Starting phenix.real_space_refine
on Fri Aug 22 12:59:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wll_37623/08_2025/8wll_37623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wll_37623/08_2025/8wll_37623.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wll_37623/08_2025/8wll_37623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wll_37623/08_2025/8wll_37623.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wll_37623/08_2025/8wll_37623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wll_37623/08_2025/8wll_37623.map"
  }
  resolution = 3.74
  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=   0.079
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    1875      2.51       5
     N     433      2.21       5
     O     479      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2815
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 2771
          Classifications: {'peptide': 389}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 22, 'TRANS': 366}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 157
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 131
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 4, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 108
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.08, per 1000 atoms: 0.38
  Number of scatterers: 2815
  At special positions: 0
  Unit cell: (73.216, 53.248, 64.064, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     479      8.00
     N     433      7.00
     C    1875      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.26
  Conformation dependent library (CDL) restraints added in 118.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  702

  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: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 40
      removed outlier: 3.847A  pdb=" N   ILE A  22 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 54
      removed outlier: 3.625A  pdb=" N   GLU A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 156
      removed outlier: 4.112A  pdb=" N   LYS A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ALA A 139 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      Proline residue:  A 147  - end of helix
    Processing helix  chain 'A' and resid 158 through 178
      removed outlier: 3.942A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 211
      removed outlier: 3.822A  pdb=" N   ILE A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   MET A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 246
      removed outlier: 4.161A  pdb=" N   VAL A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU A 233 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      Proline residue:  A 236  - end of helix
      removed outlier: 3.540A  pdb=" N   VAL A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 270
      removed outlier: 3.518A  pdb=" N   LEU A 270 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 291
    Processing helix  chain 'A' and resid 291 through 321
      removed outlier: 3.784A  pdb=" N   ALA A 297 " --> pdb=" O   TYR A 293 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      Proline residue:  A 313  - end of helix
      Proline residue:  A 316  - end of helix
    Processing helix  chain 'A' and resid 328 through 349
      removed outlier: 4.544A  pdb=" N   VAL A 332 " --> pdb=" O   TRP A 328 " (cutoff:3.500A)
      Proline residue:  A 336  - end of helix
    Processing helix  chain 'A' and resid 351 through 356
    Processing helix  chain 'A' and resid 356 through 375
    Processing helix  chain 'A' and resid 376 through 378
      No H-bonds generated for 'chain 'A' and resid 376 through 378'
    Processing helix  chain 'A' and resid 384 through 414
      Proline residue:  A 404  - end of helix
      removed outlier: 3.998A  pdb=" N   GLY A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 447
      Proline residue:  A 437  - end of helix
      removed outlier: 4.142A  pdb=" N   ALA A 446 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 464
    Processing helix  chain 'A' and resid 465 through 471

    243 hydrogen bonds defined for protein.
    717 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.39

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        0.63 -     0.87: 2
        0.87 -     1.10: 0
        1.10 -     1.34: 842
        1.34 -     1.58: 1987
        1.58 -     1.82: 52
  Bond restraints: 2883
  Sorted by residual:
  bond pdb=" C6  YHR A 501 "
       pdb=" C7  YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.521  0.629  0.892 2.00e-02 2.50e+03 1.99e+03
  bond pdb=" C13 YHR A 501 "
       pdb=" C14 YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.527  0.839  0.688 2.00e-02 2.50e+03 1.18e+03
  bond pdb=" C5  YHR A 501 "
       pdb=" C6  YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.527  1.276  0.251 2.00e-02 2.50e+03 1.57e+02
  bond pdb=" C12 YHR A 501 "
       pdb=" C13 YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.503  1.745 -0.242 2.00e-02 2.50e+03 1.46e+02
  bond pdb=" C16 YHR A 501 "
       pdb=" C3  YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.531  1.299  0.232 2.00e-02 2.50e+03 1.34e+02
  ... (remaining 2878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 3768
