Starting phenix.real_space_refine
on Fri Aug 22 14:07:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdn_37140/08_2025/8kdn_37140.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdn_37140/08_2025/8kdn_37140.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdn_37140/08_2025/8kdn_37140.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdn_37140/08_2025/8kdn_37140.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdn_37140/08_2025/8kdn_37140.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdn_37140/08_2025/8kdn_37140.map"
  }
  resolution = 4.12
  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=   0.002 sd=   0.010
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      22      5.16       5
     C    2635      2.51       5
     N     615      2.21       5
     O     658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3930
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 409
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 2, 'TRANS': 49}
    Chain: "B"
      Number of atoms: 3509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3509
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 23, 'TRANS': 430}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 1.21, per 1000 atoms: 0.31
  Number of scatterers: 3930
  At special positions: 0
  Unit cell: (76.725, 85.932, 79.794, 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      22     16.00
     O     658      8.00
     N     615      7.00
     C    2635      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.11

  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: 0.34
  Conformation dependent library (CDL) restraints added in 162.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  934

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 4.327A  pdb=" N   LYS A 171 " --> pdb=" O   GLU A 167 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 207
      removed outlier: 4.001A  pdb=" N   TRP A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 65
      removed outlier: 3.685A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   GLY B  65 " --> pdb=" O   GLY B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 72 through 80
      removed outlier: 4.397A  pdb=" N   GLU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.907A  pdb=" N   GLY B  93 " --> pdb=" O   TRP B  89 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU B 106 " --> pdb=" O   CYS B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 125
      removed outlier: 3.663A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.581A  pdb=" N   LYS B 132 " --> pdb=" O   PRO B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 157
      removed outlier: 3.616A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR B 155 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 161
    Processing helix  chain 'B' and resid 167 through 188
    Processing helix  chain 'B' and resid 189 through 221
    Processing helix  chain 'B' and resid 239 through 255
      removed outlier: 4.510A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY B 250 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   PHE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 267
      removed outlier: 4.192A  pdb=" N   LEU B 260 " --> pdb=" O   TRP B 257 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ASN B 261 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR B 264 " --> pdb=" O   ASN B 261 " (cutoff:3.500A)
      removed outlier: 5.728A  pdb=" N   GLU B 265 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 300
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
      removed outlier: 3.594A  pdb=" N   PHE B 297 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 308
    Processing helix  chain 'B' and resid 310 through 320
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.563A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 365
      removed outlier: 3.531A  pdb=" N   LEU B 363 " --> pdb=" O   PRO B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 387
      removed outlier: 3.578A  pdb=" N   LEU B 377 " --> pdb=" O   PRO B 373 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   TYR B 387 " --> pdb=" O   MET B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 390
      No H-bonds generated for 'chain 'B' and resid 388 through 390'
    Processing helix  chain 'B' and resid 393 through 422
      removed outlier: 3.838A  pdb=" N   ILE B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   PHE B 403 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN B 404 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 454
      removed outlier: 3.874A  pdb=" N   LEU B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 467
      removed outlier: 3.550A  pdb=" N   THR B 463 " --> pdb=" O   GLY B 459 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER B 467 " --> pdb=" O   THR B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 4.145A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 3.707A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)

    292 hydrogen bonds defined for protein.
