Starting phenix.real_space_refine
on Wed Sep 17 03:18:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d7k_46607/09_2025/9d7k_46607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d7k_46607/09_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_46607/09_2025/9d7k_46607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d7k_46607/09_2025/9d7k_46607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d7k_46607/09_2025/9d7k_46607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d7k_46607/09_2025/9d7k_46607.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 0.85, per 1000 atoms: 0.30
  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: 0.23
  Conformation dependent library (CDL) restraints added in 77.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.12
  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: 0.40

  Time building geometry restraints manager: 0.29 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:             0.540
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.650
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.820
-------------------------------------------------------------------------------
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= 0.105
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (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
 ARG   0.005   0.001   ARG S 298 
 TYR   0.007   0.001   TYR S 253 
 PHE   0.019   0.001   PHE S 212 
 TRP   0.007   0.001   TRP S 299 
 HIS   0.003   0.001   HIS S 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 2899)
  covalent geometry    : angle       0.55439 ( 3924)
  hydrogen bonds       : bond        0.18741 (  130)
  hydrogen bonds       : angle       7.96775 (  372)

*********************** 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  : 0.110 
Fit side-chains
REVERT: S   58 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.5653 (t80)
REVERT: S   87 LEU cc_start: 0.7953 (tp) cc_final: 0.7666 (tm)
REVERT: S  145 GLU cc_start: 0.7722 (pt0) cc_final: 0.7144 (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: 0.5585 (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: 0.3573
  time to fit residues: 45.2048
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  : 0.102 
-------------------------------------------------------------------------------
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 24 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4054 r_free = 0.4054 target = 0.152995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.140057 restraints weight = 5178.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 3.35
r_work: 0.3776 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   2899  Z= 0.205
  Angle     :  0.731   7.697   3924  Z= 0.378
  Chirality :  0.048   0.250    455
  Planarity :  0.005   0.039    499
  Dihedral  :  6.186  58.420    385
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 30.35 %
    Favored  : 66.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.47), residues: 355
  helix:  1.65 (0.50), residues: 116
  sheet:  0.34 (0.59), residues: 91
  loop : -0.31 (0.53), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG S 152 
 TYR   0.020   0.002   TYR S 253 
 PHE   0.022   0.003   PHE S 212 
 TRP   0.007   0.002   TRP S 217 
 HIS   0.005   0.002   HIS S 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 2899)
  covalent geometry    : angle       0.73063 ( 3924)
  hydrogen bonds       : bond        0.03812 (  130)
  hydrogen bonds       : angle       5.60009 (  372)

*********************** 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
  128 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: S   63 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8194 (tp40)
REVERT: S   87 LEU cc_start: 0.8327 (tp) cc_final: 0.7963 (tm)
REVERT: S  144 LYS cc_start: 0.8110 (tttp) cc_final: 0.7747 (tptm)
REVERT: S  145 GLU cc_start: 0.8161 (pt0) cc_final: 0.7471 (pt0)
REVERT: S  185 LYS cc_start: 0.8432 (tmtt) cc_final: 0.8192 (tmtp)
REVERT: S  191 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7899 (mmtt)
REVERT: S  233 LEU cc_start: 0.8239 (mt) cc_final: 0.7970 (mp)
REVERT: S  243 MET cc_start: 0.7315 (mtm) cc_final: 0.6879 (mtm)
REVERT: S  275 LEU cc_start: 0.7384 (tp) cc_final: 0.7149 (pp)
REVERT: S  284 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.6792 (tmm)
REVERT: S  333 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7559 (pt)
REVERT: S  334 GLU cc_start: 0.7384 (pt0) cc_final: 0.7092 (pm20)
REVERT: S  362 VAL cc_start: 0.8525 (p) cc_final: 0.8310 (p)
  outliers start: 10
  outliers final: 4
  residues processed: 119
  average time/residue: 0.5019
  time to fit residues: 61.2973
Evaluate side-chains
  119 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
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  284 MET
Chi-restraints excluded: chain S residue  333 ILE
Chi-restraints excluded: chain S residue  392 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 25 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 15 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4029 r_free = 0.4029 target = 0.151041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.138658 restraints weight = 5025.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 3.10
r_work: 0.3758 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2899  Z= 0.192
  Angle     :  0.678   6.286   3924  Z= 0.348
  Chirality :  0.045   0.151    455
  Planarity :  0.006   0.076    499
  Dihedral  :  5.679  37.718    383
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 28.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.47), residues: 355
  helix:  1.47 (0.49), residues: 116
  sheet: -0.06 (0.57), residues: 96
  loop : -0.22 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG S 152 
 TYR   0.020   0.002   TYR S 253 
 PHE   0.021   0.003   PHE S 153 
 TRP   0.005   0.002   TRP S 217 
 HIS   0.003   0.001   HIS S 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 2899)
  covalent geometry    : angle       0.67832 ( 3924)
  hydrogen bonds       : bond        0.03897 (  130)
  hydrogen bonds       : angle       5.49065 (  372)

