Starting phenix.real_space_refine
on Fri Aug 22 13:48:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qt7_18645/08_2025/8qt7_18645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qt7_18645/08_2025/8qt7_18645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qt7_18645/08_2025/8qt7_18645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qt7_18645/08_2025/8qt7_18645.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qt7_18645/08_2025/8qt7_18645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qt7_18645/08_2025/8qt7_18645.map"
  }
  resolution = 2.2
  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=   0.082
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: 6
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     P       5      5.49       5
     S      11      5.16       5
     C    2282      2.51       5
     N     555      2.21       5
     O     661      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 3516
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3264
          Classifications: {'peptide': 399}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 385}
    Chain: "A"
      Number of atoms: 252
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 252
          Unusual residues: {'FAD': 1, 'HEM': 2, 'NDP': 1}
          Classifications: {'undetermined': 4, 'water': 65}
          Link IDs: {None: 68}
  Time building chain proxies: 1.05, per 1000 atoms: 0.30
  Number of scatterers: 3516
  At special positions: 0
  Unit cell: (59.592, 67.8432, 92.5968, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      2     26.01
     S      11     16.00
     P       5     15.00
     O     661      8.00
     N     555      7.00
     C    2282      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 82.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  740

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 2 sheets defined
      56.1% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 6
      No H-bonds generated for 'chain 'A' and resid 4 through 6'
    Processing helix  chain 'A' and resid 7 through 29
    Processing helix  chain 'A' and resid 32 through 48
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 61 through 88
    Processing helix  chain 'A' and resid 94 through 116
      removed outlier: 3.501A  pdb=" N   GLY A 100 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 130
    Processing helix  chain 'A' and resid 131 through 147
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 155 through 178
    Processing helix  chain 'A' and resid 178 through 183
    Processing helix  chain 'A' and resid 253 through 263
      removed outlier: 3.535A  pdb=" N   LEU A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 296 through 306
    Processing helix  chain 'A' and resid 321 through 325
      removed outlier: 3.638A  pdb=" N   ALA A 325 " --> pdb=" O   ASP A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 338
    Processing helix  chain 'A' and resid 372 through 387
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 195
      removed outlier: 8.084A  pdb=" N   TYR A 186 " --> pdb=" O   PRO A 210 " (cutoff:3.500A)
      removed outlier: 8.346A  pdb=" N   GLY A 188 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   SER A 208 " --> pdb=" O   GLY A 188 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   ILE A 190 " --> pdb=" O   HIS A 206 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   HIS A 206 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   HIS A 192 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   GLN A 243 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   TYR A 246 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   THR A 248 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   SER A 236 " --> pdb=" O   THR A 248 " (cutoff:3.500A)
      removed outlier: 8.777A  pdb=" N   LYS A 250 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   PHE A 220 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   ARG A 273 " --> pdb=" O   PHE A 220 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   LYS A 222 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   LEU A 271 " --> pdb=" O   LYS A 222 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   PHE A 224 " --> pdb=" O   VAL A 269 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   VAL A 269 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347
      removed outlier: 6.726A  pdb=" N   GLN A 287 " --> pdb=" O   HIS A 314 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   TYR A 316 " --> pdb=" O   GLN A 287 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   TRP A 289 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   SER A 318 " --> pdb=" O   TRP A 289 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ALA A 291 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLU A 391 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)

    193 hydrogen bonds defined for protein.