    852 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: 0.56

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 664
        1.33 -     1.45: 1057
        1.45 -     1.58: 2279
        1.58 -     1.70: 2
        1.70 -     1.82: 31
  Bond restraints: 4033
  Sorted by residual:
  bond pdb=" CB  SER B 338 "
       pdb=" OG  SER B 338 "
    ideal  model  delta    sigma   weight residual
    1.417  1.488 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" C   VAL B 166 "
       pdb=" N   PRO B 167 "
    ideal  model  delta    sigma   weight residual
    1.332  1.365 -0.033 1.12e-02 7.97e+03 8.50e+00
  bond pdb=" C   SER B 143 "
       pdb=" O   SER B 143 "
    ideal  model  delta    sigma   weight residual
    1.237  1.203  0.034 1.19e-02 7.06e+03 8.12e+00
  bond pdb=" CA  LEU B 274 "
       pdb=" C   LEU B 274 "
    ideal  model  delta    sigma   weight residual
    1.521  1.551 -0.030 1.08e-02 8.57e+03 7.71e+00
  bond pdb=" C   LEU B 180 "
       pdb=" O   LEU B 180 "
    ideal  model  delta    sigma   weight residual
    1.237  1.205  0.031 1.16e-02 7.43e+03 7.35e+00
  ... (remaining 4028 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 4131
        1.78 -     3.56: 1131
        3.56 -     5.34: 207
        5.34 -     7.11: 32
        7.11 -     8.89: 4
  Bond angle restraints: 5505
  Sorted by residual:
  angle pdb=" CA  ASP B 116 "
        pdb=" CB  ASP B 116 "
        pdb=" CG  ASP B 116 "
      ideal   model   delta    sigma   weight residual
     112.60  118.63   -6.03 1.00e+00 1.00e+00 3.64e+01
  angle pdb=" CA  PHE B 200 "
        pdb=" CB  PHE B 200 "
        pdb=" CG  PHE B 200 "
      ideal   model   delta    sigma   weight residual
     113.80  107.96    5.84 1.00e+00 1.00e+00 3.41e+01
  angle pdb=" C   PHE B 389 "
        pdb=" CA  PHE B 389 "
        pdb=" CB  PHE B 389 "
      ideal   model   delta    sigma   weight residual
     111.74  119.36   -7.62 1.37e+00 5.33e-01 3.09e+01
  angle pdb=" CA  PHE B 445 "
        pdb=" CB  PHE B 445 "
        pdb=" CG  PHE B 445 "
      ideal   model   delta    sigma   weight residual
     113.80  119.22   -5.42 1.00e+00 1.00e+00 2.94e+01
  angle pdb=" N   TYR B 259 "
        pdb=" CA  TYR B 259 "
        pdb=" C   TYR B 259 "
      ideal   model   delta    sigma   weight residual
     111.36  116.60   -5.24 1.09e+00 8.42e-01 2.31e+01
  ... (remaining 5500 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 2151
       17.97 -    35.94: 151
       35.94 -    53.91: 20
       53.91 -    71.88: 3
       71.88 -    89.85: 4
  Dihedral angle restraints: 2329
    sinusoidal: 876
      harmonic: 1453
  Sorted by residual:
  dihedral pdb=" CA  PRO B 455 "
           pdb=" C   PRO B 455 "
           pdb=" N   VAL B 456 "
           pdb=" CA  VAL B 456 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.56  -29.44     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  TRP B 477 "
           pdb=" C   TRP B 477 "
           pdb=" N   TRP B 478 "
           pdb=" CA  TRP B 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.28  -27.72     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" CA  ILE B 139 "
           pdb=" C   ILE B 139 "
           pdb=" N   ILE B 140 "
           pdb=" CA  ILE B 140 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.56  -25.44     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 2326 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 430
       0.072 -    0.145: 173
       0.145 -    0.217: 51
       0.217 -    0.290: 10
       0.290 -    0.362: 1
  Chirality restraints: 665
  Sorted by residual:
  chirality pdb=" CA  SER B 113 "
            pdb=" N   SER B 113 "
            pdb=" C   SER B 113 "
            pdb=" CB  SER B 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.27e+00
  chirality pdb=" CB  ILE B 147 "
            pdb=" CA  ILE B 147 "
            pdb=" CG1 ILE B 147 "
            pdb=" CG2 ILE B 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  THR B 194 "
            pdb=" N   THR B 194 "
            pdb=" C   THR B 194 "
            pdb=" CB  THR B 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 662 not shown)

  Planarity restraints: 660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 141 "    0.316 9.50e-02 1.11e+02   1.42e-01 1.27e+01
        pdb=" NE  ARG B 141 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 141 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 141 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 141 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 348 "    0.314 9.50e-02 1.11e+02   1.41e-01 1.22e+01
