Starting phenix.real_space_refine
on Tue Mar 11 16:41:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zbq_39907/03_2025/8zbq_39907_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zbq_39907/03_2025/8zbq_39907.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zbq_39907/03_2025/8zbq_39907.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zbq_39907/03_2025/8zbq_39907.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zbq_39907/03_2025/8zbq_39907_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zbq_39907/03_2025/8zbq_39907_neut.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.081
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      36      5.16       5
     C    4072      2.51       5
     N    1052      2.21       5
     O    1186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6346
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
    Chain: "F"
      Number of atoms: 1476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1476
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 11, 'TRANS': 170}
  Time building chain proxies: 4.09, per 1000 atoms: 0.64
  Number of scatterers: 6346
  At special positions: 0
  Unit cell: (75.9, 97.9, 105.6, 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      36     16.00
     O    1186      8.00
     N    1052      7.00
     C    4072      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 336 " - pdb=" SG  CYS F 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 480 " - pdb=" SG  CYS F 488 " distance=2.01

  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: 1.42
  Conformation dependent library (CDL) restraints added in 819.2 milliseconds
  

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1470

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 5 sheets defined
      53.5% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'D' and resid 21 through 23
      No H-bonds generated for 'chain 'D' and resid 21 through 23'
    Processing helix  chain 'D' and resid 24 through 53
    Processing helix  chain 'D' and resid 55 through 81
    Processing helix  chain 'D' and resid 82 through 83
      No H-bonds generated for 'chain 'D' and resid 82 through 83'
    Processing helix  chain 'D' and resid 84 through 88
    Processing helix  chain 'D' and resid 92 through 101
    Processing helix  chain 'D' and resid 109 through 129
      removed outlier: 3.514A  pdb=" N   LYS D 114 " --> pdb=" O   GLU D 110 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG D 115 " --> pdb=" O   ASP D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 155
    Processing helix  chain 'D' and resid 158 through 163
    Processing helix  chain 'D' and resid 165 through 171
    Processing helix  chain 'D' and resid 172 through 193
      Proline residue:  D 178  - end of helix
      removed outlier: 3.616A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 218 through 247
      removed outlier: 3.748A  pdb=" N   LEU D 222 " --> pdb=" O   SER D 218 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   GLU D 232 " --> pdb=" O   HIS D 228 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 279
    Processing helix  chain 'D' and resid 292 through 296
      removed outlier: 4.113A  pdb=" N   ASP D 295 " --> pdb=" O   ASP D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 305 through 318
      removed outlier: 3.978A  pdb=" N   ALA D 311 " --> pdb=" O   ILE D 307 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   PHE D 314 " --> pdb=" O   GLU D 310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 329
      removed outlier: 3.726A  pdb=" N   TRP D 328 " --> pdb=" O   THR D 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 400 through 414
    Processing helix  chain 'D' and resid 416 through 421
      removed outlier: 4.072A  pdb=" N   SER D 420 " --> pdb=" O   LYS D 416 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE D 421 " --> pdb=" O   HIS D 417 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 416 through 421'
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.737A  pdb=" N   THR D 445 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 449 through 465
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 484
      removed outlier: 3.542A  pdb=" N   ARG D 482 " --> pdb=" O   TRP D 478 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 498 through 503
    Processing helix  chain 'D' and resid 512 through 533
      removed outlier: 4.226A  pdb=" N   TYR D 516 " --> pdb=" O   PHE D 512 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 550 through 559
      removed outlier: 3.706A  pdb=" N   LEU D 554 " --> pdb=" O   ALA D 550 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   ASN D 556 " --> pdb=" O   GLN D 552 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 574
    Processing helix  chain 'D' and resid 581 through 588
    Processing helix  chain 'D' and resid 588 through 599
      removed outlier: 6.071A  pdb=" N   TRP D 594 " --> pdb=" O   PRO D 590 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 611 through 615
    Processing helix  chain 'F' and resid 340 through 344
      removed outlier: 3.604A  pdb=" N   ALA F 344 " --> pdb=" O   VAL F 341 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 364 through 371
    Processing helix  chain 'F' and resid 403 through 407
      removed outlier: 3.509A  pdb=" N   VAL F 407 " --> pdb=" O   GLY F 404 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'D' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263
      removed outlier: 5.805A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'F' and resid 354 through 358
      removed outlier: 4.755A  pdb=" N   ILE F 434 " --> pdb=" O   VAL F 511 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   CYS F 432 " --> pdb=" O   LEU F 513 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 452 through 454

    280 hydrogen bonds defined for protein.
