Starting phenix.real_space_refine
on Mon Jan 13 14:58:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d7k_46607/01_2025/9d7k_46607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d7k_46607/01_2025/9d7k_46607.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d7k_46607/01_2025/9d7k_46607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d7k_46607/01_2025/9d7k_46607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d7k_46607/01_2025/9d7k_46607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d7k_46607/01_2025/9d7k_46607.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001 sd=   0.022
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      13      5.16       5
     C    1826      2.51       5
     N     466      2.21       5
     O     538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 2843
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "S"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 2843
          Classifications: {'peptide': 359}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 12, 'TRANS': 346}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 2.42, per 1000 atoms: 0.85
  Number of scatterers: 2843
  At special positions: 0
  Unit cell: (73.44, 74.52, 66.96, 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      13     16.00
     O     538      8.00
     N     466      7.00
     C    1826      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: 0.70
  Conformation dependent library (CDL) restraints added in 938.5 milliseconds
  

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  692

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 4 sheets defined
      37.0% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'S' and resid 48 through 68
      removed outlier: 3.693A  pdb=" N   ALA S  52 " --> pdb=" O   GLY S  48 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 76 through 89
    Processing helix  chain 'S' and resid 92 through 102
      removed outlier: 3.505A  pdb=" N   LEU S  96 " --> pdb=" O   HIS S  92 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   THR S  97 " --> pdb=" O   ASN S  93 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 103 through 105
      No H-bonds generated for 'chain 'S' and resid 103 through 105'
    Processing helix  chain 'S' and resid 111 through 128
    Processing helix  chain 'S' and resid 150 through 160
    Processing helix  chain 'S' and resid 172 through 188
      removed outlier: 3.671A  pdb=" N   LYS S 178 " --> pdb=" O   ALA S 174 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 222 through 226
    Processing helix  chain 'S' and resid 283 through 290
    Processing helix  chain 'S' and resid 292 through 302
      removed outlier: 3.516A  pdb=" N   ARG S 298 " --> pdb=" O   GLU S 294 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 324 through 332
    Processing helix  chain 'S' and resid 334 through 338
      removed outlier: 3.606A  pdb=" N   THR S 338 " --> pdb=" O   GLU S 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'S' and resid 73 through 75
      removed outlier: 3.563A  pdb=" N   PHE S 413 " --> pdb=" O   ILE S 403 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   CYS S 261 " --> pdb=" O   ASP S 256 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE S 251 " --> pdb=" O   ARG S 306 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU S 304 " --> pdb=" O   TYR S 253 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 134 through 137
      removed outlier: 3.740A  pdb=" N   SER S 136 " --> pdb=" O   PHE S 212 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL S 206 " --> pdb=" O   PHE S 142 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   THR S 168 " --> pdb=" O   MET S 141 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL S 143 " --> pdb=" O   THR S 168 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 134 through 137
      removed outlier: 3.740A  pdb=" N   SER S 136 " --> pdb=" O   PHE S 212 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ILE S 211 " --> pdb=" O   LYS S 360 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   PHE S 213 " --> pdb=" O   VAL S 362 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA S 361 " --> pdb=" O   ARG S 320 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ARG S 320 " --> pdb=" O   ALA S 361 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'S' and resid 227 through 232
      removed outlier: 3.628A  pdb=" N   SER S 229 " --> pdb=" O   VAL S 241 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU S 311 " --> pdb=" O   LEU S 246 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   ILE S 308 " --> pdb=" O   THR S 391 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   VAL S 393 " --> pdb=" O   ILE S 308 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   GLU S 310 " --> pdb=" O   VAL S 393 " (cutoff:3.500A)

    133 hydrogen bonds defined for protein.
    372 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: 0.79