        2.20 -     4.40: 119
        4.40 -     6.60: 41
        6.60 -     8.80: 10
        8.80 -    11.00: 5
  Bond angle restraints: 3943
  Sorted by residual:
  angle pdb=" CB  MET A 397 "
        pdb=" CG  MET A 397 "
        pdb=" SD  MET A 397 "
      ideal   model   delta    sigma   weight residual
     112.70  123.70  -11.00 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" C7  YHR A 501 "
        pdb=" N8  YHR A 501 "
        pdb=" C9  YHR A 501 "
      ideal   model   delta    sigma   weight residual
     111.89  122.57  -10.68 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" C33 YHR A 501 "
        pdb=" C31 YHR A 501 "
        pdb=" O30 YHR A 501 "
      ideal   model   delta    sigma   weight residual
     112.77  122.76   -9.99 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" N   GLY A 235 "
        pdb=" CA  GLY A 235 "
        pdb=" C   GLY A 235 "
      ideal   model   delta    sigma   weight residual
     112.34  118.82   -6.48 2.04e+00 2.40e-01 1.01e+01
  angle pdb=" CB  MET A 403 "
        pdb=" CG  MET A 403 "
        pdb=" SD  MET A 403 "
      ideal   model   delta    sigma   weight residual
     112.70  121.92   -9.22 3.00e+00 1.11e-01 9.45e+00
  ... (remaining 3938 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.56: 1468
       11.56 -    23.11: 147
       23.11 -    34.66: 72
       34.66 -    46.22: 27
       46.22 -    57.77: 5
  Dihedral angle restraints: 1719
    sinusoidal: 619
      harmonic: 1100
  Sorted by residual:
  dihedral pdb=" CA  ARG A 326 "
           pdb=" C   ARG A 326 "
           pdb=" N   LYS A 327 "
           pdb=" CA  LYS A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.96   19.04     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  GLY A 235 "
           pdb=" C   GLY A 235 "
           pdb=" N   PRO A 236 "
           pdb=" CA  PRO A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.87  -18.13     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CG  ARG A 357 "
           pdb=" CD  ARG A 357 "
           pdb=" NE  ARG A 357 "
           pdb=" CZ  ARG A 357 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  130.81  -40.81     2      1.50e+01 4.44e-03 9.11e+00
  ... (remaining 1716 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.348: 483
       0.348 -    0.695: 1
       0.695 -    1.043: 1
       1.043 -    1.391: 0
       1.391 -    1.738: 1
  Chirality restraints: 486
  Sorted by residual:
  chirality pdb=" C6  YHR A 501 "
            pdb=" C15 YHR A 501 "
            pdb=" C5  YHR A 501 "
            pdb=" C7  YHR A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    0.79    1.74 2.00e-01 2.50e+01 7.55e+01
  chirality pdb=" C13 YHR A 501 "
            pdb=" C12 YHR A 501 "
            pdb=" C14 YHR A 501 "
            pdb=" N8  YHR A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -1.46   -0.83 2.00e-01 2.50e+01 1.71e+01
  chirality pdb=" C3  YHR A 501 "
            pdb=" C16 YHR A 501 "
            pdb=" C4  YHR A 501 "
            pdb=" O2  YHR A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.11    0.47 2.00e-01 2.50e+01 5.64e+00
  ... (remaining 483 not shown)

  Planarity restraints: 479
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 291 "   -0.055 5.00e-02 4.00e+02   8.32e-02 1.11e+01
        pdb=" N   PRO A 292 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 292 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 292 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 250 "   -0.045 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO A 251 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 251 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 251 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 375 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO A 376 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 376 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 376 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 476 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 552
        2.77 -     3.30: 3075
        3.30 -     3.84: 4819
        3.84 -     4.37: 5149
        4.37 -     4.90: 9055
  Nonbonded interactions: 22650
  Sorted by model distance:
  nonbonded pdb=" C15 YHR A 501 "
            pdb=" N8  YHR A 501 "
     model   vdw
     2.238 2.840
  nonbonded pdb=" OG  SER A 137 "
            pdb=" OG  SER A 190 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   PHE A 170 "
            pdb=" OG1 THR A 173 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   ALA A 297 "
            pdb=" OG  SER A 300 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OG  SER A 325 "
            pdb=" OE1 GLN A 329 "
     model   vdw
     2.314 3.040
  ... (remaining 22645 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.950
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
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      :  0.024   0.892   2883  Z= 1.204
  Angle     :  1.058  11.003   3943  Z= 0.473
  Chirality :  0.102   1.738    486
  Planarity :  0.007   0.083    479
  Dihedral  : 13.070  57.774   1017
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.58 (0.44), residues: 385
  helix:  0.87 (0.30), residues: 323
  sheet:  None (None), residues: 0