        pdb=" NE  ARG B 348 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 348 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 348 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 348 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 182 "    0.269 9.50e-02 1.11e+02   1.21e-01 9.11e+00
        pdb=" NE  ARG A 182 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 182 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 182 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 182 "    0.012 2.00e-02 2.50e+03
  ... (remaining 657 not shown)

  Histogram of nonbonded interaction distances:
        2.61 -     3.07: 2508
        3.07 -     3.53: 4300
        3.53 -     3.98: 6293
        3.98 -     4.44: 7251
        4.44 -     4.90: 11235
  Nonbonded interactions: 31587
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 288 "
            pdb=" OG1 THR B 292 "
     model   vdw
     2.610 3.040
  nonbonded pdb=" OH  TYR B 103 "
            pdb=" OD1 ASP B 116 "
     model   vdw
     2.614 3.040
  nonbonded pdb=" NH2 ARG A 182 "
            pdb=" O   LYS B 498 "
     model   vdw
     2.633 3.120
  nonbonded pdb=" OG  SER B 395 "
            pdb=" OE1 GLU B 457 "
     model   vdw
     2.635 3.040
  nonbonded pdb=" O   ALA B 295 "
            pdb=" OG1 THR B 298 "
     model   vdw
     2.635 3.040
  ... (remaining 31582 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.070
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.160
  Find NCS groups from input model:        0.020
  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:             0.010
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6349
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      :  0.011   0.077   4034  Z= 0.703
  Angle     :  1.682   8.893   5507  Z= 1.133
  Chirality :  0.084   0.362    665
  Planarity :  0.012   0.142    660
  Dihedral  : 13.038  89.853   1392
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 0.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  4.45 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.21 %
  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: -2.77 (0.31), residues: 500
  helix: -1.67 (0.21), residues: 378
  sheet:  None (None), residues: 0
  loop : -1.70 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 141 
 TYR   0.021   0.005   TYR B 146 
 PHE   0.024   0.005   PHE B  69 
 TRP   0.037   0.004   TRP B 257 
 HIS   0.004   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.01104 ( 4033)
  covalent geometry    : angle       1.67985 ( 5505)
  SS BOND              : bond        0.07680 (    1)
  SS BOND              : angle       4.38125 (    2)
  hydrogen bonds       : bond        0.17033 (  292)
  hydrogen bonds       : angle       8.07243 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 169
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 VAL cc_start: 0.7315 (t) cc_final: 0.7075 (p)
REVERT: B  111 SER cc_start: 0.8071 (p) cc_final: 0.7536 (m)
REVERT: B  141 ARG cc_start: 0.6753 (tpp-160) cc_final: 0.6444 (tpp-160)
REVERT: B  239 ASP cc_start: 0.6811 (t0) cc_final: 0.6452 (t0)
REVERT: B  249 SER cc_start: 0.8405 (m) cc_final: 0.8157 (p)
REVERT: B  272 ARG cc_start: 0.5694 (ttt180) cc_final: 0.5404 (tpt170)
REVERT: B  297 PHE cc_start: 0.7492 (m-80) cc_final: 0.7155 (m-80)
REVERT: B  298 THR cc_start: 0.8119 (p) cc_final: 0.7838 (p)
REVERT: B  315 PHE cc_start: 0.8096 (t80) cc_final: 0.7843 (t80)
REVERT: B  318 TYR cc_start: 0.9131 (t80) cc_final: 0.8884 (t80)
REVERT: B  319 HIS cc_start: 0.6702 (m-70) cc_final: 0.5654 (m-70)
REVERT: B  365 MET cc_start: 0.8073 (mmt) cc_final: 0.7718 (mmt)
REVERT: B  367 HIS cc_start: 0.7775 (t-90) cc_final: 0.7168 (t-90)
REVERT: B  369 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8028 (mp10)
REVERT: B  391 LYS cc_start: 0.7614 (tptm) cc_final: 0.7241 (mmtt)
REVERT: B  394 PHE cc_start: 0.6433 (t80) cc_final: 0.6163 (t80)
REVERT: B  500 MET cc_start: 0.5676 (mmt) cc_final: 0.4931 (mtm)
  outliers start: 5
  outliers final: 1
  residues processed: 170
  average time/residue: 0.0590
  time to fit residues: 12.5589
Evaluate side-chains
  116 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.119967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.096558 restraints weight = 6486.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.099765 restraints weight = 3655.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.101664 restraints weight = 2551.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.103250 restraints weight = 2037.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.103696 restraints weight = 1737.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4034  Z= 0.153
  Angle     :  0.665   6.497   5507  Z= 0.340
