 0
  loop : -0.97 (0.74), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 423 
 TYR   0.012   0.001   TYR A 117 
 PHE   0.010   0.001   PHE A 496 
 TRP   0.007   0.001   TRP A 201 
 HIS   0.001   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 3456)
  covalent geometry    : angle       0.47441 ( 4731)
  hydrogen bonds       : bond        0.12146 (  272)
  hydrogen bonds       : angle       5.41640 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  512 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7550 (tppt)
  outliers start: 2
  outliers final: 2
  residues processed: 57
  average time/residue: 1.0129
  time to fit residues: 59.6978
Evaluate side-chains
  37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  404 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.103022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.084130 restraints weight = 15363.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.98
r_work: 0.2918 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3456  Z= 0.156
  Angle     :  0.518   5.535   4731  Z= 0.277
  Chirality :  0.034   0.107    569
  Planarity :  0.005   0.059    558
  Dihedral  :  5.802  55.839    666
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 17.23 %
    Favored  : 81.92 %
  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 aren not related in a simple way.
  whole:  3.98 (0.41), residues: 417
  helix:  3.14 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -0.66 (0.75), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 423 
 TYR   0.021   0.001   TYR A 117 
 PHE   0.012   0.001   PHE A 496 
 TRP   0.008   0.001   TRP A 201 
 HIS   0.006   0.002   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3456)
  covalent geometry    : angle       0.51827 ( 4731)
  hydrogen bonds       : bond        0.05236 (  272)
  hydrogen bonds       : angle       4.17459 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  396 LYS cc_start: 0.8583 (mptt) cc_final: 0.8334 (mmpt)
REVERT: A  452 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7514 (tp30)
  outliers start: 3
  outliers final: 2
  residues processed: 36
  average time/residue: 1.2097
  time to fit residues: 44.9785
Evaluate side-chains
  39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  452 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3345 r_free = 0.3345 target = 0.102677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.084450 restraints weight = 15735.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 1.96
r_work: 0.2992 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3456  Z= 0.163
  Angle     :  0.494   5.255   4731  Z= 0.267
  Chirality :  0.034   0.116    569
  Planarity :  0.005   0.052    558
  Dihedral  :  5.730  55.637    666
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.12 %
    Favored  : 84.18 %
  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 aren not related in a simple way.
  whole:  3.75 (0.41), residues: 417
  helix:  3.00 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -0.89 (0.73), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 223 
 TYR   0.021   0.001   TYR A 117 
 PHE   0.015   0.001   PHE A 114 
 TRP   0.009   0.001   TRP A 201 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3456)
  covalent geometry    : angle       0.49407 ( 4731)
  hydrogen bonds       : bond        0.05466 (  272)
  hydrogen bonds       : angle       4.10750 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8255 (mmm160)
REVERT: A  330 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8531 (mptm)
REVERT: A  452 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7732 (tp30)
  outliers start: 6
  outliers final: 3
  residues processed: 39
  average time/residue: 1.0715
  time to fit residues: 43.0767
Evaluate side-chains
  35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  452 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0980
   chunk 2 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3267 r_free = 0.3267 target = 0.098983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.080271 restraints weight = 15601.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.97
r_work: 0.2861 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3456  Z= 0.143
  Angle     :  0.481   5.091   4731  Z= 0.258
  Chirality :  0.033   0.114    569
  Planarity :  0.004   0.050    558
  Dihedral  :  5.569  55.219    664
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.41 %
    Favored  : 83.62 %
  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 aren not related in a simple way.
  whole:  3.92 (0.41), residues: 417
  helix:  3.12 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.66 (0.73), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.020   0.001   TYR A 117 
 PHE   0.010   0.001   PHE A 114 
 TRP   0.009   0.001   TRP A 201 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3456)
  covalent geometry    : angle       0.48148 ( 4731)
  hydrogen bonds       : bond        0.04991 (  272)
  hydrogen bonds       : angle       4.01115 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  330 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8551 (mptm)
REVERT: A  452 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7598 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 37
  average time/residue: 0.8762
  time to fit residues: 33.6027
Evaluate side-chains
  34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  452 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0040
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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 = 0.3350 r_free = 0.3350 target = 0.102816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.084583 restraints weight = 15997.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 1.98
r_work: 0.2981 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3456  Z= 0.146
  Angle     :  0.477   5.152   4731  Z= 0.257
  Chirality :  0.034   0.116    569
  Planarity :  0.004   0.048    558
  Dihedral  :  5.619  54.882    664
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.28 %
    Favored  : 84.46 %
  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 aren not related in a simple way.