  loop : -1.89 (0.79), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  19 
 TYR   0.016   0.002   TYR A  47 
 PHE   0.020   0.002   PHE A 166 
 TRP   0.009   0.002   TRP A 451 
 HIS   0.002   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.02419 ( 2883)
  covalent geometry    : angle       1.05800 ( 3943)
  hydrogen bonds       : bond        0.10037 (  243)
  hydrogen bonds       : angle       5.45979 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  144 ILE cc_start: 0.8518 (mm) cc_final: 0.8285 (mm)
REVERT: A  287 THR cc_start: 0.7984 (p) cc_final: 0.7783 (p)
REVERT: A  408 TYR cc_start: 0.8277 (t80) cc_final: 0.7731 (t80)
REVERT: A  453 MET cc_start: 0.7950 (mmm) cc_final: 0.7587 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0434
  time to fit residues: 7.9441
Evaluate side-chains
  111 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0570
   chunk 16 optimal weight:    0.0020
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4506

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.148473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.129409 restraints weight = 5242.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.133119 restraints weight = 3182.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.135674 restraints weight = 2133.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.137609 restraints weight = 1565.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.139051 restraints weight = 1202.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   2883  Z= 0.156
  Angle     :  0.806   8.838   3943  Z= 0.380
  Chirality :  0.045   0.191    486
  Planarity :  0.006   0.055    479
  Dihedral  :  6.989  52.780    467
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 17.99 %
    Favored  : 78.06 %
  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:  0.81 (0.44), residues: 385
  helix:  1.12 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -3.00 (0.75), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 326 
 TYR   0.022   0.002   TYR A 341 
 PHE   0.019   0.001   PHE A  27 
 TRP   0.010   0.001   TRP A 451 
 HIS   0.002   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 2883)
  covalent geometry    : angle       0.80601 ( 3943)
  hydrogen bonds       : bond        0.04158 (  243)
  hydrogen bonds       : angle       4.58099 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7667 (tt) cc_final: 0.6956 (mp)
REVERT: A  133 LEU cc_start: 0.8379 (mm) cc_final: 0.8034 (mm)
REVERT: A  144 ILE cc_start: 0.8389 (mm) cc_final: 0.8188 (mm)
REVERT: A  170 PHE cc_start: 0.8775 (t80) cc_final: 0.8369 (t80)
REVERT: A  355 MET cc_start: 0.7894 (ppp) cc_final: 0.7685 (ppp)
REVERT: A  388 ASN cc_start: 0.8695 (m-40) cc_final: 0.8447 (m110)
REVERT: A  402 MET cc_start: 0.8233 (mmp) cc_final: 0.8023 (mmp)
REVERT: A  408 TYR cc_start: 0.8293 (t80) cc_final: 0.7730 (t80)
REVERT: A  452 LEU cc_start: 0.8657 (tt) cc_final: 0.8311 (tt)
REVERT: A  453 MET cc_start: 0.8161 (mmm) cc_final: 0.7572 (mmm)
  outliers start: 11
  outliers final: 8
  residues processed: 151
  average time/residue: 0.0407
  time to fit residues: 7.8973
Evaluate side-chains
  122 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  350 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.144439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125503 restraints weight = 5324.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.129044 restraints weight = 3194.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.131694 restraints weight = 2149.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.133520 restraints weight = 1552.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.134948 restraints weight = 1194.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   2883  Z= 0.175
  Angle     :  0.789   7.479   3943  Z= 0.379
  Chirality :  0.044   0.169    486
  Planarity :  0.005   0.043    479
  Dihedral  :  6.237  53.106    467
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 26.26 %
    Favored  : 69.42 %
  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:  0.92 (0.44), residues: 385
  helix:  1.18 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -2.94 (0.81), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 326 
 TYR   0.012   0.002   TYR A 341 
 PHE   0.020   0.001   PHE A  27 
 TRP   0.007   0.001   TRP A 451 
 HIS   0.002   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 2883)
  covalent geometry    : angle       0.78852 ( 3943)
  hydrogen bonds       : bond        0.03894 (  243)
  hydrogen bonds       : angle       4.61876 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  355 MET cc_start: 0.7905 (ppp) cc_final: 0.7680 (tmm)
REVERT: A  388 ASN cc_start: 0.8751 (m-40) cc_final: 0.8444 (m110)
REVERT: A  408 TYR cc_start: 0.8313 (t80) cc_final: 0.7808 (t80)
  outliers start: 12
  outliers final: 9
  residues processed: 131
  average time/residue: 0.0362
  time to fit residues: 6.1633
Evaluate side-chains
  126 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  375 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0270