  Chirality :  0.043   0.153    665
  Planarity :  0.004   0.030    660
  Dihedral  :  5.379  21.883    534
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  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:  0.59 (0.36), residues: 500
  helix:  0.90 (0.25), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.05 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 355 
 TYR   0.022   0.001   TYR B 103 
 PHE   0.019   0.002   PHE B 200 
 TRP   0.019   0.002   TRP B 452 
 HIS   0.003   0.001   HIS B 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4033)
  covalent geometry    : angle       0.66446 ( 5505)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       1.01461 (    2)
  hydrogen bonds       : bond        0.04073 (  292)
  hydrogen bonds       : angle       4.75234 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8182 (pm20) cc_final: 0.7621 (pm20)
REVERT: B  205 LEU cc_start: 0.8463 (mt) cc_final: 0.8138 (mt)
REVERT: B  254 TYR cc_start: 0.8257 (m-80) cc_final: 0.7773 (m-80)
REVERT: B  297 PHE cc_start: 0.8145 (m-80) cc_final: 0.7525 (m-80)
REVERT: B  335 CYS cc_start: 0.9090 (m) cc_final: 0.8714 (m)
REVERT: B  365 MET cc_start: 0.7791 (mmt) cc_final: 0.7191 (mmt)
REVERT: B  394 PHE cc_start: 0.7778 (t80) cc_final: 0.7168 (t80)
REVERT: B  398 ASN cc_start: 0.7910 (m-40) cc_final: 0.7210 (m-40)
REVERT: B  415 MET cc_start: 0.9195 (tmm) cc_final: 0.8772 (ttp)
REVERT: B  500 MET cc_start: 0.6363 (mmt) cc_final: 0.5474 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0532
  time to fit residues: 9.6304
Evaluate side-chains
  100 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0770
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.1942

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.122836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.099374 restraints weight = 6392.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.102702 restraints weight = 3603.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.104715 restraints weight = 2491.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.106258 restraints weight = 1980.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.106979 restraints weight = 1696.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4034  Z= 0.129
  Angle     :  0.604   6.805   5507  Z= 0.303
  Chirality :  0.041   0.155    665
  Planarity :  0.004   0.035    660
  Dihedral  :  4.667  18.498    534
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.37), residues: 500
  helix:  1.49 (0.25), residues: 385
  sheet:  None (None), residues: 0
  loop : -0.81 (0.59), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 355 
 TYR   0.016   0.002   TYR B 289 
 PHE   0.016   0.002   PHE B 200 
 TRP   0.019   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4033)
  covalent geometry    : angle       0.60357 ( 5505)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       0.73425 (    2)
  hydrogen bonds       : bond        0.03690 (  292)
  hydrogen bonds       : angle       4.17639 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8345 (pm20) cc_final: 0.8077 (pm20)
REVERT: B   46 LEU cc_start: 0.8008 (mt) cc_final: 0.7779 (mt)
REVERT: B   54 ASN cc_start: 0.7223 (m-40) cc_final: 0.6604 (m-40)
REVERT: B  178 CYS cc_start: 0.8453 (t) cc_final: 0.8222 (t)
REVERT: B  194 THR cc_start: 0.7682 (p) cc_final: 0.7204 (p)
REVERT: B  205 LEU cc_start: 0.8371 (mt) cc_final: 0.8130 (mt)
REVERT: B  254 TYR cc_start: 0.8238 (m-80) cc_final: 0.7512 (m-80)
REVERT: B  297 PHE cc_start: 0.8432 (m-80) cc_final: 0.8005 (m-80)
REVERT: B  319 HIS cc_start: 0.7759 (m-70) cc_final: 0.7556 (m-70)
REVERT: B  365 MET cc_start: 0.7683 (mmt) cc_final: 0.7459 (mmm)
REVERT: B  394 PHE cc_start: 0.7646 (t80) cc_final: 0.7339 (t80)
REVERT: B  398 ASN cc_start: 0.7894 (m-40) cc_final: 0.7417 (m-40)
REVERT: B  407 CYS cc_start: 0.7405 (t) cc_final: 0.7082 (t)
REVERT: B  500 MET cc_start: 0.6436 (mmt) cc_final: 0.5322 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0560
  time to fit residues: 9.0147
Evaluate side-chains
  97 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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 = 0.3440 r_free = 0.3440 target = 0.122618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.099830 restraints weight = 6363.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.103058 restraints weight = 3522.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.105266 restraints weight = 2430.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.106178 restraints weight = 1916.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.107187 restraints weight = 1706.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.4486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4034  Z= 0.127