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 917
        1.34 -     1.46: 560
        1.46 -     1.57: 1397
        1.57 -     1.69: 0
        1.69 -     1.80: 25
  Bond restraints: 2899
  Sorted by residual:
  bond pdb=" CB  ASP S 321 "
       pdb=" CG  ASP S 321 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.28e+00
  bond pdb=" CA  ASP S 321 "
       pdb=" CB  ASP S 321 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.013 1.55e-02 4.16e+03 7.20e-01
  bond pdb=" CA  GLU S 371 "
       pdb=" CB  GLU S 371 "
    ideal  model  delta    sigma   weight residual
    1.527  1.539 -0.012 1.61e-02 3.86e+03 5.12e-01
  bond pdb=" CB  PHE S  58 "
       pdb=" CG  PHE S  58 "
    ideal  model  delta    sigma   weight residual
    1.502  1.486  0.016 2.30e-02 1.89e+03 5.09e-01
  bond pdb=" CB  ASP S  70 "
       pdb=" CG  ASP S  70 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 2.50e-02 1.60e+03 4.98e-01
  ... (remaining 2894 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 3843
        1.60 -     3.20: 64
        3.20 -     4.80: 13
        4.80 -     6.40: 2
        6.40 -     7.99: 2
  Bond angle restraints: 3924
  Sorted by residual:
  angle pdb=" C   ASP S 321 "
        pdb=" CA  ASP S 321 "
        pdb=" CB  ASP S 321 "
      ideal   model   delta    sigma   weight residual
     109.48  113.79   -4.31 1.68e+00 3.54e-01 6.59e+00
  angle pdb=" CA  ASP S 321 "
        pdb=" CB  ASP S 321 "
        pdb=" CG  ASP S 321 "
      ideal   model   delta    sigma   weight residual
     112.60  114.97   -2.37 1.00e+00 1.00e+00 5.61e+00
  angle pdb=" CA  LEU S 133 "
        pdb=" CB  LEU S 133 "
        pdb=" CG  LEU S 133 "
      ideal   model   delta    sigma   weight residual
     116.30  124.29   -7.99 3.50e+00 8.16e-02 5.22e+00
  angle pdb=" C   ALA S 349 "
        pdb=" N   ARG S 350 "
        pdb=" CA  ARG S 350 "
      ideal   model   delta    sigma   weight residual
     121.54  125.54   -4.00 1.91e+00 2.74e-01 4.38e+00
  angle pdb=" CA  LEU S 195 "
        pdb=" CB  LEU S 195 "
        pdb=" CG  LEU S 195 "
      ideal   model   delta    sigma   weight residual
     116.30  123.43   -7.13 3.50e+00 8.16e-02 4.15e+00
  ... (remaining 3919 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 1495
       17.15 -    34.30: 180
       34.30 -    51.45: 59
       51.45 -    68.60: 13
       68.60 -    85.75: 5
  Dihedral angle restraints: 1752
    sinusoidal: 694
      harmonic: 1058
  Sorted by residual:
  dihedral pdb=" CA  LYS S 101 "
           pdb=" C   LYS S 101 "
           pdb=" N   GLY S 102 "
           pdb=" CA  GLY S 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.20   16.80     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CG  ARG S 350 "
           pdb=" CD  ARG S 350 "
           pdb=" NE  ARG S 350 "
           pdb=" CZ  ARG S 350 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.78  -44.22     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CA  ASN S 181 "
           pdb=" CB  ASN S 181 "
           pdb=" CG  ASN S 181 "
           pdb=" OD1 ASN S 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -154.79   64.79     2      2.00e+01 2.50e-03 9.82e+00
  ... (remaining 1749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 264
       0.027 -    0.055: 120
       0.055 -    0.082: 37
       0.082 -    0.110: 25
       0.110 -    0.137: 9
  Chirality restraints: 455
  Sorted by residual:
  chirality pdb=" CA  ILE S 251 "
            pdb=" N   ILE S 251 "
            pdb=" C   ILE S 251 "
            pdb=" CB  ILE S 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.71e-01
  chirality pdb=" CA  ILE S 277 "
            pdb=" N   ILE S 277 "
            pdb=" C   ILE S 277 "
            pdb=" CB  ILE S 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  VAL S 357 "
            pdb=" N   VAL S 357 "
            pdb=" C   VAL S 357 "
            pdb=" CB  VAL S 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 452 not shown)