*********************** 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
  137 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: S   80 ILE cc_start: 0.7978 (mm) cc_final: 0.7748 (tp)
REVERT: S   87 LEU cc_start: 0.8330 (tp) cc_final: 0.7991 (tm)
REVERT: S  145 GLU cc_start: 0.8102 (pt0) cc_final: 0.7532 (pt0)
REVERT: S  185 LYS cc_start: 0.8373 (tmtt) cc_final: 0.8104 (tmtp)
REVERT: S  228 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7494 (tp-100)
REVERT: S  233 LEU cc_start: 0.8130 (mt) cc_final: 0.7854 (mp)
REVERT: S  240 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5727 (mtt)
REVERT: S  284 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6931 (tmm)
REVERT: S  360 LYS cc_start: 0.7989 (tttt) cc_final: 0.7698 (tttt)
REVERT: S  362 VAL cc_start: 0.8463 (p) cc_final: 0.8202 (p)
REVERT: S  363 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7878 (tp)
REVERT: S  399 PHE cc_start: 0.8347 (p90) cc_final: 0.7827 (p90)
REVERT: S  404 VAL cc_start: 0.8342 (m) cc_final: 0.8110 (t)
  outliers start: 18
  outliers final: 5
  residues processed: 125
  average time/residue: 0.4874
  time to fit residues: 62.6481
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  : 0.106 
-------------------------------------------------------------------------------
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  228 GLN
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  257 GLU
Chi-restraints excluded: chain S residue  284 MET
Chi-restraints excluded: chain S residue  363 LEU
Chi-restraints excluded: chain S residue  408 THR
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 32 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4006 r_free = 0.4006 target = 0.149066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.136340 restraints weight = 4918.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 3.18
r_work: 0.3733 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   2899  Z= 0.215
  Angle     :  0.747  10.360   3924  Z= 0.383
  Chirality :  0.046   0.171    455
  Planarity :  0.006   0.081    499
  Dihedral  :  5.172  20.543    379
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 32.59 %
    Favored  : 62.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.46), residues: 355
  helix:  1.47 (0.48), residues: 116
  sheet: -0.21 (0.55), residues: 96
  loop : -0.30 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG S 397 
 TYR   0.020   0.002   TYR S 253 
 PHE   0.019   0.003   PHE S 212 
 TRP   0.006   0.002   TRP S 238 
 HIS   0.003   0.001   HIS S 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 2899)
  covalent geometry    : angle       0.74663 ( 3924)
  hydrogen bonds       : bond        0.04168 (  130)
  hydrogen bonds       : angle       5.52366 (  372)

*********************** 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
  123 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: S   55 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6665 (t70)
REVERT: S   87 LEU cc_start: 0.8391 (tp) cc_final: 0.8047 (tm)
REVERT: S  145 GLU cc_start: 0.8049 (pt0) cc_final: 0.7379 (pt0)
REVERT: S  185 LYS cc_start: 0.8440 (tmtt) cc_final: 0.8196 (tmtp)
REVERT: S  201 SER cc_start: 0.8316 (m) cc_final: 0.7783 (t)
REVERT: S  240 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5526 (mtt)
REVERT: S  275 LEU cc_start: 0.7698 (pp) cc_final: 0.7441 (pp)
REVERT: S  284 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6857 (tmm)
REVERT: S  298 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7307 (ttp80)
REVERT: S  320 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.6700 (mmm-85)
REVERT: S  354 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7538 (t)
REVERT: S  360 LYS cc_start: 0.8156 (tttt) cc_final: 0.7771 (tttt)
  outliers start: 15
  outliers final: 4
  residues processed: 115
  average time/residue: 0.4865
  time to fit residues: 57.4917
Evaluate side-chains
  112 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   55 ASP
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  243 MET
Chi-restraints excluded: chain S residue  277 ILE
Chi-restraints excluded: chain S residue  284 MET
Chi-restraints excluded: chain S residue  354 VAL
Chi-restraints excluded: chain S residue  392 ILE
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 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 29 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
S 202 GLN
S 228 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 = 0.4021 r_free = 0.4021 target = 0.150062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.137789 restraints weight = 4924.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 3.11
r_work: 0.3758 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.4272