  Angle     :  0.606   6.639   5507  Z= 0.297
  Chirality :  0.041   0.156    665
  Planarity :  0.004   0.039    660
  Dihedral  :  4.369  17.526    534
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.38), residues: 500
  helix:  1.71 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.33 (0.63), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 419 
 TYR   0.016   0.001   TYR B 103 
 PHE   0.014   0.001   PHE B  95 
 TRP   0.009   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4033)
  covalent geometry    : angle       0.60576 ( 5505)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       0.62594 (    2)
  hydrogen bonds       : bond        0.03425 (  292)
  hydrogen bonds       : angle       4.09116 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8388 (pm20) cc_final: 0.8104 (pm20)
REVERT: B   46 LEU cc_start: 0.7694 (mt) cc_final: 0.7250 (tp)
REVERT: B  122 GLU cc_start: 0.8150 (tt0) cc_final: 0.7950 (tt0)
REVERT: B  178 CYS cc_start: 0.8520 (t) cc_final: 0.8297 (t)
REVERT: B  194 THR cc_start: 0.7520 (p) cc_final: 0.7274 (p)
REVERT: B  205 LEU cc_start: 0.8339 (mt) cc_final: 0.8117 (mt)
REVERT: B  254 TYR cc_start: 0.8304 (m-80) cc_final: 0.7800 (m-80)
REVERT: B  294 LEU cc_start: 0.8531 (tp) cc_final: 0.8273 (tp)
REVERT: B  394 PHE cc_start: 0.7605 (t80) cc_final: 0.7090 (t80)
REVERT: B  398 ASN cc_start: 0.7935 (m-40) cc_final: 0.7376 (m-40)
REVERT: B  412 ILE cc_start: 0.7367 (mm) cc_final: 0.7145 (mm)
REVERT: B  432 ASN cc_start: 0.7182 (t0) cc_final: 0.6861 (t0)
REVERT: B  500 MET cc_start: 0.6891 (mmt) cc_final: 0.5742 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0573
  time to fit residues: 8.4499
Evaluate side-chains
  91 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 48 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.124786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.101694 restraints weight = 6341.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.104975 restraints weight = 3505.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.107327 restraints weight = 2419.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.108377 restraints weight = 1903.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.108677 restraints weight = 1675.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.4756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4034  Z= 0.119
  Angle     :  0.592   7.199   5507  Z= 0.289
  Chirality :  0.040   0.153    665
  Planarity :  0.004   0.038    660
  Dihedral  :  4.198  16.711    534
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  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:  2.17 (0.38), residues: 500
  helix:  1.94 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop : -0.28 (0.63), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 211 
 TYR   0.027   0.001   TYR B 103 
 PHE   0.013   0.001   PHE B  95 
 TRP   0.012   0.001   TRP B 257 
 HIS   0.004   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4033)
  covalent geometry    : angle       0.59165 ( 5505)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       0.45258 (    2)
  hydrogen bonds       : bond        0.03270 (  292)
  hydrogen bonds       : angle       3.93916 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8408 (pm20) cc_final: 0.8090 (pm20)
REVERT: B  112 LYS cc_start: 0.7859 (mtmt) cc_final: 0.7588 (mtpt)
REVERT: B  136 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7158 (mm-30)
REVERT: B  178 CYS cc_start: 0.8566 (t) cc_final: 0.8317 (t)
REVERT: B  194 THR cc_start: 0.7520 (p) cc_final: 0.7233 (p)
REVERT: B  254 TYR cc_start: 0.8158 (m-80) cc_final: 0.7581 (m-80)
REVERT: B  319 HIS cc_start: 0.7491 (m-70) cc_final: 0.7076 (m170)
REVERT: B  394 PHE cc_start: 0.7549 (t80) cc_final: 0.6959 (t80)
REVERT: B  398 ASN cc_start: 0.7934 (m-40) cc_final: 0.7255 (m-40)
REVERT: B  407 CYS cc_start: 0.7247 (t) cc_final: 0.6909 (t)
REVERT: B  500 MET cc_start: 0.6877 (mmt) cc_final: 0.5851 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0589
  time to fit residues: 8.6158
Evaluate side-chains
  95 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0870
   overall best weight:    0.7362

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

Flipped N/Q/H residues before XYZ refinement:
