Starting phenix.real_space_refine
on Wed Mar  5 16:41:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d7k_46607/03_2025/9d7k_46607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d7k_46607/03_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_46607/03_2025/9d7k_46607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d7k_46607/03_2025/9d7k_46607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d7k_46607/03_2025/9d7k_46607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d7k_46607/03_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-5624/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: 2.31, per 1000 atoms: 0.81
  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: 0.72
  Conformation dependent library (CDL) restraints added in 336.2 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: 0.35
  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: 0.74

  Time building geometry restraints manager: 0.87 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:             0.340
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.960
  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:11.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.780
-------------------------------------------------------------------------------
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  : 0.307 
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: 0.6976
  time to fit residues: 88.3905
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  : 0.251 
-------------------------------------------------------------------------------
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:    0.9990
   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 = 21)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.143009 restraints weight = 5092.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 3.32
r_work: 0.3825 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
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  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: S   87 LEU cc_start: 0.8214 (tp) cc_final: 0.7863 (tm)
REVERT: S  144 LYS cc_start: 0.8023 (tttp) cc_final: 0.7734 (tptm)
REVERT: S  145 GLU cc_start: 0.8124 (pt0) cc_final: 0.7528 (pt0)
REVERT: S  185 LYS cc_start: 0.8330 (tmtt) cc_final: 0.8103 (tmtp)
REVERT: S  204 MET cc_start: 0.7073 (mmt) cc_final: 0.6802 (mmm)
REVERT: S  258 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7309 (mm-30)
REVERT: S  298 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7123 (ttp80)
REVERT: S  333 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7388 (pt)
REVERT: S  362 VAL cc_start: 0.8546 (p) cc_final: 0.8325 (p)
REVERT: S  402 ILE cc_start: 0.8254 (mp) cc_final: 0.7962 (OUTLIER)
  outliers start: 11
  outliers final: 5
  residues processed: 113
  average time/residue: 0.9916
  time to fit residues: 115.3632
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  : 0.295 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4019 r_free = 0.4019 target = 0.150091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.137637 restraints weight = 4974.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 3.04
r_work: 0.3753 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2899  Z= 0.287
  Angle     :  0.693   6.243   3924  Z= 0.358
  Chirality :  0.046   0.148    455
  Planarity :  0.006   0.076    499
  Dihedral  :  5.680  38.341    383
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 30.03 %
    Favored  : 66.13 %
  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 (0.46), residues: 355
  helix:  1.46 (0.49), residues: 116
  sheet: -0.16 (0.57), residues: 94
  loop : -0.29 (0.53), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP S 217 
 HIS   0.004   0.001   HIS S 359 
 PHE   0.035   0.003   PHE S  75 
 TYR   0.019   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
  136 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   87 LEU cc_start: 0.8328 (tp) cc_final: 0.7974 (tm)
REVERT: S  145 GLU cc_start: 0.8057 (pt0) cc_final: 0.7419 (pt0)
REVERT: S  185 LYS cc_start: 0.8342 (tmtt) cc_final: 0.8098 (tmtp)
REVERT: S  233 LEU cc_start: 0.8141 (mt) cc_final: 0.7885 (mp)
REVERT: S  240 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5662 (mtt)
REVERT: S  277 ILE cc_start: 0.8206 (mt) cc_final: 0.8004 (mt)
REVERT: S  284 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.6966 (tmm)
REVERT: S  357 VAL cc_start: 0.7337 (t) cc_final: 0.7013 (p)
REVERT: S  360 LYS cc_start: 0.8016 (tttt) cc_final: 0.7697 (tttt)
REVERT: S  362 VAL cc_start: 0.8504 (p) cc_final: 0.8286 (p)
REVERT: S  363 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7893 (tp)
  outliers start: 12
  outliers final: 3
  residues processed: 127
  average time/residue: 0.9529
  time to fit residues: 124.5838
Evaluate side-chains
  125 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 33 optimal weight:    0.0770
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
S 228 GLN
S 248 HIS
S 351 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.150580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.138077 restraints weight = 5041.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 3.17
r_work: 0.3753 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2899  Z= 0.241
  Angle     :  0.745  11.413   3924  Z= 0.368
  Chirality :  0.045   0.145    455
  Planarity :  0.006   0.071    499
  Dihedral  :  4.959  20.744    379
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 36.74 %
    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:  0.34 (0.46), residues: 355
  helix:  1.41 (0.49), residues: 116
  sheet: -0.02 (0.58), residues: 87
  loop : -0.47 (0.53), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP S 217 
 HIS   0.002   0.001   HIS S 121 
 PHE   0.032   0.003   PHE S 212 
 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
  133 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   87 LEU cc_start: 0.8307 (tp) cc_final: 0.7957 (tm)
REVERT: S  145 GLU cc_start: 0.8000 (pt0) cc_final: 0.7387 (pt0)
REVERT: S  185 LYS cc_start: 0.8392 (tmtt) cc_final: 0.8114 (tmtp)
REVERT: S  200 ASP cc_start: 0.7444 (t0) cc_final: 0.7233 (t0)
REVERT: S  201 SER cc_start: 0.8318 (m) cc_final: 0.7951 (t)
REVERT: S  240 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5603 (mtt)
REVERT: S  284 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6922 (tmm)
REVERT: S  298 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7221 (ttp80)
REVERT: S  357 VAL cc_start: 0.7462 (t) cc_final: 0.7158 (p)
REVERT: S  360 LYS cc_start: 0.8027 (tttt) cc_final: 0.7790 (tttt)
REVERT: S  363 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7810 (tp)
REVERT: S  399 PHE cc_start: 0.8329 (p90) cc_final: 0.7816 (p90)
  outliers start: 11
  outliers final: 4
  residues processed: 126
  average time/residue: 0.9264
  time to fit residues: 120.2044
Evaluate side-chains
  123 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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  292 LEU
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  414 MET
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:    0.0970
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    0.2980
   chunk 7 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.3178