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= 0.158
  Angle     :  0.757   9.927   3924  Z= 0.378
  Chirality :  0.046   0.176    455
  Planarity :  0.004   0.035    499
  Dihedral  :  5.099  20.385    379
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 32.27 %
    Favored  : 61.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.47), residues: 355
  helix:  1.63 (0.49), residues: 116
  sheet:  0.21 (0.58), residues: 87
  loop : -0.57 (0.54), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG S 397 
 TYR   0.018   0.002   TYR S 253 
 PHE   0.020   0.002   PHE S 212 
 TRP   0.006   0.001   TRP S 299 
 HIS   0.002   0.001   HIS S 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 2899)
  covalent geometry    : angle       0.75699 ( 3924)
  hydrogen bonds       : bond        0.03536 (  130)
  hydrogen bonds       : angle       5.39777 (  372)

*********************** 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
  124 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: S   84 LEU cc_start: 0.8631 (mm) cc_final: 0.8385 (mm)
REVERT: S   87 LEU cc_start: 0.8313 (tp) cc_final: 0.7952 (tm)
REVERT: S  132 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7574 (mp0)
REVERT: S  139 ASN cc_start: 0.7758 (p0) cc_final: 0.7555 (p0)
REVERT: S  145 GLU cc_start: 0.7990 (pt0) cc_final: 0.7349 (pt0)
REVERT: S  240 MET cc_start: 0.6198 (OUTLIER) cc_final: 0.5451 (mtt)
REVERT: S  298 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7289 (ttp80)
REVERT: S  320 ARG cc_start: 0.7511 (mmm-85) cc_final: 0.7019 (mmm-85)
REVERT: S  360 LYS cc_start: 0.8177 (tttt) cc_final: 0.7831 (tttt)
  outliers start: 20
  outliers final: 7
  residues processed: 110
  average time/residue: 0.5019
  time to fit residues: 56.6260
Evaluate side-chains
  120 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
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  172 ASP
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  243 MET
Chi-restraints excluded: chain S residue  257 GLU
Chi-restraints excluded: chain S residue  307 GLU
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 2 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0170
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.150057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.137536 restraints weight = 5010.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 3.19
r_work: 0.3751 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.4388

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= 0.164
  Angle     :  0.793  12.145   3924  Z= 0.386
  Chirality :  0.046   0.178    455
  Planarity :  0.005   0.067    499
  Dihedral  :  5.140  20.739    379
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 36.42 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.47), residues: 355
  helix:  1.55 (0.47), residues: 119
  sheet:  0.05 (0.57), residues: 93
  loop : -0.37 (0.56), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG S 397 
 TYR   0.017   0.002   TYR S 253 
 PHE   0.023   0.002   PHE S 212 
 TRP   0.005   0.001   TRP S 238 
 HIS   0.003   0.001   HIS S 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 2899)
  covalent geometry    : angle       0.79302 ( 3924)
  hydrogen bonds       : bond        0.03600 (  130)
  hydrogen bonds       : angle       5.37102 (  372)

*********************** 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
  121 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   87 LEU cc_start: 0.8309 (tp) cc_final: 0.7965 (tm)
REVERT: S  132 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7590 (mp0)
REVERT: S  145 GLU cc_start: 0.7908 (pt0) cc_final: 0.7273 (pt0)
REVERT: S  192 ILE cc_start: 0.8411 (mm) cc_final: 0.8115 (mp)
REVERT: S  240 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5509 (mtt)
REVERT: S  298 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7237 (ttp80)
REVERT: S  320 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7147 (mmm-85)
REVERT: S  360 LYS cc_start: 0.8194 (tttt) cc_final: 0.7899 (tttt)
  outliers start: 14
  outliers final: 6
  residues processed: 110
  average time/residue: 0.4542
  time to fit residues: 51.3928
Evaluate side-chains
  112 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
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  141 MET
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  243 MET
Chi-restraints excluded: chain S residue  257 GLU
Chi-restraints excluded: chain S residue  416 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    0.1980
   chunk 30 optimal weight:    0.0060
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0670
   chunk 16 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.2934