B 497 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.126746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.103771 restraints weight = 6395.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.107220 restraints weight = 3481.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.109539 restraints weight = 2366.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.110575 restraints weight = 1844.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.111892 restraints weight = 1622.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.5015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4034  Z= 0.113
  Angle     :  0.577   6.580   5507  Z= 0.281
  Chirality :  0.040   0.156    665
  Planarity :  0.004   0.035    660
  Dihedral  :  4.076  16.157    534
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  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:  2.22 (0.38), residues: 500
  helix:  2.00 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop : -0.34 (0.61), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 421 
 TYR   0.022   0.001   TYR B 103 
 PHE   0.019   0.001   PHE B 474 
 TRP   0.010   0.001   TRP B 405 
 HIS   0.001   0.000   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 4033)
  covalent geometry    : angle       0.57716 ( 5505)
  SS BOND              : bond        0.00099 (    1)
  SS BOND              : angle       0.35568 (    2)
  hydrogen bonds       : bond        0.03216 (  292)
  hydrogen bonds       : angle       3.90913 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8368 (pm20) cc_final: 0.7844 (pm20)
REVERT: A  202 VAL cc_start: 0.9008 (t) cc_final: 0.8790 (p)
REVERT: B   54 ASN cc_start: 0.7664 (m-40) cc_final: 0.7344 (m-40)
REVERT: B  105 GLU cc_start: 0.5652 (tp30) cc_final: 0.5127 (tp30)
REVERT: B  136 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6632 (mm-30)
REVERT: B  178 CYS cc_start: 0.8593 (t) cc_final: 0.8341 (t)
REVERT: B  212 ILE cc_start: 0.8111 (mm) cc_final: 0.7830 (mm)
REVERT: B  254 TYR cc_start: 0.7928 (m-80) cc_final: 0.7449 (m-80)
REVERT: B  313 VAL cc_start: 0.8042 (p) cc_final: 0.7812 (p)
REVERT: B  319 HIS cc_start: 0.7550 (m-70) cc_final: 0.7341 (m170)
REVERT: B  365 MET cc_start: 0.8113 (mmp) cc_final: 0.7684 (mmp)
REVERT: B  383 MET cc_start: 0.9168 (mmm) cc_final: 0.8960 (tpt)
REVERT: B  404 ASN cc_start: 0.7950 (m-40) cc_final: 0.7697 (m-40)
REVERT: B  407 CYS cc_start: 0.7075 (t) cc_final: 0.6565 (t)
REVERT: B  421 ARG cc_start: 0.7792 (mmp-170) cc_final: 0.7536 (mmp80)
REVERT: B  500 MET cc_start: 0.6883 (mmt) cc_final: 0.5836 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0573
  time to fit residues: 8.8085
Evaluate side-chains
  94 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 4 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 17 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 398 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.121726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.098066 restraints weight = 6632.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.101327 restraints weight = 3736.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.103327 restraints weight = 2609.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.104784 restraints weight = 2090.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.105277 restraints weight = 1807.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.4948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4034  Z= 0.173
  Angle     :  0.646   6.606   5507  Z= 0.323
  Chirality :  0.043   0.153    665
  Planarity :  0.004   0.036    660
  Dihedral  :  4.363  18.777    534
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.37), residues: 500
  helix:  1.74 (0.25), residues: 387
  sheet:  None (None), residues: 0
  loop : -0.35 (0.62), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 141 
 TYR   0.031   0.002   TYR B 289 
 PHE   0.020   0.002   PHE B 473 
 TRP   0.011   0.001   TRP B 257 
 HIS   0.004   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 4033)
  covalent geometry    : angle       0.64610 ( 5505)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.74037 (    2)
  hydrogen bonds       : bond        0.03772 (  292)
  hydrogen bonds       : angle       4.16928 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8523 (pm20) cc_final: 0.7975 (pm20)
REVERT: A  191 LEU cc_start: 0.8588 (mm) cc_final: 0.8343 (mm)
REVERT: B  105 GLU cc_start: 0.6336 (tm-30) cc_final: 0.5540 (tp30)
REVERT: B  136 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7573 (mm-30)
REVERT: B  178 CYS cc_start: 0.8692 (t) cc_final: 0.8461 (t)
REVERT: B  194 THR cc_start: 0.7678 (p) cc_final: 0.7396 (p)
REVERT: B  254 TYR cc_start: 0.8123 (m-80) cc_final: 0.7645 (m-80)
REVERT: B  319 HIS cc_start: 0.7756 (m-70) cc_final: 0.7541 (m170)
REVERT: B  335 CYS cc_start: 0.9052 (m) cc_final: 0.8625 (m)
REVERT: B  365 MET cc_start: 0.8101 (mmp) cc_final: 0.7840 (mmp)