  whole:  3.85 (0.41), residues: 417
  helix:  3.09 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.82 (0.72), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 516 
 TYR   0.020   0.001   TYR A 117 
 PHE   0.012   0.001   PHE A 114 
 TRP   0.008   0.001   TRP A 201 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3456)
  covalent geometry    : angle       0.47718 ( 4731)
  hydrogen bonds       : bond        0.05052 (  272)
  hydrogen bonds       : angle       4.00111 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: A  330 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8595 (mptm)
REVERT: A  452 GLU cc_start: 0.7940 (tp30) cc_final: 0.7676 (tp30)
  outliers start: 8
  outliers final: 3
  residues processed: 37
  average time/residue: 0.9995
  time to fit residues: 38.3521
Evaluate side-chains
  34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  350 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0470
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.3255 r_free = 0.3255 target = 0.098220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.079459 restraints weight = 15731.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 1.99
r_work: 0.2849 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3456  Z= 0.136
  Angle     :  0.474   5.128   4731  Z= 0.255
  Chirality :  0.033   0.118    569
  Planarity :  0.004   0.048    558
  Dihedral  :  5.632  54.776    664
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.84 %
    Favored  : 84.18 %
  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 aren not related in a simple way.
  whole:  3.83 (0.41), residues: 417
  helix:  3.08 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.77 (0.73), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 516 
 TYR   0.019   0.001   TYR A 117 
 PHE   0.011   0.001   PHE A 114 
 TRP   0.007   0.001   TRP A 201 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3456)
  covalent geometry    : angle       0.47418 ( 4731)
  hydrogen bonds       : bond        0.04915 (  272)
  hydrogen bonds       : angle       3.96008 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8483 (mp)
REVERT: A  294 ILE cc_start: 0.8808 (mm) cc_final: 0.8603 (mt)
REVERT: A  330 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8551 (mptm)
REVERT: A  452 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7625 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 35
  average time/residue: 0.9322
  time to fit residues: 33.9514
Evaluate side-chains
  36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  452 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3251 r_free = 0.3251 target = 0.097852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.079264 restraints weight = 15412.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.97
r_work: 0.2852 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3456  Z= 0.139
  Angle     :  0.474   5.236   4731  Z= 0.255
  Chirality :  0.034   0.119    569
  Planarity :  0.004   0.047    558
  Dihedral  :  5.723  54.645    664
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.56 %
    Favored  : 84.46 %
  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 aren not related in a simple way.
  whole:  3.82 (0.41), residues: 417
  helix:  3.07 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.77 (0.74), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 516 
 TYR   0.018   0.001   TYR A 117 
 PHE   0.011   0.001   PHE A 114 
 TRP   0.008   0.001   TRP A 201 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3456)
  covalent geometry    : angle       0.47357 ( 4731)
  hydrogen bonds       : bond        0.04882 (  272)
  hydrogen bonds       : angle       3.94145 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8440 (mp)
REVERT: A  330 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8576 (mptm)
REVERT: A  452 GLU cc_start: 0.7955 (tp30) cc_final: 0.7685 (tp30)
  outliers start: 7
  outliers final: 4
  residues processed: 35
  average time/residue: 0.9023
  time to fit residues: 32.7473
Evaluate side-chains
  38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  445 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 3 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3306 r_free = 0.3306 target = 0.100737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.082180 restraints weight = 16106.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 2.04
r_work: 0.2944 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3456  Z= 0.137
  Angle     :  0.472   5.176   4731  Z= 0.253
  Chirality :  0.034   0.119    569
  Planarity :  0.004   0.047    558
  Dihedral  :  5.808  54.771    664
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.56 %
    Favored  : 84.75 %
  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 aren not related in a simple way.