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.146217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127291 restraints weight = 5243.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.130832 restraints weight = 3157.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.133345 restraints weight = 2130.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.134915 restraints weight = 1561.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.136381 restraints weight = 1245.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   2883  Z= 0.151
  Angle     :  0.769   7.017   3943  Z= 0.365
  Chirality :  0.044   0.164    486
  Planarity :  0.005   0.038    479
  Dihedral  :  5.988  52.269    467
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 28.06 %
    Favored  : 68.71 %
  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:  1.09 (0.44), residues: 385
  helix:  1.29 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.89 (0.83), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 357 
 TYR   0.017   0.001   TYR A  47 
 PHE   0.019   0.001   PHE A  27 
 TRP   0.007   0.001   TRP A 451 
 HIS   0.002   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 2883)
  covalent geometry    : angle       0.76920 ( 3943)
  hydrogen bonds       : bond        0.03779 (  243)
  hydrogen bonds       : angle       4.47264 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A   49 TYR cc_start: 0.8152 (t80) cc_final: 0.7754 (t80)
REVERT: A  191 LEU cc_start: 0.7886 (tt) cc_final: 0.7570 (tt)
REVERT: A  341 TYR cc_start: 0.8173 (t80) cc_final: 0.7750 (t80)
REVERT: A  388 ASN cc_start: 0.8743 (m-40) cc_final: 0.8422 (m110)
REVERT: A  408 TYR cc_start: 0.8312 (t80) cc_final: 0.7805 (t80)
REVERT: A  453 MET cc_start: 0.8283 (mmm) cc_final: 0.7841 (mmm)
  outliers start: 9
  outliers final: 6
  residues processed: 128
  average time/residue: 0.0400
  time to fit residues: 6.6077
Evaluate side-chains
  128 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    0.1980
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.144635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.125924 restraints weight = 5268.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.129517 restraints weight = 3129.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.132221 restraints weight = 2088.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.133894 restraints weight = 1496.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.135211 restraints weight = 1167.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   2883  Z= 0.159
  Angle     :  0.786   7.729   3943  Z= 0.374
  Chirality :  0.044   0.143    486
  Planarity :  0.004   0.038    479
  Dihedral  :  5.828  51.751    467
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 29.86 %
    Favored  : 65.11 %
  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:  1.12 (0.44), residues: 385
  helix:  1.32 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.91 (0.83), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 326 
 TYR   0.012   0.001   TYR A  47 
 PHE   0.019   0.001   PHE A  27 
 TRP   0.006   0.001   TRP A 451 
 HIS   0.005   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 2883)
  covalent geometry    : angle       0.78615 ( 3943)
  hydrogen bonds       : bond        0.03752 (  243)
  hydrogen bonds       : angle       4.52844 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   49 TYR cc_start: 0.8140 (t80) cc_final: 0.7774 (t80)
REVERT: A  191 LEU cc_start: 0.7961 (tt) cc_final: 0.7635 (tt)
REVERT: A  315 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8553 (mp)
REVERT: A  408 TYR cc_start: 0.8313 (t80) cc_final: 0.7789 (t80)
REVERT: A  453 MET cc_start: 0.8285 (mmm) cc_final: 0.7844 (mmm)
  outliers start: 14
  outliers final: 11
  residues processed: 133
  average time/residue: 0.0393
  time to fit residues: 6.7856
Evaluate side-chains
  138 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 18 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.125231 restraints weight = 5359.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.128844 restraints weight = 3100.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.131125 restraints weight = 2028.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.133069 restraints weight = 1477.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.134251 restraints weight = 1117.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   2883  Z= 0.172
  Angle     :  0.818   9.762   3943  Z= 0.391
  Chirality :  0.044   0.134    486
  Planarity :  0.005   0.037    479
  Dihedral  :  5.875  51.840    467
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 30.94 %
    Favored  : 62.23 %
  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 (0.44), residues: 385
  helix:  1.24 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.98 (0.83), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 326 
 TYR   0.014   0.001   TYR A  47 
 PHE   0.020   0.001   PHE A  27 
 TRP   0.006   0.001   TRP A 451 
 HIS   0.010   0.003   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 2883)
  covalent geometry    : angle       0.81794 ( 3943)
  hydrogen bonds       : bond        0.03824 (  243)
  hydrogen bonds       : angle       4.65520 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  191 LEU cc_start: 0.8084 (tt) cc_final: 0.7732 (tt)
REVERT: A  315 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8611 (mp)