    555 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: 0.49

  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:
        1.21 -     1.39: 1513
        1.39 -     1.57: 2020
        1.57 -     1.75: 8
        1.75 -     1.93: 22
        1.93 -     2.12: 7
  Bond restraints: 3570
  Sorted by residual:
  bond pdb=" O2B NDP A 501 "
       pdb=" P2B NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.833  1.599  0.234 3.80e-02 6.93e+02 3.78e+01
  bond pdb=" O5D NDP A 501 "
       pdb=" PN  NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.757  1.590  0.167 3.50e-02 8.16e+02 2.29e+01
  bond pdb=" C3B HEM A 503 "
       pdb=" CAB HEM A 503 "
    ideal  model  delta    sigma   weight residual
    1.544  1.458  0.086 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" O2X NDP A 501 "
       pdb=" P2B NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.532  1.490  0.042 1.00e-02 1.00e+04 1.78e+01
  bond pdb=" O2N NDP A 501 "
       pdb=" PN  NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.513  1.475  0.038 1.00e-02 1.00e+04 1.41e+01
  ... (remaining 3565 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.53: 4857
        5.53 -    11.05: 21
       11.05 -    16.58: 1
       16.58 -    22.10: 1
       22.10 -    27.63: 1
  Bond angle restraints: 4881
  Sorted by residual:
  angle pdb=" PA  NDP A 501 "
        pdb=" O3  NDP A 501 "
        pdb=" PN  NDP A 501 "
      ideal   model   delta    sigma   weight residual
     107.74  135.37  -27.63 1.95e+00 2.62e-01 2.00e+02
  angle pdb=" C5B NDP A 501 "
        pdb=" O5B NDP A 501 "
        pdb=" PA  NDP A 501 "
      ideal   model   delta    sigma   weight residual
     103.84  121.33  -17.49 1.91e+00 2.73e-01 8.34e+01
  angle pdb=" C5D NDP A 501 "
        pdb=" O5D NDP A 501 "
        pdb=" PN  NDP A 501 "
      ideal   model   delta    sigma   weight residual
     104.93  120.33  -15.40 2.66e+00 1.41e-01 3.35e+01
  angle pdb=" O1X NDP A 501 "
        pdb=" P2B NDP A 501 "
        pdb=" O3X NDP A 501 "
      ideal   model   delta    sigma   weight residual
     117.46  111.64    5.82 1.17e+00 7.36e-01 2.50e+01
  angle pdb=" O3  NDP A 501 "
        pdb=" PA  NDP A 501 "
        pdb=" O5B NDP A 501 "
      ideal   model   delta    sigma   weight residual
     108.94   98.09   10.85 2.49e+00 1.62e-01 1.90e+01
  ... (remaining 4876 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.28: 1740
       20.28 -    40.57: 199
       40.57 -    60.85: 58
       60.85 -    81.13: 8
       81.13 -   101.42: 7
  Dihedral angle restraints: 2012
    sinusoidal: 850
      harmonic: 1162
  Sorted by residual:
  dihedral pdb=" C2B HEM A 503 "
           pdb=" C3B HEM A 503 "
           pdb=" CAB HEM A 503 "
           pdb=" CBB HEM A 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00   49.42  -49.42     2      1.00e+01 1.00e-02 2.77e+01
  dihedral pdb=" C5B NDP A 501 "
           pdb=" O5B NDP A 501 "
           pdb=" PA  NDP A 501 "
           pdb=" O3  NDP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.04  -83.54 -101.42     1      3.00e+01 1.11e-03 1.28e+01
  dihedral pdb=" C1A HEM A 504 "
           pdb=" C2A HEM A 504 "
           pdb=" CAA HEM A 504 "
           pdb=" CBA HEM A 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   94.44   85.56     2      2.00e+01 2.50e-03 1.19e+01
  ... (remaining 2009 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 416
       0.053 -    0.106: 74
       0.106 -    0.158: 17
       0.158 -    0.211: 1
       0.211 -    0.264: 1
  Chirality restraints: 509
  Sorted by residual:
  chirality pdb=" C4D NDP A 501 "
            pdb=" C3D NDP A 501 "
            pdb=" C5D NDP A 501 "
            pdb=" O4D NDP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.45   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" C2D NDP A 501 "
            pdb=" C1D NDP A 501 "
            pdb=" C3D NDP A 501 "
            pdb=" O2D NDP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.50   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C3B NDP A 501 "
            pdb=" C2B NDP A 501 "
            pdb=" C4B NDP A 501 "
            pdb=" O3B NDP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.59   -0.15 2.00e-01 2.50e+01 5.97e-01
  ... (remaining 506 not shown)

  Planarity restraints: 581
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C4N NDP A 501 "   -0.013 2.00e-02 2.50e+03   2.14e-02 4.58e+00
        pdb=" C5N NDP A 501 "    0.027 2.00e-02 2.50e+03
        pdb=" C6N NDP A 501 "   -0.028 2.00e-02 2.50e+03
        pdb=" N1N NDP A 501 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1A HEM A 503 "   -0.010 2.00e-02 2.50e+03   1.33e-02 3.98e+00
        pdb=" C2A HEM A 503 "   -0.014 2.00e-02 2.50e+03
        pdb=" C3A HEM A 503 "    0.001 2.00e-02 2.50e+03
        pdb=" C4A HEM A 503 "   -0.000 2.00e-02 2.50e+03
        pdb=" CAA HEM A 503 "    0.003 2.00e-02 2.50e+03
        pdb=" CHA HEM A 503 "    0.024 2.00e-02 2.50e+03
        pdb=" CHB HEM A 503 "    0.015 2.00e-02 2.50e+03