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.151860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.138890 restraints weight = 4976.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 3.31
r_work: 0.3770 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.4039

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= 0.215
  Angle     :  0.732  11.512   3924  Z= 0.362
  Chirality :  0.044   0.158    455
  Planarity :  0.005   0.072    499
  Dihedral  :  4.900  20.527    379
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 38.02 %
    Favored  : 58.15 %
  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:  1.56 (0.48), residues: 116
  sheet: -0.10 (0.57), residues: 94
  loop : -0.33 (0.55), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP S 299 
 HIS   0.001   0.000   HIS S 116 
 PHE   0.026   0.003   PHE S 212 
 TYR   0.016   0.002   TYR S 253 
 ARG   0.006   0.001   ARG S 300 

*********************** 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
  128 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: S   87 LEU cc_start: 0.8326 (tp) cc_final: 0.7951 (tm)
REVERT: S  144 LYS cc_start: 0.7948 (tttp) cc_final: 0.7745 (tttp)
REVERT: S  145 GLU cc_start: 0.8021 (pt0) cc_final: 0.7349 (pt0)
REVERT: S  185 LYS cc_start: 0.8371 (tmtt) cc_final: 0.8109 (tmtp)
REVERT: S  201 SER cc_start: 0.8153 (m) cc_final: 0.7780 (t)
REVERT: S  357 VAL cc_start: 0.7271 (t) cc_final: 0.6883 (p)
REVERT: S  360 LYS cc_start: 0.8102 (tttt) cc_final: 0.7877 (tttt)
REVERT: S  399 PHE cc_start: 0.8340 (p90) cc_final: 0.7789 (p90)
  outliers start: 12
  outliers final: 4
  residues processed: 119
  average time/residue: 0.9897
  time to fit residues: 121.0443
Evaluate side-chains
  119 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  172 ASP
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  416 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 5 optimal weight:    0.4980
   chunk 34 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 0 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5380

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.151187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.138380 restraints weight = 5105.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 3.25
r_work: 0.3762 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.4313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2899  Z= 0.234
  Angle     :  0.754  11.721   3924  Z= 0.370
  Chirality :  0.045   0.164    455
  Planarity :  0.005   0.064    499
  Dihedral  :  4.911  20.175    379
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 36.74 %
    Favored  : 58.47 %
  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:  0.46 (0.46), residues: 355
  helix:  1.52 (0.47), residues: 119
  sheet: -0.08 (0.57), residues: 94
  loop : -0.36 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP S 299 
 HIS   0.002   0.001   HIS S 121 
 PHE   0.024   0.003   PHE S 212 
 TYR   0.016   0.002   TYR S 253 
 ARG   0.005   0.001   ARG S 300 