    753 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: 1.96

  Time building geometry restraints manager: 1.72 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1060
        1.31 -     1.44: 1921
        1.44 -     1.58: 3494
        1.58 -     1.72: 0
        1.72 -     1.86: 57
  Bond restraints: 6532
  Sorted by residual:
  bond pdb=" CA  ALA F 348 "
       pdb=" C   ALA F 348 "
    ideal  model  delta    sigma   weight residual
    1.527  1.419  0.108 1.35e-02 5.49e+03 6.35e+01
  bond pdb=" CA  LYS F 478 "
       pdb=" C   LYS F 478 "
    ideal  model  delta    sigma   weight residual
    1.523  1.424  0.099 1.31e-02 5.83e+03 5.67e+01
  bond pdb=" C   ASP F 442 "
       pdb=" O   ASP F 442 "
    ideal  model  delta    sigma   weight residual
    1.232  1.171  0.061 1.01e-02 9.80e+03 3.61e+01
  bond pdb=" N   GLU D 110 "
       pdb=" CA  GLU D 110 "
    ideal  model  delta    sigma   weight residual
    1.457  1.519 -0.062 1.17e-02 7.31e+03 2.77e+01
  bond pdb=" C   LYS F 478 "
       pdb=" O   LYS F 478 "
    ideal  model  delta    sigma   weight residual
    1.241  1.184  0.057 1.14e-02 7.69e+03 2.50e+01
  ... (remaining 6527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 8587
        2.25 -     4.51: 224
        4.51 -     6.76: 46
        6.76 -     9.02: 11
        9.02 -    11.27: 7
  Bond angle restraints: 8875
  Sorted by residual:
  angle pdb=" C   LYS F 478 "
        pdb=" CA  LYS F 478 "
        pdb=" CB  LYS F 478 "
      ideal   model   delta    sigma   weight residual
     110.33  101.27    9.06 1.02e+00 9.61e-01 7.88e+01
  angle pdb=" N   ASN F 477 "
        pdb=" CA  ASN F 477 "
        pdb=" C   ASN F 477 "
      ideal   model   delta    sigma   weight residual
     112.41  123.68  -11.27 1.30e+00 5.92e-01 7.52e+01
  angle pdb=" N   PRO F 499 "
        pdb=" CA  PRO F 499 "
        pdb=" C   PRO F 499 "
      ideal   model   delta    sigma   weight residual
     113.98  103.70   10.28 1.29e+00 6.01e-01 6.35e+01
  angle pdb=" N   VAL D 298 "
        pdb=" CA  VAL D 298 "
        pdb=" C   VAL D 298 "
      ideal   model   delta    sigma   weight residual
     113.71  106.57    7.14 9.50e-01 1.11e+00 5.66e+01
  angle pdb=" N   TYR D 158 "
        pdb=" CA  TYR D 158 "
        pdb=" C   TYR D 158 "
      ideal   model   delta    sigma   weight residual
     114.04  105.17    8.87 1.24e+00 6.50e-01 5.12e+01
  ... (remaining 8870 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3367
       17.97 -    35.95: 365
       35.95 -    53.92: 79
       53.92 -    71.90: 27
       71.90 -    89.87: 11
  Dihedral angle restraints: 3849
    sinusoidal: 1559
      harmonic: 2290
  Sorted by residual:
  dihedral pdb=" CB  CYS F 336 "
           pdb=" SG  CYS F 336 "
           pdb=" SG  CYS F 361 "
           pdb=" CB  CYS F 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   22.87   70.13     1      1.00e+01 1.00e-02 6.34e+01
  dihedral pdb=" CB  CYS D 133 "
           pdb=" SG  CYS D 133 "
           pdb=" SG  CYS D 141 "
           pdb=" CB  CYS D 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.22   52.78     1      1.00e+01 1.00e-02 3.79e+01
  dihedral pdb=" C   LYS F 478 "
           pdb=" N   LYS F 478 "
           pdb=" CA  LYS F 478 "
           pdb=" CB  LYS F 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.54  -15.06     0      2.50e+00 1.60e-01 3.63e+01
  ... (remaining 3846 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 743
       0.055 -    0.109: 144
       0.109 -    0.164: 23
       0.164 -    0.218: 6
       0.218 -    0.273: 2
  Chirality restraints: 918
  Sorted by residual:
  chirality pdb=" CA  GLU D 110 "
            pdb=" N   GLU D 110 "
            pdb=" C   GLU D 110 "
            pdb=" CB  GLU D 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  LYS D 234 "
            pdb=" N   LYS D 234 "
            pdb=" C   LYS D 234 "
            pdb=" CB  LYS D 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ASP D 111 "
            pdb=" N   ASP D 111 "
            pdb=" C   ASP D 111 "
            pdb=" CB  ASP D 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 915 not shown)

  Planarity restraints: 1150
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F 476 "   -0.021 2.00e-02 2.50e+03   4.34e-02 1.88e+01
        pdb=" C   GLY F 476 "    0.075 2.00e-02 2.50e+03