        pdb=" CMA HEM A 503 "    0.003 2.00e-02 2.50e+03
        pdb=" NA  HEM A 503 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  HEM A 503 "    0.008 2.00e-02 2.50e+03   1.01e-02 2.28e+00
        pdb=" C1B HEM A 503 "    0.012 2.00e-02 2.50e+03
        pdb=" C2B HEM A 503 "    0.002 2.00e-02 2.50e+03
        pdb=" C3B HEM A 503 "    0.013 2.00e-02 2.50e+03
        pdb=" C4B HEM A 503 "    0.006 2.00e-02 2.50e+03
        pdb=" CAB HEM A 503 "   -0.005 2.00e-02 2.50e+03
        pdb=" CHB HEM A 503 "   -0.014 2.00e-02 2.50e+03
        pdb=" CHC HEM A 503 "   -0.015 2.00e-02 2.50e+03
        pdb=" CMB HEM A 503 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 578 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 141
        2.72 -     3.26: 3343
        3.26 -     3.81: 6373
        3.81 -     4.35: 8207
        4.35 -     4.90: 13086
  Nonbonded interactions: 31150
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A  69 "
            pdb="FE   HEM A 504 "
     model   vdw
     2.169 3.080
  nonbonded pdb=" NE2 HIS A 142 "
            pdb="FE   HEM A 503 "
     model   vdw
     2.174 3.080
  nonbonded pdb=" O1P FAD A 502 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" CG2 THR A  28 "
            pdb=" O   HOH A 662 "
     model   vdw
     2.230 3.460
  nonbonded pdb=" OE1 GLU A 229 "
            pdb=" O   HOH A 602 "
     model   vdw
     2.232 3.040
  ... (remaining 31145 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:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.820
  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:6.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
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      :  0.009   0.234   3572  Z= 0.361
  Angle     :  0.959  27.630   4881  Z= 0.431
  Chirality :  0.045   0.264    509
  Planarity :  0.003   0.021    581
  Dihedral  : 19.299 101.415   1272
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 19.31 %
    Favored  : 79.83 %
  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:  1.00 (0.42), residues: 397
  helix:  1.33 (0.37), residues: 193
  sheet:  0.26 (0.52), residues: 96
  loop :  0.05 (0.64), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.011   0.001   TYR A 275 
 PHE   0.010   0.001   PHE A 218 
 TRP   0.004   0.001   TRP A 127 
 HIS   0.006   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00930 ( 3570)
  covalent geometry    : angle       0.95881 ( 4881)
  hydrogen bonds       : bond        0.14620 (  193)
  hydrogen bonds       : angle       6.89758 (  555)
  Misc. bond           : bond        0.03082 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7138 (tt0) cc_final: 0.6912 (mp0)
  outliers start: 3
  outliers final: 3
  residues processed: 51
  average time/residue: 0.4379
  time to fit residues: 23.1976
Evaluate side-chains
  48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 SER
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue  160 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0970
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.129713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.110374 restraints weight = 3342.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.27
r_work: 0.3166 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.0802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.227   3572  Z= 0.127
  Angle     :  0.606  13.764   4881  Z= 0.266
  Chirality :  0.040   0.136    509
  Planarity :  0.003   0.020    581
  Dihedral  : 12.361 106.343    513
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.00 %
    Favored  : 80.12 %
  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:  1.77 (0.43), residues: 397
  helix:  2.29 (0.36), residues: 196
  sheet:  0.31 (0.53), residues: 96
  loop : -0.03 (0.64), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.012   0.001   TYR A 275 
 PHE   0.011   0.001   PHE A 218 
 TRP   0.011   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3570)
  covalent geometry    : angle       0.60616 ( 4881)
  hydrogen bonds       : bond        0.04168 (  193)
  hydrogen bonds       : angle       4.66471 (  555)
  Misc. bond           : bond        0.21690 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7784 (tt0) cc_final: 0.7082 (mp0)
REVERT: A  323 GLU cc_start: 0.6819 (pm20) cc_final: 0.6332 (pm20)
REVERT: A  385 LYS cc_start: 0.7068 (tmmt) cc_final: 0.6321 (tttp)
  outliers start: 10
  outliers final: 5
  residues processed: 63
  average time/residue: 0.5817
  time to fit residues: 37.8590
Evaluate side-chains
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 SER
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  353 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   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 = 0.3496 r_free = 0.3496 target = 0.129278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.109792 restraints weight = 3317.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.27