*********************** 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
  137 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.302 
Fit side-chains
REVERT: S   87 LEU cc_start: 0.8267 (tp) cc_final: 0.7920 (tm)
REVERT: S  132 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7563 (mp0)
REVERT: S  145 GLU cc_start: 0.7983 (pt0) cc_final: 0.7442 (pt0)
REVERT: S  191 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7885 (mtpp)
REVERT: S  201 SER cc_start: 0.8334 (m) cc_final: 0.7825 (t)
REVERT: S  228 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7160 (mm-40)
REVERT: S  240 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5491 (mtt)
REVERT: S  284 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6181 (tmm)
REVERT: S  298 ARG cc_start: 0.7742 (ttp80) cc_final: 0.7225 (ttp80)
REVERT: S  357 VAL cc_start: 0.7348 (t) cc_final: 0.7026 (p)
REVERT: S  360 LYS cc_start: 0.8137 (tttt) cc_final: 0.7910 (tttt)
REVERT: S  397 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8189 (mtm-85)
REVERT: S  399 PHE cc_start: 0.8361 (p90) cc_final: 0.7830 (p90)
  outliers start: 15
  outliers final: 3
  residues processed: 126
  average time/residue: 0.9338
  time to fit residues: 121.0657
Evaluate side-chains
  122 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  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  233 LEU
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  284 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 20 optimal weight:    0.0270
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
S 139 ASN
S 330 GLN
S 351 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.152526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.139658 restraints weight = 5079.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 3.24
r_work: 0.3772 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.4468

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= 0.224
  Angle     :  0.813  12.152   3924  Z= 0.393
  Chirality :  0.045   0.166    455
  Planarity :  0.005   0.065    499
  Dihedral  :  5.026  19.684    379
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 39.30 %
    Favored  : 56.87 %
  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:  0.55 (0.46), residues: 355
  helix:  1.66 (0.47), residues: 116
  sheet: -0.03 (0.57), residues: 94
  loop : -0.33 (0.55), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP S 299 
 HIS   0.001   0.001   HIS S 247 
 PHE   0.023   0.003   PHE S 316 
 TYR   0.015   0.002   TYR S 253 
 ARG   0.005   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
  123 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.321 
Fit side-chains
REVERT: S   60 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8089 (tp)
REVERT: S   87 LEU cc_start: 0.8252 (tp) cc_final: 0.7895 (tm)
REVERT: S  132 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7542 (mp0)
REVERT: S  145 GLU cc_start: 0.7855 (pt0) cc_final: 0.7290 (pt0)
REVERT: S  228 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7363 (mm110)
REVERT: S  350 ARG cc_start: 0.7796 (ptm160) cc_final: 0.7554 (ptp-110)
REVERT: S  357 VAL cc_start: 0.7424 (t) cc_final: 0.7075 (p)
REVERT: S  397 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.8162 (mtm-85)
REVERT: S  414 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.5473 (ttp)
  outliers start: 12
  outliers final: 7
  residues processed: 115
  average time/residue: 1.0075
  time to fit residues: 119.0559
Evaluate side-chains
  113 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   60 LEU
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  132 GLU
Chi-restraints excluded: chain S residue  139 ASN
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  414 MET
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:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0070
   chunk 29 optimal weight:    0.6980
   chunk 10 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.5398

-------------------------------------------------------------------------------
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 = 0.4044 r_free = 0.4044 target = 0.151820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.138918 restraints weight = 5003.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 3.23
r_work: 0.3767 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.4624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   2899  Z= 0.240
  Angle     :  0.817  12.358   3924  Z= 0.396
  Chirality :  0.045   0.176    455
  Planarity :  0.006   0.070    499
  Dihedral  :  5.031  19.768    379
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 39.62 %
    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 (0.46), residues: 355
  helix:  1.54 (0.47), residues: 119
  sheet:  0.02 (0.57), residues: 94
  loop : -0.44 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP S 299 
 HIS   0.002   0.001   HIS S 121 
 PHE   0.026   0.003   PHE S 316 
 TYR   0.015   0.002   TYR S 253 
 ARG   0.006   0.001   ARG S 300 

*********************** 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
  118 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.286 
Fit side-chains
REVERT: S   60 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8148 (tp)
REVERT: S   84 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8363 (mm)
REVERT: S   87 LEU cc_start: 0.8277 (tp) cc_final: 0.7923 (tm)
REVERT: S  132 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7551 (mp0)
REVERT: S  145 GLU cc_start: 0.7873 (pt0) cc_final: 0.7320 (pt0)
REVERT: S  191 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7886 (mmtt)
REVERT: S  228 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7368 (mm110)
REVERT: S  240 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5323 (mtt)
REVERT: S  350 ARG cc_start: 0.7754 (ptm160) cc_final: 0.7477 (ptp-110)
REVERT: S  360 LYS cc_start: 0.8196 (tttt) cc_final: 0.7744 (ttpt)
REVERT: S  414 MET cc_start: 0.5845 (OUTLIER) cc_final: 0.5629 (ttm)
  outliers start: 13
  outliers final: 6
  residues processed: 112
  average time/residue: 1.0217
  time to fit residues: 117.5367
Evaluate side-chains
  112 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   60 LEU
Chi-restraints excluded: chain S residue   84 LEU
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  132 GLU
Chi-restraints excluded: chain S residue  172 ASP
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  213 PHE
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  414 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4048 r_free = 0.4048 target = 0.151987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.139329 restraints weight = 4956.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 3.15
r_work: 0.3778 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.4768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   2899  Z= 0.241
  Angle     :  0.831  12.537   3924  Z= 0.408
  Chirality :  0.046   0.187    455
  Planarity :  0.006   0.074    499
  Dihedral  :  5.189  19.477    379
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 41.21 %
    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:  0.42 (0.46), residues: 355
  helix:  1.57 (0.47), residues: 116
  sheet: -0.04 (0.56), residues: 94
  loop : -0.47 (0.54), 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 121 
 PHE   0.027   0.003   PHE S 316 
 TYR   0.015   0.002   TYR S 253 
 ARG   0.006   0.001   ARG S 350 