        pdb=" O   GLY F 476 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ASN F 477 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F 498 "   -0.054 5.00e-02 4.00e+02   8.23e-02 1.08e+01
        pdb=" N   PRO F 499 "    0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO F 499 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO F 499 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 233 "    0.016 2.00e-02 2.50e+03   3.25e-02 1.05e+01
        pdb=" C   ILE D 233 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ILE D 233 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LYS D 234 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1147 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1774
        2.79 -     3.32: 6510
        3.32 -     3.84: 11877
        3.84 -     4.37: 14524
        4.37 -     4.90: 23235
  Nonbonded interactions: 57920
  Sorted by model distance:
  nonbonded pdb=" O   PHE D 327 "
            pdb=" OG  SER D 331 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OE2 GLU D 527 "
            pdb=" NE2 GLN D 531 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" O   SER D  47 "
            pdb=" ND2 ASN D  51 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" NH2 ARG F 454 "
            pdb=" O   ASP F 467 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" NH1 ARG D 482 "
            pdb=" O   THR D 608 "
     model   vdw
     2.300 3.120
  ... (remaining 57915 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 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:             1.890
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.820
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
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      :  0.006   0.108   6532  Z= 0.370
  Angle     :  0.919  11.273   8875  Z= 0.584
  Chirality :  0.048   0.273    918
  Planarity :  0.006   0.082   1150
  Dihedral  : 16.508  89.870   2361
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 24.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.81 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  :  3.50 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.30), residues: 775
  helix: -0.65 (0.28), residues: 351
  sheet: -1.62 (0.82), residues: 39
  loop : -2.01 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP F 353 
 HIS   0.008   0.002   HIS D 378 
 PHE   0.022   0.002   PHE F 375 
 TYR   0.021   0.001   TYR D 381 
 ARG   0.002   0.000   ARG D 482 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 139
  time to evaluate  : 0.720 
Fit side-chains
REVERT: D   63 ASN cc_start: 0.7280 (m110) cc_final: 0.6760 (m110)
REVERT: D  111 ASP cc_start: 0.7840 (p0) cc_final: 0.7497 (p0)
REVERT: D  189 GLU cc_start: 0.7186 (mp0) cc_final: 0.6461 (mp0)
REVERT: F  500 THR cc_start: 0.6869 (OUTLIER) cc_final: 0.6573 (t)
  outliers start: 44
  outliers final: 6
  residues processed: 165
  average time/residue: 0.2044
  time to fit residues: 43.7736
Evaluate side-chains
  111 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  143 LEU
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  501 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0970
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D  58 ASN
D 175 GLN
D 378 HIS
F 493 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.162284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.131207 restraints weight = 7410.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.45
r_work: 0.3295 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   6532  Z= 0.300
  Angle     :  0.648   6.247   8875  Z= 0.348
  Chirality :  0.046   0.162    918
  Planarity :  0.005   0.053   1150
  Dihedral  :  6.376  53.232    858
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 11.37 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.30), residues: 775
  helix: -0.56 (0.26), residues: 364
  sheet: -1.48 (0.87), residues: 36
  loop : -1.56 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 302 
 HIS   0.006   0.001   HIS D 374 
 PHE   0.020   0.002   PHE D 523 
 TYR   0.027   0.002   TYR D 385 
 ARG   0.007   0.001   ARG F 454 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.781 
Fit side-chains
REVERT: D   62 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7242 (ttt)
REVERT: D   63 ASN cc_start: 0.7337 (m110) cc_final: 0.6707 (m110)
REVERT: D  120 LEU cc_start: 0.8727 (mt) cc_final: 0.8519 (mt)