  whole:  3.85 (0.41), residues: 417
  helix:  3.08 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.66 (0.75), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 516 
 TYR   0.018   0.001   TYR A 117 
 PHE   0.011   0.001   PHE A 114 
 TRP   0.008   0.001   TRP A 201 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3456)
  covalent geometry    : angle       0.47222 ( 4731)
  hydrogen bonds       : bond        0.04853 (  272)
  hydrogen bonds       : angle       3.91693 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8399 (mp)
REVERT: A  330 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8564 (mptm)
REVERT: A  452 GLU cc_start: 0.7933 (tp30) cc_final: 0.7651 (tp30)
  outliers start: 6
  outliers final: 3
  residues processed: 39
  average time/residue: 1.0401
  time to fit residues: 41.9051
Evaluate side-chains
  35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  350 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 308 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.100199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.082400 restraints weight = 16390.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 1.95
r_work: 0.2947 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3456  Z= 0.161
  Angle     :  0.492   5.270   4731  Z= 0.265
  Chirality :  0.034   0.122    569
  Planarity :  0.004   0.047    558
  Dihedral  :  6.005  55.286    664
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.56 %
    Favored  : 84.46 %
  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 aren not related in a simple way.
  whole:  3.79 (0.41), residues: 417
  helix:  3.02 (0.27), residues: 352
  sheet:  None (None), residues: 0
  loop : -0.63 (0.76), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 516 
 TYR   0.019   0.001   TYR A 117 
 PHE   0.013   0.001   PHE A 114 
 TRP   0.007   0.001   TRP A 201 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3456)
  covalent geometry    : angle       0.49193 ( 4731)
  hydrogen bonds       : bond        0.05101 (  272)
  hydrogen bonds       : angle       3.97991 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A  259 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8564 (mp)
REVERT: A  294 ILE cc_start: 0.8932 (mm) cc_final: 0.8719 (mt)
REVERT: A  330 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8658 (mptm)
REVERT: A  452 GLU cc_start: 0.8016 (tp30) cc_final: 0.7741 (tp30)
  outliers start: 7
  outliers final: 4
  residues processed: 36
  average time/residue: 0.9146
  time to fit residues: 34.1409
Evaluate side-chains
  35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  445 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 27 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0770
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.3344 r_free = 0.3344 target = 0.102277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.084494 restraints weight = 16168.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 1.96
r_work: 0.2981 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3456  Z= 0.122
  Angle     :  0.467   5.079   4731  Z= 0.250
  Chirality :  0.033   0.117    569
  Planarity :  0.004   0.046    558
  Dihedral  :  5.901  55.280    664
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.12 %
    Favored  : 84.75 %
  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 aren not related in a simple way.
  whole:  3.90 (0.41), residues: 417
  helix:  3.09 (0.27), residues: 352
  sheet:  None (None), residues: 0
  loop : -0.59 (0.76), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 516 
 TYR   0.018   0.001   TYR A 117 
 PHE   0.009   0.001   PHE A 496 
 TRP   0.008   0.001   TRP A 201 
 HIS   0.001   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3456)
  covalent geometry    : angle       0.46656 ( 4731)
  hydrogen bonds       : bond        0.04685 (  272)
  hydrogen bonds       : angle       3.87062 (  816)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 ILE cc_start: 0.8918 (mm) cc_final: 0.8702 (mt)
REVERT: A  330 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8684 (mptm)
REVERT: A  452 GLU cc_start: 0.8008 (tp30) cc_final: 0.7735 (tp30)
  outliers start: 4
  outliers final: 2
  residues processed: 35
  average time/residue: 1.1578
  time to fit residues: 41.9910
Evaluate side-chains
  36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  350 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0170
   chunk 15 optimal weight:    0.0980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.3818

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
A 127 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.102549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.085049 restraints weight = 16117.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.93
r_work: 0.2996 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3456  Z= 0.116
  Angle     :  0.460   5.094   4731  Z= 0.246
  Chirality :  0.033   0.115    569
  Planarity :  0.004   0.046    558
  Dihedral  :  5.765  56.298    664
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.84 %
    Favored  : 85.03 %
  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 aren not related in a simple way.
  whole:  3.96 (0.41), residues: 417
  helix:  3.15 (0.27), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.67 (0.75), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 223 
 TYR   0.017   0.001   TYR A 117 
 PHE   0.009   0.001   PHE A 496 
 TRP   0.006   0.001   TRP A 201 
 HIS   0.001   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 3456)
  covalent geometry    : angle       0.46017 ( 4731)
  hydrogen bonds       : bond        0.04512 (  272)
  hydrogen bonds       : angle       3.80101 (  816)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2331.10 seconds
wall clock time: 40 minutes 19.95 seconds (2419.95 seconds total)