  Planarity restraints: 499
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG S 397 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.54e+00
        pdb=" N   PRO S 398 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO S 398 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO S 398 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL S 404 "    0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO S 405 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO S 405 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO S 405 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP S 321 "   -0.006 2.00e-02 2.50e+03   1.19e-02 1.42e+00
        pdb=" C   ASP S 321 "    0.021 2.00e-02 2.50e+03
        pdb=" O   ASP S 321 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   TYR S 322 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 496 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 882
        2.83 -     3.34: 2542
        3.34 -     3.86: 4569
        3.86 -     4.38: 5079
        4.38 -     4.90: 8824
  Nonbonded interactions: 21896
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS S 116 "
            pdb=" OH  TYR S 161 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OG  SER S 317 "
            pdb=" OD1 ASP S 364 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" NE2 GLN S 117 "
            pdb=" OE1 GLN S 120 "
     model   vdw
     2.366 3.120
  nonbonded pdb=" OG  SER S  76 "
            pdb=" OG  SER S  79 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" O   THR S 338 "
            pdb=" OG1 THR S 338 "
     model   vdw
     2.416 3.040
  ... (remaining 21891 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:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.740
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   25.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2899  Z= 0.127
  Angle     :  0.554   7.995   3924  Z= 0.280
  Chirality :  0.042   0.137    455
  Planarity :  0.004   0.040    499
  Dihedral  : 17.288  85.754   1060
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 23.64 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.47), residues: 355
  helix:  1.76 (0.53), residues: 115
  sheet:  0.07 (0.66), residues: 81
  loop : -0.32 (0.48), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP S 299 
 HIS   0.003   0.001   HIS S 359 
 PHE   0.019   0.001   PHE S 212 
 TYR   0.007   0.001   TYR S 253 
 ARG   0.005   0.001   ARG S 298 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.277 
Fit side-chains
REVERT: S   58 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.5651 (t80)
REVERT: S   87 LEU cc_start: 0.7953 (tp) cc_final: 0.7667 (tm)
REVERT: S  145 GLU cc_start: 0.7722 (pt0) cc_final: 0.7145 (pt0)
REVERT: S  185 LYS cc_start: 0.7754 (tttt) cc_final: 0.7504 (tmtp)
REVERT: S  291 LEU cc_start: 0.5915 (mt) cc_final: 0.5573 (mt)
REVERT: S  333 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7202 (pt)
REVERT: S  362 VAL cc_start: 0.8579 (p) cc_final: 0.8322 (p)
  outliers start: 5
  outliers final: 1
  residues processed: 122
  average time/residue: 0.7254
  time to fit residues: 91.8043
Evaluate side-chains
  103 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   58 PHE
Chi-restraints excluded: chain S residue  246 LEU
Chi-restraints excluded: chain S residue  333 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0030
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0470
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.3488

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

Flipped N/Q/H residues before XYZ refinement:
S 139 ASN
S 186 ASN
S 351 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.155873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.143013 restraints weight = 5092.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 3.32
r_work: 0.3825 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2899  Z= 0.214
  Angle     :  0.690   8.098   3924  Z= 0.350
  Chirality :  0.046   0.242    455
  Planarity :  0.005   0.040    499
  Dihedral  :  6.083  58.780    385
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 29.71 %
    Favored  : 66.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.47), residues: 355
  helix:  1.80 (0.51), residues: 116
  sheet:  0.36 (0.59), residues: 90
  loop : -0.26 (0.51), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP S 217 
 HIS   0.003   0.001   HIS S 359 
 PHE   0.021   0.003   PHE S 212 
 TYR   0.015   0.002   TYR S 253 
 ARG   0.005   0.001   ARG S 152 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: S   87 LEU cc_start: 0.8213 (tp) cc_final: 0.7863 (tm)
REVERT: S  144 LYS cc_start: 0.8025 (tttp) cc_final: 0.7734 (tptm)
REVERT: S  145 GLU cc_start: 0.8125 (pt0) cc_final: 0.7529 (pt0)
REVERT: S  185 LYS cc_start: 0.8329 (tmtt) cc_final: 0.8101 (tmtp)
REVERT: S  204 MET cc_start: 0.7074 (mmt) cc_final: 0.6804 (mmm)
REVERT: S  258 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7308 (mm-30)
REVERT: S  298 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7122 (ttp80)
REVERT: S  333 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7385 (pt)
REVERT: S  362 VAL cc_start: 0.8544 (p) cc_final: 0.8323 (p)
REVERT: S  402 ILE cc_start: 0.8253 (mp) cc_final: 0.7962 (OUTLIER)
  outliers start: 11
  outliers final: 5
  residues processed: 113
  average time/residue: 0.9231
  time to fit residues: 107.5250
Evaluate side-chains
  106 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   58 PHE
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  254 PHE
Chi-restraints excluded: chain S residue  333 ILE
Chi-restraints excluded: chain S residue  416 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.6282