REVERT: D  228 HIS cc_start: 0.8026 (m170) cc_final: 0.7747 (m-70)
REVERT: D  306 ARG cc_start: 0.7441 (ttt180) cc_final: 0.7099 (ttt180)
REVERT: D  307 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7932 (mt)
REVERT: D  483 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8243 (pp20)
REVERT: F  346 ARG cc_start: 0.5576 (OUTLIER) cc_final: 0.4854 (tmm160)
  outliers start: 24
  outliers final: 12
  residues processed: 121
  average time/residue: 0.2112
  time to fit residues: 33.2897
Evaluate side-chains
  118 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  299 ASP
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  483 GLU
Chi-restraints excluded: chain F residue  339 HIS
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  501 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0070
   chunk 64 optimal weight:    9.9990
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
D 330 ASN
D 345 HIS
D 531 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.160980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.129900 restraints weight = 7505.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.46
r_work: 0.3264 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6532  Z= 0.254
  Angle     :  0.598   6.019   8875  Z= 0.316
  Chirality :  0.044   0.138    918
  Planarity :  0.005   0.052   1150
  Dihedral  :  5.676  45.314    850
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.29 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.30), residues: 775
  helix: -0.27 (0.27), residues: 356
  sheet: -1.56 (0.86), residues: 36
  loop : -1.42 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP F 353 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.019   0.002   PHE D 523 
 TYR   0.022   0.002   TYR D 385 
 ARG   0.005   0.001   ARG F 454 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7559 (mm-30)
REVERT: D   62 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7241 (ttt)
REVERT: D   63 ASN cc_start: 0.7321 (m110) cc_final: 0.6770 (m110)
REVERT: D  306 ARG cc_start: 0.7485 (ttt180) cc_final: 0.7036 (ttt180)
REVERT: D  307 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7957 (mt)
REVERT: D  472 GLN cc_start: 0.8645 (mt0) cc_final: 0.8428 (mt0)
REVERT: D  474 MET cc_start: 0.8883 (mmp) cc_final: 0.8622 (mmp)
REVERT: D  483 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8264 (pp20)
REVERT: D  518 ARG cc_start: 0.8320 (tmm160) cc_final: 0.8079 (tmm160)
REVERT: F  439 ASN cc_start: 0.8219 (t0) cc_final: 0.7868 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 128
  average time/residue: 0.1963
  time to fit residues: 33.8461
Evaluate side-chains
  124 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  299 ASP
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  483 GLU
Chi-restraints excluded: chain D residue  611 SER
Chi-restraints excluded: chain F residue  339 HIS
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  501 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
D 340 GLN
D 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.156455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.124956 restraints weight = 7634.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.46
r_work: 0.3220 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   6532  Z= 0.299
  Angle     :  0.611   6.156   8875  Z= 0.323
  Chirality :  0.045   0.144    918
  Planarity :  0.005   0.051   1150
  Dihedral  :  5.696  45.719    850
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 15.74 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.30), residues: 775
  helix: -0.33 (0.27), residues: 363
  sheet: -1.52 (0.87), residues: 36
  loop : -1.39 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP F 353 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.021   0.002   PHE D 523 
 TYR   0.022   0.002   TYR D 385 
 ARG   0.003   0.001   ARG D 482 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7408 (m110) cc_final: 0.6836 (m110)
REVERT: D   81 GLN cc_start: 0.7649 (mm110) cc_final: 0.7431 (mm-40)
REVERT: D  306 ARG cc_start: 0.7394 (ttt180) cc_final: 0.6999 (ttt180)
REVERT: D  307 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7980 (mt)
REVERT: D  472 GLN cc_start: 0.8728 (mt0) cc_final: 0.8497 (mt0)
REVERT: D  474 MET cc_start: 0.9058 (mmp) cc_final: 0.8458 (mmp)
REVERT: D  483 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8254 (pp20)