r_work: 0.3152 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.212   3572  Z= 0.137
  Angle     :  0.623  14.168   4881  Z= 0.270
  Chirality :  0.041   0.138    509
  Planarity :  0.003   0.021    581
  Dihedral  : 12.325 106.824    512
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.29 %
    Favored  : 80.40 %
  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:  1.70 (0.43), residues: 397
  helix:  2.27 (0.36), residues: 196
  sheet:  0.27 (0.53), residues: 95
  loop : -0.14 (0.63), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 320 
 TYR   0.012   0.002   TYR A 275 
 PHE   0.012   0.001   PHE A 218 
 TRP   0.007   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3570)
  covalent geometry    : angle       0.62331 ( 4881)
  hydrogen bonds       : bond        0.04267 (  193)
  hydrogen bonds       : angle       4.65955 (  555)
  Misc. bond           : bond        0.21031 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7803 (tt0) cc_final: 0.7088 (mp0)
REVERT: A  285 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6819 (tt0)
REVERT: A  323 GLU cc_start: 0.6801 (pm20) cc_final: 0.6371 (pm20)
REVERT: A  385 LYS cc_start: 0.7102 (tmmt) cc_final: 0.6355 (tttp)
  outliers start: 8
  outliers final: 3
  residues processed: 56
  average time/residue: 0.4987
  time to fit residues: 29.0009
Evaluate side-chains
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  353 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0000
   chunk 35 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0670
   chunk 12 optimal weight:    0.0970
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.3520

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.132772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.113496 restraints weight = 3290.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.26
r_work: 0.3203 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.180   3572  Z= 0.099
  Angle     :  0.543  11.999   4881  Z= 0.239
  Chirality :  0.039   0.138    509
  Planarity :  0.003   0.019    581
  Dihedral  : 11.879 104.143    511
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.58 %
    Favored  : 80.12 %
  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:  1.89 (0.43), residues: 397
  helix:  2.49 (0.36), residues: 196
  sheet:  0.49 (0.55), residues: 88
  loop : -0.30 (0.61), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.012   0.001   TYR A 275 
 PHE   0.010   0.001   PHE A 154 
 TRP   0.007   0.001   TRP A  25 
 HIS   0.005   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 3570)
  covalent geometry    : angle       0.54285 ( 4881)
  hydrogen bonds       : bond        0.03419 (  193)
  hydrogen bonds       : angle       4.37634 (  555)
  Misc. bond           : bond        0.17330 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7779 (tt0) cc_final: 0.7119 (mp0)
REVERT: A  285 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6804 (tt0)
REVERT: A  323 GLU cc_start: 0.6791 (pm20) cc_final: 0.6300 (pm20)
REVERT: A  385 LYS cc_start: 0.7173 (tmmt) cc_final: 0.6521 (tmmt)
  outliers start: 8
  outliers final: 3
  residues processed: 59
  average time/residue: 0.5202
  time to fit residues: 31.8020
Evaluate side-chains
  55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3504 r_free = 0.3504 target = 0.129918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.110547 restraints weight = 3313.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.26
r_work: 0.3164 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.193   3572  Z= 0.131
  Angle     :  0.605  13.710   4881  Z= 0.263
  Chirality :  0.040   0.139    509
  Planarity :  0.003   0.021    581
  Dihedral  : 12.190 107.611    511
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.44 %
    Favored  : 79.83 %
  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:  1.74 (0.43), residues: 397
  helix:  2.36 (0.36), residues: 196
  sheet:  0.23 (0.53), residues: 95
  loop : -0.18 (0.62), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.011   0.002   TYR A 275 
 PHE   0.012   0.001   PHE A 218 
 TRP   0.004   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3570)
  covalent geometry    : angle       0.60506 ( 4881)
  hydrogen bonds       : bond        0.04054 (  193)
  hydrogen bonds       : angle       4.53931 (  555)
  Misc. bond           : bond        0.19146 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7800 (tt0) cc_final: 0.7091 (mp0)
REVERT: A  285 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6825 (tt0)
REVERT: A  323 GLU cc_start: 0.6815 (pm20) cc_final: 0.6264 (pm20)
REVERT: A  385 LYS cc_start: 0.7283 (tmmt) cc_final: 0.6548 (tmmt)
  outliers start: 6
  outliers final: 3
  residues processed: 55
  average time/residue: 0.5005
  time to fit residues: 28.5400
Evaluate side-chains
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3499 r_free = 0.3499 target = 0.129514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110073 restraints weight = 3308.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.27