*********************** 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
  121 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.294 
Fit side-chains
REVERT: S   60 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8195 (tp)
REVERT: S   84 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8318 (mm)
REVERT: S   87 LEU cc_start: 0.8294 (tp) cc_final: 0.7929 (tm)
REVERT: S   93 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.6795 (t0)
REVERT: S  132 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7573 (mp0)
REVERT: S  145 GLU cc_start: 0.7863 (pt0) cc_final: 0.7291 (pt0)
REVERT: S  191 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7846 (tppp)
REVERT: S  240 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5321 (mtt)
REVERT: S  257 GLU cc_start: 0.7795 (pt0) cc_final: 0.7306 (tm-30)
REVERT: S  360 LYS cc_start: 0.8244 (tttt) cc_final: 0.7891 (ttpt)
REVERT: S  414 MET cc_start: 0.5834 (OUTLIER) cc_final: 0.5595 (ttm)
  outliers start: 13
  outliers final: 3
  residues processed: 114
  average time/residue: 0.9831
  time to fit residues: 115.1959
Evaluate side-chains
  114 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   60 LEU
Chi-restraints excluded: chain S residue   84 LEU
Chi-restraints excluded: chain S residue   93 ASN
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  233 LEU
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  414 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0770
   chunk 17 optimal weight:    0.0970
   chunk 29 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.4936

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.151490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.138682 restraints weight = 5070.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 3.18
r_work: 0.3772 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.4882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   2899  Z= 0.233
  Angle     :  0.831  12.865   3924  Z= 0.410
  Chirality :  0.046   0.192    455
  Planarity :  0.006   0.074    499
  Dihedral  :  5.141  19.121    379
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 42.49 %
    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:  0.38 (0.45), residues: 355
  helix:  1.54 (0.46), residues: 119
  sheet: -0.17 (0.54), residues: 94
  loop : -0.47 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP S 299 
 HIS   0.001   0.001   HIS S 121 
 PHE   0.030   0.003   PHE S 221 
 TYR   0.015   0.002   TYR S 253 
 ARG   0.006   0.001   ARG S 397 

********************** 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
  109 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.323 
Fit side-chains
REVERT: S   60 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8243 (tp)
REVERT: S   84 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8346 (mm)
REVERT: S   87 LEU cc_start: 0.8341 (tp) cc_final: 0.7966 (tm)
REVERT: S  132 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7597 (mp0)
REVERT: S  145 GLU cc_start: 0.7886 (pt0) cc_final: 0.7282 (pt0)
REVERT: S  150 LEU cc_start: 0.7595 (tp) cc_final: 0.7388 (tt)
REVERT: S  204 MET cc_start: 0.7154 (mmt) cc_final: 0.6889 (mmm)
REVERT: S  240 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5388 (mtt)
REVERT: S  360 LYS cc_start: 0.8249 (tttt) cc_final: 0.7859 (ttpt)
REVERT: S  414 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5605 (ttm)
  outliers start: 10
  outliers final: 3
  residues processed: 103
  average time/residue: 0.9341
  time to fit residues: 99.1164
Evaluate side-chains
  106 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   60 LEU
Chi-restraints excluded: chain S residue   84 LEU
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  233 LEU
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  414 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0870
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
S 323 ASN
S 356 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.150825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.138813 restraints weight = 4947.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 3.06
r_work: 0.3774 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.5022

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= 0.248
  Angle     :  0.847  12.810   3924  Z= 0.417
  Chirality :  0.047   0.193    455
  Planarity :  0.006   0.076    499
  Dihedral  :  5.284  19.141    379
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 43.45 %
    Favored  : 53.04 %
  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:  0.39 (0.45), residues: 355
  helix:  1.63 (0.47), residues: 116
  sheet: -0.15 (0.55), residues: 94
  loop : -0.50 (0.54), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   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   0.011   0.001   ARG S 397 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3013.62 seconds
wall clock time: 51 minutes 59.57 seconds (3119.57 seconds total)