REVERT: D  518 ARG cc_start: 0.8356 (tmm160) cc_final: 0.8089 (tmm160)
REVERT: D  531 GLN cc_start: 0.8194 (mt0) cc_final: 0.7871 (mt0)
REVERT: F  346 ARG cc_start: 0.5413 (OUTLIER) cc_final: 0.3473 (tmm160)
REVERT: F  439 ASN cc_start: 0.8327 (t0) cc_final: 0.7934 (t0)
  outliers start: 31
  outliers final: 21
  residues processed: 128
  average time/residue: 0.2027
  time to fit residues: 35.3557
Evaluate side-chains
  126 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  299 ASP
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  483 GLU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  611 SER
Chi-restraints excluded: chain F residue  339 HIS
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  501 TYR
Chi-restraints excluded: chain F residue  503 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 46 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 75 optimal weight:    0.4980
   chunk 72 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 54 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3702 r_free = 0.3702 target = 0.156522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.124949 restraints weight = 7512.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.47
r_work: 0.3254 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6532  Z= 0.244
  Angle     :  0.574   6.244   8875  Z= 0.303
  Chirality :  0.043   0.144    918
  Planarity :  0.004   0.051   1150
  Dihedral  :  5.605  46.005    850
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 16.47 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.30), residues: 775
  helix: -0.16 (0.27), residues: 361
  sheet: -1.55 (0.86), residues: 36
  loop : -1.51 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 302 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.019   0.001   PHE D 523 
 TYR   0.019   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 482 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 110
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7384 (m110) cc_final: 0.6803 (m110)
REVERT: D  306 ARG cc_start: 0.7390 (ttt180) cc_final: 0.7022 (ttt180)
REVERT: D  307 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8024 (mt)
REVERT: D  472 GLN cc_start: 0.8758 (mt0) cc_final: 0.8458 (mt0)
REVERT: D  474 MET cc_start: 0.9014 (mmp) cc_final: 0.8416 (mmp)
REVERT: D  483 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8215 (pp20)
REVERT: D  531 GLN cc_start: 0.8153 (mt0) cc_final: 0.7883 (mt0)
REVERT: F  346 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.3866 (tmm160)
REVERT: F  439 ASN cc_start: 0.8326 (t0) cc_final: 0.7906 (t0)
  outliers start: 33
  outliers final: 24
  residues processed: 132
  average time/residue: 0.1790
  time to fit residues: 32.1894
Evaluate side-chains
  132 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  299 ASP
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  483 GLU
Chi-restraints excluded: chain D residue  485 VAL
Chi-restraints excluded: chain D residue  527 GLU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  611 SER
Chi-restraints excluded: chain F residue  339 HIS
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  501 TYR
Chi-restraints excluded: chain F residue  503 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0050
   chunk 57 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 58 optimal weight:    0.2980
   chunk 68 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 56 optimal weight:    0.2980
   overall best weight:    0.3794

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.159691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.128914 restraints weight = 7431.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.46
r_work: 0.3277 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6532  Z= 0.203
  Angle     :  0.549   7.078   8875  Z= 0.289
  Chirality :  0.042   0.138    918
  Planarity :  0.004   0.052   1150
  Dihedral  :  5.453  46.040    850
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 17.06 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.30), residues: 775
  helix:  0.13 (0.28), residues: 343
  sheet: -1.87 (0.69), residues: 48
  loop : -1.36 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP F 353 
 HIS   0.006   0.001   HIS D 374 
 PHE   0.021   0.001   PHE F 371 
 TYR   0.018   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 582 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7402 (m110) cc_final: 0.6814 (m110)