-------------------------------------------------------------------------------
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 = 0.4051 r_free = 0.4051 target = 0.152830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.140423 restraints weight = 4954.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 3.13
r_work: 0.3789 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.4565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   2899  Z= 0.138
  Angle     :  0.792  12.108   3924  Z= 0.385
  Chirality :  0.046   0.184    455
  Planarity :  0.005   0.066    499
  Dihedral  :  4.969  19.644    379
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 36.74 %
    Favored  : 58.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.46), residues: 355
  helix:  1.78 (0.47), residues: 115
  sheet:  0.47 (0.58), residues: 87
  loop : -0.66 (0.54), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG S 397 
 TYR   0.016   0.002   TYR S 253 
 PHE   0.022   0.002   PHE S 316 
 TRP   0.004   0.001   TRP S 238 
 HIS   0.002   0.001   HIS S 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2899)
  covalent geometry    : angle       0.79221 ( 3924)
  hydrogen bonds       : bond        0.03303 (  130)
  hydrogen bonds       : angle       5.23171 (  372)

*********************** 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
  126 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.122 
Fit side-chains
REVERT: S   87 LEU cc_start: 0.8274 (tp) cc_final: 0.7936 (tm)
REVERT: S  132 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7568 (mp0)
REVERT: S  145 GLU cc_start: 0.7904 (pt0) cc_final: 0.7294 (pt0)
REVERT: S  191 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7887 (mtpp)
REVERT: S  240 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5382 (mtt)
REVERT: S  320 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.7111 (mmm-85)
REVERT: S  322 TYR cc_start: 0.8442 (m-80) cc_final: 0.8235 (m-10)
REVERT: S  399 PHE cc_start: 0.8312 (p90) cc_final: 0.7834 (p90)
  outliers start: 14
  outliers final: 3
  residues processed: 114
  average time/residue: 0.4849
  time to fit residues: 56.7361
Evaluate side-chains
  107 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  132 GLU
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  243 MET
Chi-restraints excluded: chain S residue  257 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0970
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 8 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0270
   chunk 9 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.3636

-------------------------------------------------------------------------------
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 = 0.4047 r_free = 0.4047 target = 0.153144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.140192 restraints weight = 4952.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 3.19
r_work: 0.3787 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.4678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   2899  Z= 0.152
  Angle     :  0.854  12.466   3924  Z= 0.413
  Chirality :  0.046   0.184    455
  Planarity :  0.005   0.067    499
  Dihedral  :  5.127  19.521    379
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.46), residues: 355
  helix:  1.54 (0.46), residues: 119
  sheet:  0.11 (0.56), residues: 93
  loop : -0.49 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG S 397 
 TYR   0.015   0.002   TYR S 253 
 PHE   0.026   0.002   PHE S 316 
 TRP   0.006   0.001   TRP S 299 
 HIS   0.002   0.001   HIS S 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 2899)
  covalent geometry    : angle       0.85447 ( 3924)
  hydrogen bonds       : bond        0.03325 (  130)
  hydrogen bonds       : angle       5.35957 (  372)

*********************** 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
  106 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.107 
Fit side-chains
REVERT: S   87 LEU cc_start: 0.8252 (tp) cc_final: 0.7922 (tm)
REVERT: S  106 ASN cc_start: 0.6673 (OUTLIER) cc_final: 0.5691 (m-40)
REVERT: S  132 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7540 (mp0)
REVERT: S  145 GLU cc_start: 0.7798 (pt0) cc_final: 0.7225 (pt0)
REVERT: S  191 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7813 (mtpp)
REVERT: S  320 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.7134 (mmm-85)
REVERT: S  350 ARG cc_start: 0.7784 (ptm160) cc_final: 0.7549 (ptp-110)
  outliers start: 10
  outliers final: 6
  residues processed: 99
  average time/residue: 0.4544
  time to fit residues: 46.1739
Evaluate side-chains
  104 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
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  243 MET
Chi-restraints excluded: chain S residue  257 GLU
Chi-restraints excluded: chain S residue  290 MET
Chi-restraints excluded: chain S residue  292 LEU
Chi-restraints excluded: chain S residue  363 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 5 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 = 0.4049 r_free = 0.4049 target = 0.152867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.140001 restraints weight = 5023.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 3.18
r_work: 0.3780 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   2899  Z= 0.165
  Angle     :  0.866  13.612   3924  Z= 0.415
  Chirality :  0.047   0.189    455
  Planarity :  0.006   0.072    499
  Dihedral  :  5.130  19.913    379
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 39.62 %
    Favored  : 57.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.46), residues: 355
  helix:  1.46 (0.46), residues: 119
  sheet:  0.16 (0.57), residues: 93
  loop : -0.51 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG S 300 
 TYR   0.015   0.002   TYR S 253 
 PHE   0.025   0.002   PHE S 316 
 TRP   0.006   0.002   TRP S 299 
 HIS   0.002   0.001   HIS S 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 2899)
  covalent geometry    : angle       0.86574 ( 3924)
  hydrogen bonds       : bond        0.03449 (  130)
  hydrogen bonds       : angle       5.40676 (  372)