REVERT: B  367 HIS cc_start: 0.7366 (t-90) cc_final: 0.7042 (t-90)
REVERT: B  394 PHE cc_start: 0.7406 (t80) cc_final: 0.7185 (t80)
REVERT: B  421 ARG cc_start: 0.7769 (mmp-170) cc_final: 0.7430 (mmp-170)
REVERT: B  500 MET cc_start: 0.6997 (mmt) cc_final: 0.6034 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0547
  time to fit residues: 8.1018
Evaluate side-chains
  93 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    7.9990
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.121975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.098577 restraints weight = 6493.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.101755 restraints weight = 3689.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.103694 restraints weight = 2584.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.105247 restraints weight = 2081.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.105669 restraints weight = 1783.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.5041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4034  Z= 0.156
  Angle     :  0.635   6.327   5507  Z= 0.313
  Chirality :  0.042   0.149    665
  Planarity :  0.004   0.034    660
  Dihedral  :  4.316  18.243    534
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.37), residues: 500
  helix:  1.68 (0.25), residues: 392
  sheet:  None (None), residues: 0
  loop : -0.29 (0.65), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 141 
 TYR   0.022   0.001   TYR B 289 
 PHE   0.020   0.002   PHE B 474 
 TRP   0.020   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 4033)
  covalent geometry    : angle       0.63521 ( 5505)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.62315 (    2)
  hydrogen bonds       : bond        0.03596 (  292)
  hydrogen bonds       : angle       4.11568 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8482 (pm20) cc_final: 0.7948 (pm20)
REVERT: A  191 LEU cc_start: 0.8591 (mm) cc_final: 0.8334 (mm)
REVERT: B  178 CYS cc_start: 0.8676 (t) cc_final: 0.8471 (t)
REVERT: B  194 THR cc_start: 0.7638 (p) cc_final: 0.7395 (p)
REVERT: B  249 SER cc_start: 0.8664 (m) cc_final: 0.8456 (t)
REVERT: B  254 TYR cc_start: 0.8180 (m-80) cc_final: 0.7696 (m-80)
REVERT: B  287 LEU cc_start: 0.8216 (tp) cc_final: 0.7999 (tp)
REVERT: B  291 LEU cc_start: 0.8429 (mm) cc_final: 0.8185 (mm)
REVERT: B  335 CYS cc_start: 0.9041 (m) cc_final: 0.8604 (m)
REVERT: B  365 MET cc_start: 0.7988 (mmp) cc_final: 0.7523 (mmp)
REVERT: B  367 HIS cc_start: 0.7344 (t-90) cc_final: 0.7027 (t-90)
REVERT: B  407 CYS cc_start: 0.7272 (t) cc_final: 0.6856 (t)
REVERT: B  421 ARG cc_start: 0.7711 (mmp-170) cc_final: 0.7453 (mmp-170)
REVERT: B  500 MET cc_start: 0.7002 (mmt) cc_final: 0.6085 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0554
  time to fit residues: 7.8271
Evaluate side-chains
  94 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.125818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.102490 restraints weight = 6504.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.106027 restraints weight = 3566.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.108154 restraints weight = 2431.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.109815 restraints weight = 1918.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.110608 restraints weight = 1625.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.5276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4034  Z= 0.118
  Angle     :  0.602   6.373   5507  Z= 0.296
  Chirality :  0.040   0.150    665
  Planarity :  0.004   0.034    660
  Dihedral  :  4.132  18.765    534
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.38), residues: 500
  helix:  1.75 (0.26), residues: 395
  sheet:  None (None), residues: 0
  loop : -0.35 (0.65), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 141 
 TYR   0.023   0.001   TYR B 103 
 PHE   0.019   0.001   PHE B 474 
 TRP   0.021   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4033)
  covalent geometry    : angle       0.60243 ( 5505)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.34020 (    2)
  hydrogen bonds       : bond        0.03359 (  292)
  hydrogen bonds       : angle       3.92946 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8413 (pm20) cc_final: 0.7912 (pm20)
REVERT: A  191 LEU cc_start: 0.8570 (mm) cc_final: 0.8313 (mm)
REVERT: A  209 ARG cc_start: 0.6373 (mmt180) cc_final: 0.5917 (mmm-85)
REVERT: B  178 CYS cc_start: 0.8683 (t) cc_final: 0.8426 (t)
REVERT: B  212 ILE cc_start: 0.8470 (mm) cc_final: 0.8222 (mm)
REVERT: B  254 TYR cc_start: 0.8126 (m-80) cc_final: 0.7645 (m-80)
REVERT: B  265 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6887 (mp0)