r_work: 0.3155 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.203   3572  Z= 0.139
  Angle     :  0.613  13.499   4881  Z= 0.270
  Chirality :  0.041   0.139    509
  Planarity :  0.003   0.021    581
  Dihedral  : 12.292 109.199    511
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.87 %
    Favored  : 80.40 %
  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:  1.66 (0.43), residues: 397
  helix:  2.29 (0.36), residues: 196
  sheet:  0.19 (0.53), residues: 95
  loop : -0.22 (0.62), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.011   0.002   TYR A 275 
 PHE   0.012   0.001   PHE A 218 
 TRP   0.004   0.001   TRP A  25 
 HIS   0.008   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3570)
  covalent geometry    : angle       0.61332 ( 4881)
  hydrogen bonds       : bond        0.04190 (  193)
  hydrogen bonds       : angle       4.61919 (  555)
  Misc. bond           : bond        0.20216 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7786 (tt0) cc_final: 0.7095 (mp0)
REVERT: A  285 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6825 (tt0)
REVERT: A  323 GLU cc_start: 0.6689 (pm20) cc_final: 0.6190 (pm20)
REVERT: A  385 LYS cc_start: 0.7301 (tmmt) cc_final: 0.6575 (tmmt)
  outliers start: 6
  outliers final: 3
  residues processed: 53
  average time/residue: 0.5148
  time to fit residues: 28.3213
Evaluate side-chains
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0980
   chunk 6 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0670
   chunk 33 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0000
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.3322

-------------------------------------------------------------------------------
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 = 0.3542 r_free = 0.3542 target = 0.133132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.113858 restraints weight = 3342.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.27
r_work: 0.3207 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.176   3572  Z= 0.097
  Angle     :  0.534  11.460   4881  Z= 0.237
  Chirality :  0.039   0.140    509
  Planarity :  0.003   0.020    581
  Dihedral  : 11.864 105.818    511
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.44 %
    Favored  : 80.12 %
  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:  1.87 (0.43), residues: 397
  helix:  2.49 (0.36), residues: 197
  sheet:  0.39 (0.55), residues: 88
  loop : -0.28 (0.60), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.011   0.001   TYR A 275 
 PHE   0.011   0.001   PHE A 154 
 TRP   0.007   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 3570)
  covalent geometry    : angle       0.53416 ( 4881)
  hydrogen bonds       : bond        0.03329 (  193)
  hydrogen bonds       : angle       4.31263 (  555)
  Misc. bond           : bond        0.17299 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7777 (tt0) cc_final: 0.7090 (mp0)
REVERT: A  285 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6811 (tt0)
REVERT: A  323 GLU cc_start: 0.6808 (pm20) cc_final: 0.6248 (pm20)
REVERT: A  385 LYS cc_start: 0.7148 (tmmt) cc_final: 0.6444 (tmmt)
  outliers start: 5
  outliers final: 3
  residues processed: 56
  average time/residue: 0.5164
  time to fit residues: 29.9677
Evaluate side-chains
  55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0770
   chunk 21 optimal weight:    0.3980
   chunk 37 optimal weight:    0.4980
   chunk 19 optimal weight:    0.7980
   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 = 0.3530 r_free = 0.3530 target = 0.132168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.112743 restraints weight = 3414.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.29
r_work: 0.3193 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.167   3572  Z= 0.105
  Angle     :  0.556  12.385   4881  Z= 0.243
  Chirality :  0.039   0.140    509
  Planarity :  0.003   0.020    581
  Dihedral  : 11.926 106.133    511
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.16 %
    Favored  : 80.12 %
  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:  1.89 (0.43), residues: 397
  helix:  2.50 (0.36), residues: 197
  sheet:  0.41 (0.55), residues: 88
  loop : -0.28 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 201 
 TYR   0.012   0.001   TYR A 275 
 PHE   0.012   0.001   PHE A 154 
 TRP   0.005   0.001   TRP A  25 
 HIS   0.006   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 3570)
  covalent geometry    : angle       0.55600 ( 4881)
  hydrogen bonds       : bond        0.03524 (  193)
  hydrogen bonds       : angle       4.34234 (  555)
  Misc. bond           : bond        0.16701 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7792 (tt0) cc_final: 0.7091 (mp0)
REVERT: A  285 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6814 (tt0)
REVERT: A  323 GLU cc_start: 0.6807 (pm20) cc_final: 0.6242 (pm20)