*********************** 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
  107 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.109 
Fit side-chains
REVERT: S   87 LEU cc_start: 0.8303 (tp) cc_final: 0.7986 (tm)
REVERT: S  106 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.5807 (m-40)
REVERT: S  132 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7552 (mp0)
REVERT: S  144 LYS cc_start: 0.7841 (tttp) cc_final: 0.7578 (tptp)
REVERT: S  145 GLU cc_start: 0.7801 (pt0) cc_final: 0.7235 (pt0)
REVERT: S  191 LYS cc_start: 0.8334 (mmtt) cc_final: 0.7928 (mmtt)
REVERT: S  240 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.5442 (mtt)
REVERT: S  258 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7253 (mm-30)
REVERT: S  320 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7256 (mmm-85)
REVERT: S  350 ARG cc_start: 0.7765 (ptm160) cc_final: 0.7508 (ptp-110)
REVERT: S  360 LYS cc_start: 0.8131 (tttt) cc_final: 0.7753 (ttpt)
  outliers start: 9
  outliers final: 3
  residues processed: 100
  average time/residue: 0.4728
  time to fit residues: 48.4990
Evaluate side-chains
  106 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
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  240 MET
Chi-restraints excluded: chain S residue  243 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 27 optimal weight:    0.0050
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 8 optimal weight:    0.2980
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.152148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.139580 restraints weight = 5012.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 3.13
r_work: 0.3779 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.4949

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= 0.167
  Angle     :  0.856  11.140   3924  Z= 0.416
  Chirality :  0.047   0.190    455
  Planarity :  0.006   0.073    499
  Dihedral  :  5.230  20.017    379
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 39.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.46), residues: 355
  helix:  1.53 (0.46), residues: 119
  sheet:  0.20 (0.57), residues: 93
  loop : -0.54 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG S 397 
 TYR   0.019   0.002   TYR S 253 
 PHE   0.025   0.002   PHE S 316 
 TRP   0.006   0.002   TRP S 238 
 HIS   0.002   0.001   HIS S 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 2899)
  covalent geometry    : angle       0.85634 ( 3924)
  hydrogen bonds       : bond        0.03528 (  130)
  hydrogen bonds       : angle       5.38418 (  372)

********************** 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
  114 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.112 
Fit side-chains
REVERT: S   87 LEU cc_start: 0.8340 (tp) cc_final: 0.8022 (tm)
REVERT: S  132 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7604 (mp0)
REVERT: S  145 GLU cc_start: 0.7832 (pt0) cc_final: 0.7200 (pt0)
REVERT: S  147 LEU cc_start: 0.7943 (pt) cc_final: 0.7740 (pt)
REVERT: S  191 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7922 (mmtt)
REVERT: S  240 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5398 (mtt)
REVERT: S  320 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7340 (mmm-85)
REVERT: S  350 ARG cc_start: 0.7734 (ptm160) cc_final: 0.7460 (ptp-110)
REVERT: S  360 LYS cc_start: 0.8239 (tttt) cc_final: 0.7846 (ttpt)
REVERT: S  399 PHE cc_start: 0.8322 (p90) cc_final: 0.7896 (p90)
  outliers start: 7
  outliers final: 2
  residues processed: 108
  average time/residue: 0.4697
  time to fit residues: 52.1408
Evaluate side-chains
  106 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  132 GLU
Chi-restraints excluded: chain S residue  196 ILE
Chi-restraints excluded: chain S residue  240 MET
Chi-restraints excluded: chain S residue  243 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0970
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.151953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.139479 restraints weight = 4991.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 3.14
r_work: 0.3777 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.5042

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= 0.167
  Angle     :  0.871  12.461   3924  Z= 0.422
  Chirality :  0.047   0.189    455
  Planarity :  0.006   0.063    499
  Dihedral  :  5.243  19.889    379
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 39.62 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.47), residues: 355
  helix:  1.62 (0.47), residues: 119
  sheet:  0.23 (0.57), residues: 93
  loop : -0.60 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG S 298 
 TYR   0.016   0.002   TYR S 253 
 PHE   0.025   0.002   PHE S 316 
 TRP   0.006   0.002   TRP S 299 
 HIS   0.002   0.001   HIS S 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 2899)
  covalent geometry    : angle       0.87116 ( 3924)
  hydrogen bonds       : bond        0.03474 (  130)
  hydrogen bonds       : angle       5.40558 (  372)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1482.07 seconds
wall clock time: 26 minutes 5.02 seconds (1565.02 seconds total)