REVERT: B  365 MET cc_start: 0.7963 (mmp) cc_final: 0.7623 (mmp)
REVERT: B  367 HIS cc_start: 0.7234 (t-90) cc_final: 0.6957 (t-90)
REVERT: B  500 MET cc_start: 0.7024 (mmt) cc_final: 0.6114 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0602
  time to fit residues: 8.5665
Evaluate side-chains
  90 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 46 optimal weight:    0.3980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.126019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.102981 restraints weight = 6406.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.106445 restraints weight = 3541.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.108772 restraints weight = 2417.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.110062 restraints weight = 1882.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.110954 restraints weight = 1620.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.5398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4034  Z= 0.117
  Angle     :  0.607   6.798   5507  Z= 0.297
  Chirality :  0.040   0.155    665
  Planarity :  0.004   0.033    660
  Dihedral  :  4.076  18.730    534
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  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:  2.01 (0.38), residues: 500
  helix:  1.80 (0.26), residues: 395
  sheet:  None (None), residues: 0
  loop : -0.37 (0.65), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 421 
 TYR   0.013   0.001   TYR B 289 
 PHE   0.020   0.001   PHE B 474 
 TRP   0.020   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4033)
  covalent geometry    : angle       0.60688 ( 5505)
  SS BOND              : bond        0.00096 (    1)
  SS BOND              : angle       0.32883 (    2)
  hydrogen bonds       : bond        0.03240 (  292)
  hydrogen bonds       : angle       3.85220 (  852)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8406 (pm20) cc_final: 0.7926 (pm20)
REVERT: A  209 ARG cc_start: 0.6380 (mmt180) cc_final: 0.5918 (mmm-85)
REVERT: B   89 TRP cc_start: 0.8110 (m100) cc_final: 0.7715 (m100)
REVERT: B  121 LEU cc_start: 0.8728 (tp) cc_final: 0.8416 (tp)
REVERT: B  133 LEU cc_start: 0.8981 (tp) cc_final: 0.8766 (tt)
REVERT: B  178 CYS cc_start: 0.8612 (t) cc_final: 0.8359 (t)
REVERT: B  254 TYR cc_start: 0.8058 (m-80) cc_final: 0.7445 (m-80)
REVERT: B  265 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7034 (mp0)
REVERT: B  365 MET cc_start: 0.8120 (mmp) cc_final: 0.7788 (mmp)
REVERT: B  367 HIS cc_start: 0.7209 (t-90) cc_final: 0.6952 (t-90)
REVERT: B  394 PHE cc_start: 0.7155 (t80) cc_final: 0.6584 (t80)
REVERT: B  398 ASN cc_start: 0.7429 (m110) cc_final: 0.6961 (m110)
REVERT: B  407 CYS cc_start: 0.7183 (t) cc_final: 0.6927 (t)
REVERT: B  500 MET cc_start: 0.7044 (mmt) cc_final: 0.6133 (mtm)
REVERT: B  501 GLN cc_start: 0.7672 (tt0) cc_final: 0.7440 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0566
  time to fit residues: 8.0620
Evaluate side-chains
  93 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0040
   chunk 23 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0270
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5050

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.128219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.105143 restraints weight = 6378.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.108594 restraints weight = 3520.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.110853 restraints weight = 2404.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.112052 restraints weight = 1887.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.113105 restraints weight = 1637.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.5613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4034  Z= 0.113
  Angle     :  0.606   7.624   5507  Z= 0.294
  Chirality :  0.040   0.138    665
  Planarity :  0.004   0.034    660
  Dihedral  :  4.025  17.275    534
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.38), residues: 500
  helix:  1.70 (0.26), residues: 403
  sheet:  None (None), residues: 0
  loop : -0.34 (0.66), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 421 
 TYR   0.023   0.001   TYR B 103 
 PHE   0.021   0.001   PHE B  95 
 TRP   0.020   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4033)
  covalent geometry    : angle       0.60601 ( 5505)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.27765 (    2)
  hydrogen bonds       : bond        0.03217 (  292)
  hydrogen bonds       : angle       3.83392 (  852)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 777.83 seconds
wall clock time: 14 minutes 10.43 seconds (850.43 seconds total)