REVERT: A  373 ILE cc_start: 0.8070 (tp) cc_final: 0.7791 (tp)
REVERT: A  385 LYS cc_start: 0.7162 (tmmt) cc_final: 0.6451 (tmmt)
  outliers start: 6
  outliers final: 4
  residues processed: 56
  average time/residue: 0.5234
  time to fit residues: 30.2996
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 8 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3502 r_free = 0.3502 target = 0.129774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.110623 restraints weight = 3286.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.25
r_work: 0.3165 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.189   3572  Z= 0.136
  Angle     :  0.610  13.518   4881  Z= 0.269
  Chirality :  0.041   0.139    509
  Planarity :  0.003   0.021    581
  Dihedral  : 12.229 111.148    511
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.73 %
    Favored  : 79.83 %
  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:  1.75 (0.43), residues: 397
  helix:  2.34 (0.36), residues: 197
  sheet:  0.21 (0.54), residues: 95
  loop : -0.13 (0.62), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.011   0.002   TYR A 275 
 PHE   0.013   0.001   PHE A 154 
 TRP   0.004   0.001   TRP A 125 
 HIS   0.007   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3570)
  covalent geometry    : angle       0.61026 ( 4881)
  hydrogen bonds       : bond        0.04087 (  193)
  hydrogen bonds       : angle       4.56295 (  555)
  Misc. bond           : bond        0.18935 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7801 (tt0) cc_final: 0.7102 (mp0)
REVERT: A  285 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6800 (tt0)
REVERT: A  323 GLU cc_start: 0.6686 (pm20) cc_final: 0.6169 (pm20)
REVERT: A  385 LYS cc_start: 0.7235 (tmmt) cc_final: 0.6500 (tmmt)
  outliers start: 5
  outliers final: 4
  residues processed: 54
  average time/residue: 0.5616
  time to fit residues: 31.4036
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 30 optimal weight:    0.3980
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3513 r_free = 0.3513 target = 0.130693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.111363 restraints weight = 3355.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.27
r_work: 0.3174 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.191   3572  Z= 0.122
  Angle     :  0.586  12.925   4881  Z= 0.259
  Chirality :  0.040   0.139    509
  Planarity :  0.003   0.020    581
  Dihedral  : 12.167 111.679    511
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.16 %
    Favored  : 80.12 %
  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:  1.75 (0.43), residues: 397
  helix:  2.36 (0.36), residues: 197
  sheet:  0.19 (0.54), residues: 95
  loop : -0.14 (0.62), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.012   0.001   TYR A 275 
 PHE   0.011   0.001   PHE A 218 
 TRP   0.004   0.001   TRP A  25 
 HIS   0.007   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3570)
  covalent geometry    : angle       0.58567 ( 4881)
  hydrogen bonds       : bond        0.03854 (  193)
  hydrogen bonds       : angle       4.50127 (  555)
  Misc. bond           : bond        0.18969 (    2)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  226 GLU cc_start: 0.7811 (tt0) cc_final: 0.7100 (mp0)
REVERT: A  285 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6809 (tt0)
REVERT: A  323 GLU cc_start: 0.6706 (pm20) cc_final: 0.6188 (pm20)
REVERT: A  385 LYS cc_start: 0.7168 (tmmt) cc_final: 0.6432 (tmmt)
  outliers start: 6
  outliers final: 4
  residues processed: 56
  average time/residue: 0.5442
  time to fit residues: 31.5581
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  285 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3504 r_free = 0.3504 target = 0.129906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.110641 restraints weight = 3326.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.26
r_work: 0.3164 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.194   3572  Z= 0.133
  Angle     :  0.602  13.322   4881  Z= 0.265
  Chirality :  0.041   0.139    509
  Planarity :  0.003   0.021    581
  Dihedral  : 12.271 113.185    511
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.44 %
    Favored  : 80.12 %
  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:  1.72 (0.43), residues: 397
  helix:  2.32 (0.36), residues: 197
  sheet:  0.20 (0.54), residues: 95
  loop : -0.13 (0.62), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.011   0.002   TYR A 275 
 PHE   0.012   0.001   PHE A 218 
 TRP   0.004   0.001   TRP A  25 
 HIS   0.008   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3570)
  covalent geometry    : angle       0.60155 ( 4881)
  hydrogen bonds       : bond        0.04056 (  193)
  hydrogen bonds       : angle       4.54333 (  555)
  Misc. bond           : bond        0.19390 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1710.71 seconds
wall clock time: 29 minutes 58.77 seconds (1798.77 seconds total)