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

Flipped N/Q/H residues before XYZ refinement:
S 228 GLN
S 330 GLN
S 351 ASN
S 356 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.152537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.139974 restraints weight = 4966.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 3.01
r_work: 0.3790 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2899  Z= 0.237
  Angle     :  0.666   6.664   3924  Z= 0.337
  Chirality :  0.044   0.139    455
  Planarity :  0.005   0.074    499
  Dihedral  :  5.436  40.784    383
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 29.71 %
    Favored  : 67.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.47), residues: 355
  helix:  1.67 (0.50), residues: 116
  sheet: -0.06 (0.58), residues: 94
  loop : -0.16 (0.54), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP S 217 
 HIS   0.004   0.001   HIS S 359 
 PHE   0.033   0.003   PHE S  75 
 TYR   0.017   0.002   TYR S 253 
 ARG   0.005   0.001   ARG S 152 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   80 ILE cc_start: 0.7992 (mm) cc_final: 0.7786 (tp)
REVERT: S   87 LEU cc_start: 0.8267 (tp) cc_final: 0.7925 (tm)
REVERT: S  145 GLU cc_start: 0.8051 (pt0) cc_final: 0.7448 (pt0)
REVERT: S  185 LYS cc_start: 0.8322 (tmtt) cc_final: 0.8097 (tmtp)
REVERT: S  233 LEU cc_start: 0.8217 (mt) cc_final: 0.7967 (mp)
REVERT: S  284 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.6949 (tmm)
REVERT: S  362 VAL cc_start: 0.8463 (p) cc_final: 0.8250 (p)
REVERT: S  363 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7861 (tp)
  outliers start: 10
  outliers final: 3
  residues processed: 124
  average time/residue: 0.9757
  time to fit residues: 124.4893
Evaluate side-chains
  115 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  172 ASP
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  284 MET
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  416 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
S 202 GLN
S 351 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.152365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.139332 restraints weight = 5013.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 3.29
r_work: 0.3764 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2899  Z= 0.256
  Angle     :  0.738  11.134   3924  Z= 0.367
  Chirality :  0.045   0.154    455
  Planarity :  0.005   0.068    499
  Dihedral  :  4.826  19.757    379
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 35.78 %
    Favored  : 60.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.46), residues: 355
  helix:  1.62 (0.49), residues: 116
  sheet:  0.04 (0.58), residues: 87
  loop : -0.45 (0.52), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP S 217 
 HIS   0.003   0.001   HIS S 359 
 PHE   0.025   0.003   PHE S  75 
 TYR   0.019   0.002   TYR S 253 
 ARG   0.007   0.001   ARG S 397 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   87 LEU cc_start: 0.8310 (tp) cc_final: 0.7973 (tm)
REVERT: S  145 GLU cc_start: 0.8052 (pt0) cc_final: 0.7441 (pt0)
REVERT: S  185 LYS cc_start: 0.8385 (tmtt) cc_final: 0.8136 (tmtp)
REVERT: S  200 ASP cc_start: 0.7367 (t0) cc_final: 0.7147 (t0)
REVERT: S  218 GLU cc_start: 0.7344 (tt0) cc_final: 0.7134 (tp30)
REVERT: S  240 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5642 (mtt)
REVERT: S  284 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6929 (tmm)
REVERT: S  298 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7155 (ttp80)
REVERT: S  360 LYS cc_start: 0.7981 (tttt) cc_final: 0.7749 (tttt)
REVERT: S  362 VAL cc_start: 0.8422 (p) cc_final: 0.8157 (p)
REVERT: S  363 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7826 (tp)
  outliers start: 11
  outliers final: 2
  residues processed: 113
  average time/residue: 1.0933
  time to fit residues: 126.8835
Evaluate side-chains
  111 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  284 MET
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  416 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 20 optimal weight:    0.0010
   chunk 17 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0670
   chunk 14 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.4324