REVERT: A  341 TYR cc_start: 0.8124 (t80) cc_final: 0.7759 (t80)
REVERT: A  388 ASN cc_start: 0.8692 (m110) cc_final: 0.8468 (m110)
REVERT: A  408 TYR cc_start: 0.8333 (t80) cc_final: 0.7800 (t80)
REVERT: A  453 MET cc_start: 0.8341 (mmm) cc_final: 0.7860 (mmm)
  outliers start: 19
  outliers final: 12
  residues processed: 134
  average time/residue: 0.0370
  time to fit residues: 6.4490
Evaluate side-chains
  136 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.142270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.124498 restraints weight = 5291.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.128085 restraints weight = 3066.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.130623 restraints weight = 2015.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.132452 restraints weight = 1446.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.133462 restraints weight = 1104.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   2883  Z= 0.166
  Angle     :  0.863  14.012   3943  Z= 0.406
  Chirality :  0.045   0.143    486
  Planarity :  0.004   0.037    479
  Dihedral  :  5.833  51.363    467
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 33.81 %
    Favored  : 60.79 %
  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:  0.89 (0.44), residues: 385
  helix:  1.16 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.95 (0.83), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  19 
 TYR   0.018   0.002   TYR A 211 
 PHE   0.019   0.001   PHE A  27 
 TRP   0.006   0.001   TRP A 451 
 HIS   0.007   0.002   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 2883)
  covalent geometry    : angle       0.86346 ( 3943)
  hydrogen bonds       : bond        0.03803 (  243)
  hydrogen bonds       : angle       4.72021 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  175 MET cc_start: 0.7900 (mtp) cc_final: 0.7565 (mtp)
REVERT: A  191 LEU cc_start: 0.8036 (tt) cc_final: 0.7681 (tt)
REVERT: A  315 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8588 (mp)
REVERT: A  341 TYR cc_start: 0.8101 (t80) cc_final: 0.7736 (t80)
REVERT: A  388 ASN cc_start: 0.8712 (m110) cc_final: 0.8457 (m110)
REVERT: A  408 TYR cc_start: 0.8340 (t80) cc_final: 0.7788 (t80)
REVERT: A  453 MET cc_start: 0.8337 (mmm) cc_final: 0.7852 (mmm)
  outliers start: 15
  outliers final: 12
  residues processed: 131
  average time/residue: 0.0381
  time to fit residues: 6.5098
Evaluate side-chains
  133 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0870
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.1762

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.141028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.123535 restraints weight = 5478.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.127080 restraints weight = 3144.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.129624 restraints weight = 2065.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131219 restraints weight = 1469.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.132708 restraints weight = 1141.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   2883  Z= 0.179
  Angle     :  0.858  12.633   3943  Z= 0.409
  Chirality :  0.046   0.138    486
  Planarity :  0.005   0.036    479
  Dihedral  :  5.847  51.574    467
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 34.53 %
    Favored  : 59.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.44), residues: 385
  helix:  1.07 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -3.11 (0.82), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 357 
 TYR   0.014   0.002   TYR A 211 
 PHE   0.019   0.001   PHE A  27 
 TRP   0.005   0.001   TRP A 451 
 HIS   0.006   0.002   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 2883)
  covalent geometry    : angle       0.85755 ( 3943)
  hydrogen bonds       : bond        0.03885 (  243)
  hydrogen bonds       : angle       4.81951 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  175 MET cc_start: 0.7921 (mtp) cc_final: 0.7608 (mtp)
REVERT: A  191 LEU cc_start: 0.8038 (tt) cc_final: 0.7705 (tt)
REVERT: A  315 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8601 (mp)
REVERT: A  408 TYR cc_start: 0.8344 (t80) cc_final: 0.7803 (t80)
REVERT: A  453 MET cc_start: 0.8348 (mmm) cc_final: 0.7870 (mmm)
  outliers start: 17
  outliers final: 13
  residues processed: 134
  average time/residue: 0.0382
  time to fit residues: 6.6627
Evaluate side-chains
  135 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 2 optimal weight:    0.0370
   chunk 28 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   chunk 9 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 ASN
A 388 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.143762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125859 restraints weight = 5349.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.129509 restraints weight = 3067.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.132063 restraints weight = 1999.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.133854 restraints weight = 1433.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.135095 restraints weight = 1098.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   2883  Z= 0.164