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

Flipped N/Q/H residues before XYZ refinement:
S 202 GLN
S 248 HIS
S 330 GLN
S 351 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.152698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.139598 restraints weight = 4969.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 3.36
r_work: 0.3771 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2899  Z= 0.217
  Angle     :  0.733  11.541   3924  Z= 0.361
  Chirality :  0.044   0.162    455
  Planarity :  0.005   0.056    499
  Dihedral  :  4.796  19.568    379
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 37.06 %
    Favored  : 59.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.47), residues: 355
  helix:  1.63 (0.49), residues: 116
  sheet: -0.10 (0.57), residues: 94
  loop : -0.36 (0.55), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP S 238 
 HIS   0.003   0.001   HIS S 359 
 PHE   0.022   0.003   PHE S  75 
 TYR   0.016   0.002   TYR S 253 
 ARG   0.010   0.001   ARG S 397 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: S   87 LEU cc_start: 0.8258 (tp) cc_final: 0.7946 (tm)
REVERT: S  145 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7364 (pt0)
REVERT: S  185 LYS cc_start: 0.8352 (tttt) cc_final: 0.8092 (tmtp)
REVERT: S  284 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6389 (tmm)
REVERT: S  298 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7218 (ttp80)
REVERT: S  354 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7830 (m)
REVERT: S  362 VAL cc_start: 0.8335 (p) cc_final: 0.8131 (p)
REVERT: S  363 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7752 (tp)
REVERT: S  397 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8185 (mtm-85)
REVERT: S  399 PHE cc_start: 0.8320 (p90) cc_final: 0.7812 (p90)
  outliers start: 12
  outliers final: 2
  residues processed: 109
  average time/residue: 1.0569
  time to fit residues: 118.2521
Evaluate side-chains
  114 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  145 GLU
Chi-restraints excluded: chain S residue  172 ASP
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  284 MET
Chi-restraints excluded: chain S residue  354 VAL
Chi-restraints excluded: chain S residue  363 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0000
   chunk 32 optimal weight:    0.0770
   chunk 0 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   overall best weight:    0.4142

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

Flipped N/Q/H residues before XYZ refinement:
** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 202 GLN
S 330 GLN
S 351 ASN
S 356 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.152516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.139532 restraints weight = 5145.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 3.31
r_work: 0.3773 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.4072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2899  Z= 0.216
  Angle     :  0.758  11.581   3924  Z= 0.372
  Chirality :  0.045   0.169    455
  Planarity :  0.005   0.064    499
  Dihedral  :  4.851  19.752    379
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 34.82 %
    Favored  : 59.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.47), residues: 355
  helix:  1.52 (0.48), residues: 119
  sheet: -0.05 (0.58), residues: 92
  loop : -0.32 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP S 238 
 HIS   0.002   0.001   HIS S 359 
 PHE   0.020   0.003   PHE S 212 
 TYR   0.015   0.002   TYR S 253 
 ARG   0.008   0.001   ARG S 397 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.322 
Fit side-chains
REVERT: S   84 LEU cc_start: 0.8473 (mm) cc_final: 0.8238 (mm)
REVERT: S   87 LEU cc_start: 0.8233 (tp) cc_final: 0.7905 (tm)
REVERT: S  132 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7606 (mp0)
REVERT: S  144 LYS cc_start: 0.8037 (tttp) cc_final: 0.7811 (tttp)
REVERT: S  145 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7437 (pt0)
REVERT: S  185 LYS cc_start: 0.8284 (tttt) cc_final: 0.7991 (tmtp)
REVERT: S  240 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5566 (mtt)
REVERT: S  298 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7196 (ttp80)
REVERT: S  320 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6706 (mmm-85)
REVERT: S  360 LYS cc_start: 0.8041 (tttt) cc_final: 0.7809 (tttt)
REVERT: S  363 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7775 (tp)
REVERT: S  399 PHE cc_start: 0.8291 (p90) cc_final: 0.7767 (p90)
  outliers start: 17
  outliers final: 5
  residues processed: 119
  average time/residue: 0.9334
  time to fit residues: 114.3930
Evaluate side-chains
  122 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  132 GLU
Chi-restraints excluded: chain S residue  145 GLU
Chi-restraints excluded: chain S residue  172 ASP
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  290 MET
Chi-restraints excluded: chain S residue  363 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 25 optimal weight:    0.0980
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0980
   chunk 17 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 31 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0070
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0000
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.1202

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

Flipped N/Q/H residues before XYZ refinement:
S 330 GLN
S 351 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.155762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.143108 restraints weight = 5113.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 3.26
r_work: 0.3820 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   2899  Z= 0.201
  Angle     :  0.826  12.334   3924  Z= 0.394
  Chirality :  0.045   0.171    455
  Planarity :  0.005   0.063    499
  Dihedral  :  4.710  19.069    379
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 38.98 %
    Favored  : 57.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.47), residues: 355
  helix:  1.60 (0.47), residues: 119
  sheet: -0.04 (0.57), residues: 92
  loop : -0.34 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP S 299 
 HIS   0.002   0.000   HIS S 359 
 PHE   0.021   0.002   PHE S 212 
 TYR   0.013   0.001   TYR S 253 
 ARG   0.006   0.001   ARG S 300 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.339 
Fit side-chains
REVERT: S   87 LEU cc_start: 0.8162 (tp) cc_final: 0.7828 (tm)
REVERT: S  145 GLU cc_start: 0.7970 (pt0) cc_final: 0.7422 (pt0)
REVERT: S  320 ARG cc_start: 0.7035 (mmm-85) cc_final: 0.6611 (mmm-85)
REVERT: S  363 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7780 (tp)
  outliers start: 10
  outliers final: 4
  residues processed: 111
  average time/residue: 0.9421
  time to fit residues: 107.8256
Evaluate side-chains
  111 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  126 LEU
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  363 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    0.4980
   chunk 23 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0770
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 330 GLN
S 351 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.152821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.140635 restraints weight = 5020.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 3.14
r_work: 0.3783 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.4573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   2899  Z= 0.257
  Angle     :  0.842  12.432   3924  Z= 0.411
  Chirality :  0.046   0.176    455
  Planarity :  0.005   0.069    499
  Dihedral  :  5.012  19.042    379
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 41.21 %
    Favored  : 56.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.47), residues: 355
  helix:  1.61 (0.47), residues: 116
  sheet: -0.00 (0.57), residues: 92
  loop : -0.45 (0.56), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP S 238 
 HIS   0.003   0.001   HIS S 247 
 PHE   0.024   0.003   PHE S 316 
 TYR   0.016   0.002   TYR S 253 
 ARG   0.009   0.001   ARG S 298 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.295 
Fit side-chains
REVERT: S   87 LEU cc_start: 0.8223 (tp) cc_final: 0.7880 (tm)
REVERT: S  132 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7556 (mp0)
REVERT: S  145 GLU cc_start: 0.7880 (pt0) cc_final: 0.7306 (pt0)
REVERT: S  192 ILE cc_start: 0.8403 (mm) cc_final: 0.8102 (mp)
REVERT: S  240 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.5585 (mtt)
REVERT: S  298 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7262 (ttp80)
REVERT: S  320 ARG cc_start: 0.7359 (mmm-85) cc_final: 0.6922 (mmm-85)
  outliers start: 8
  outliers final: 2
  residues processed: 100
  average time/residue: 0.8408
  time to fit residues: 86.8881
Evaluate side-chains
  102 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  132 GLU
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  240 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 30 optimal weight:    0.4980
   chunk 28 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0970
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 351 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.153126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.141071 restraints weight = 4942.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 3.02
r_work: 0.3797 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   2899  Z= 0.247
  Angle     :  0.831  12.893   3924  Z= 0.406
  Chirality :  0.046   0.185    455
  Planarity :  0.006   0.069    499
  Dihedral  :  5.119  19.684    379
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 40.89 %
    Favored  : 56.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.47), residues: 355
  helix:  1.38 (0.46), residues: 119
  sheet: -0.06 (0.57), residues: 94
  loop : -0.47 (0.57), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP S 238 
 HIS   0.002   0.001   HIS S 247 
 PHE   0.028   0.002   PHE S 316 
 TYR   0.016   0.002   TYR S 253 
 ARG   0.009   0.001   ARG S 298 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.290 
Fit side-chains
REVERT: S   87 LEU cc_start: 0.8247 (tp) cc_final: 0.7893 (tm)
REVERT: S  132 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7616 (mp0)
REVERT: S  145 GLU cc_start: 0.7832 (pt0) cc_final: 0.7217 (pt0)
REVERT: S  204 MET cc_start: 0.7183 (mmt) cc_final: 0.6915 (mmm)
REVERT: S  240 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5320 (mtt)
REVERT: S  298 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7257 (ttp80)
REVERT: S  320 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7093 (mmm-85)
REVERT: S  360 LYS cc_start: 0.8208 (tttt) cc_final: 0.7833 (tttt)
REVERT: S  397 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.8047 (mtm-85)
  outliers start: 9
  outliers final: 4
  residues processed: 99
  average time/residue: 0.7995
  time to fit residues: 81.8467
Evaluate side-chains
  99 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  132 GLU
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  290 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:    0.0270
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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 = 0.4054 r_free = 0.4054 target = 0.152835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.140936 restraints weight = 5052.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 3.00
r_work: 0.3791 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2899  Z= 0.259
  Angle     :  0.845  11.967   3924  Z= 0.416
  Chirality :  0.047   0.181    455
  Planarity :  0.006   0.074    499
  Dihedral  :  5.260  19.836    379
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 42.81 %
    Favored  : 54.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.47), residues: 355
  helix:  1.54 (0.47), residues: 116
  sheet: -0.02 (0.57), residues: 94
  loop : -0.48 (0.56), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP S 299 
 HIS   0.002   0.001   HIS S 247 
 PHE   0.035   0.003   PHE S 316 
 TYR   0.016   0.002   TYR S 253 
 ARG   0.008   0.001   ARG S 298 