  Angle     :  0.883  15.770   3943  Z= 0.417
  Chirality :  0.047   0.164    486
  Planarity :  0.005   0.037    479
  Dihedral  :  6.087  52.290    467
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 36.69 %
    Favored  : 57.55 %
  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:  0.70 (0.44), residues: 385
  helix:  1.03 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.99 (0.83), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 357 
 TYR   0.015   0.002   TYR A 211 
 PHE   0.017   0.001   PHE A  27 
 TRP   0.008   0.001   TRP A 328 
 HIS   0.005   0.002   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 2883)
  covalent geometry    : angle       0.88288 ( 3943)
  hydrogen bonds       : bond        0.03907 (  243)
  hydrogen bonds       : angle       4.77359 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A  169 MET cc_start: 0.9194 (tpp) cc_final: 0.8947 (tpp)
REVERT: A  175 MET cc_start: 0.7909 (mtp) cc_final: 0.7593 (mtp)
REVERT: A  191 LEU cc_start: 0.7902 (tt) cc_final: 0.7546 (tt)
REVERT: A  315 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8565 (mp)
REVERT: A  327 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7696 (mtmm)
REVERT: A  408 TYR cc_start: 0.8313 (t80) cc_final: 0.7750 (t80)
REVERT: A  453 MET cc_start: 0.8352 (mmm) cc_final: 0.7896 (mmm)
  outliers start: 16
  outliers final: 12
  residues processed: 128
  average time/residue: 0.0350
  time to fit residues: 5.7407
Evaluate side-chains
  131 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0000
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 10 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0020
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.146053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.127908 restraints weight = 5388.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.131654 restraints weight = 3100.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.134214 restraints weight = 2031.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136050 restraints weight = 1461.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.137597 restraints weight = 1114.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   2883  Z= 0.163
  Angle     :  0.896  15.446   3943  Z= 0.424
  Chirality :  0.047   0.161    486
  Planarity :  0.005   0.036    479
  Dihedral  :  6.257  53.735    467
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 38.49 %
    Favored  : 57.55 %
  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:  0.69 (0.44), residues: 385
  helix:  1.03 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.12 (0.81), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  19 
 TYR   0.015   0.002   TYR A 341 
 PHE   0.015   0.001   PHE A 389 
 TRP   0.008   0.001   TRP A 328 
 HIS   0.005   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 2883)
  covalent geometry    : angle       0.89553 ( 3943)
  hydrogen bonds       : bond        0.03906 (  243)
  hydrogen bonds       : angle       4.77218 (  717)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A  175 MET cc_start: 0.7874 (mtp) cc_final: 0.7545 (mtp)
REVERT: A  191 LEU cc_start: 0.7885 (tt) cc_final: 0.7516 (tt)
REVERT: A  315 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8409 (mp)
REVERT: A  327 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7717 (mtmm)
REVERT: A  408 TYR cc_start: 0.8313 (t80) cc_final: 0.7743 (t80)
REVERT: A  453 MET cc_start: 0.8372 (mmm) cc_final: 0.7927 (mmm)
  outliers start: 11
  outliers final: 8
  residues processed: 123
  average time/residue: 0.0410
  time to fit residues: 6.5121
Evaluate side-chains
  124 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.4980
   chunk 4 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
A 192 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.144116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.126273 restraints weight = 5261.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.129865 restraints weight = 3045.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.132529 restraints weight = 2000.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.134338 restraints weight = 1431.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.135423 restraints weight = 1095.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   2883  Z= 0.167
  Angle     :  0.896  15.484   3943  Z= 0.426
  Chirality :  0.047   0.162    486
  Planarity :  0.005   0.036    479
  Dihedral  :  6.361  51.379    467
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 39.93 %
    Favored  : 56.83 %
  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:  0.64 (0.44), residues: 385
  helix:  1.02 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.25 (0.81), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 326 
 TYR   0.023   0.002   TYR A 341 
 PHE   0.023   0.001   PHE A 303 
 TRP   0.007   0.001   TRP A 328 
 HIS   0.005   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 2883)
  covalent geometry    : angle       0.89588 ( 3943)
  hydrogen bonds       : bond        0.03902 (  243)
  hydrogen bonds       : angle       4.80731 (  717)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 626.34 seconds
wall clock time: 11 minutes 24.17 seconds (684.17 seconds total)