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

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

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  710 Ramachandran restraints generated.
    355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.316 
Fit side-chains
REVERT: S   87 LEU cc_start: 0.8280 (tp) cc_final: 0.7942 (tm)
REVERT: S  132 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7564 (mp0)
REVERT: S  145 GLU cc_start: 0.7790 (pt0) cc_final: 0.7244 (pt0)
REVERT: S  204 MET cc_start: 0.7144 (mmt) cc_final: 0.6840 (mmm)
REVERT: S  240 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.5323 (mtt)
REVERT: S  298 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7271 (ttp80)
REVERT: S  320 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7242 (mmm-85)
REVERT: S  360 LYS cc_start: 0.8218 (tttt) cc_final: 0.7874 (ttpt)
REVERT: S  397 ARG cc_start: 0.8339 (mtm-85) cc_final: 0.8070 (mtm-85)
  outliers start: 9
  outliers final: 5
  residues processed: 102
  average time/residue: 0.8745
  time to fit residues: 92.2504
Evaluate side-chains
  102 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   58 PHE
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  132 GLU
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  240 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0370
   chunk 20 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
S 351 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.152845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.140958 restraints weight = 4909.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.96
r_work: 0.3798 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.4963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   2899  Z= 0.271
  Angle     :  0.868  12.471   3924  Z= 0.425
  Chirality :  0.047   0.181    455
  Planarity :  0.006   0.073    499
  Dihedral  :  5.301  20.873    379
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 17.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 42.49 %
    Favored  : 54.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.47), residues: 355
  helix:  1.42 (0.45), residues: 119
  sheet:  0.02 (0.58), residues: 94
  loop : -0.54 (0.57), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP S 299 
 HIS   0.002   0.001   HIS S 121 
 PHE   0.032   0.003   PHE S 221 
 TYR   0.016   0.002   TYR S 253 
 ARG   0.008   0.001   ARG S 298 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2830.14 seconds
wall clock time: 50 minutes 46.11 seconds (3046.11 seconds total)