REVERT: D  306 ARG cc_start: 0.7377 (ttt180) cc_final: 0.7008 (ttt180)
REVERT: D  307 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7976 (mt)
REVERT: D  472 GLN cc_start: 0.8688 (mt0) cc_final: 0.8443 (mt0)
REVERT: D  474 MET cc_start: 0.9021 (mmp) cc_final: 0.8412 (mmp)
REVERT: D  483 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8217 (pp20)
REVERT: D  531 GLN cc_start: 0.8090 (mt0) cc_final: 0.7872 (mt0)
REVERT: D  578 ASN cc_start: 0.7052 (t0) cc_final: 0.6589 (p0)
REVERT: F  346 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.3741 (tmm160)
REVERT: F  439 ASN cc_start: 0.8313 (t0) cc_final: 0.7939 (t0)
  outliers start: 29
  outliers final: 23
  residues processed: 136
  average time/residue: 0.1795
  time to fit residues: 33.5130
Evaluate side-chains
  130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  483 GLU
Chi-restraints excluded: chain D residue  485 VAL
Chi-restraints excluded: chain D residue  527 GLU
Chi-restraints excluded: chain D residue  611 SER
Chi-restraints excluded: chain F residue  339 HIS
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  501 TYR
Chi-restraints excluded: chain F residue  503 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0980
   chunk 59 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 56 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9990
   chunk 69 optimal weight:    0.4980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3720 r_free = 0.3720 target = 0.158051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.126978 restraints weight = 7538.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.47
r_work: 0.3256 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6532  Z= 0.225
  Angle     :  0.562   6.660   8875  Z= 0.295
  Chirality :  0.042   0.136    918
  Planarity :  0.004   0.053   1150
  Dihedral  :  5.463  47.070    850
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 17.64 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.30), residues: 775
  helix:  0.08 (0.28), residues: 351
  sheet: -1.83 (0.69), residues: 48
  loop : -1.36 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 302 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.018   0.001   PHE D 523 
 TYR   0.013   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 582 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7564 (mm-30)
REVERT: D   63 ASN cc_start: 0.7404 (m110) cc_final: 0.6805 (m110)
REVERT: D  306 ARG cc_start: 0.7381 (ttt180) cc_final: 0.6920 (ttt180)
REVERT: D  307 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7970 (mt)
REVERT: D  472 GLN cc_start: 0.8728 (mt0) cc_final: 0.8495 (mt0)
REVERT: D  474 MET cc_start: 0.9044 (mmp) cc_final: 0.8761 (mmp)
REVERT: D  483 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8213 (pp20)
REVERT: D  531 GLN cc_start: 0.8106 (mt0) cc_final: 0.7870 (mt0)
REVERT: D  578 ASN cc_start: 0.7233 (t0) cc_final: 0.6769 (p0)
REVERT: F  346 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.3691 (tmm160)
REVERT: F  439 ASN cc_start: 0.8338 (t0) cc_final: 0.7964 (t0)
  outliers start: 31
  outliers final: 24
  residues processed: 132
  average time/residue: 0.1882
  time to fit residues: 34.2390
Evaluate side-chains
  132 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  483 GLU
Chi-restraints excluded: chain D residue  485 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  527 GLU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  611 SER
Chi-restraints excluded: chain F residue  339 HIS
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  501 TYR
Chi-restraints excluded: chain F residue  503 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0570
   chunk 42 optimal weight:    0.0980
   chunk 8 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.158942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.127927 restraints weight = 7478.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.47
r_work: 0.3267 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6532  Z= 0.219
  Angle     :  0.561   6.788   8875  Z= 0.295
  Chirality :  0.043   0.181    918
  Planarity :  0.004   0.053   1150
  Dihedral  :  5.445  47.566    850
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.93 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.30), residues: 775
  helix:  0.12 (0.28), residues: 351
  sheet: -1.77 (0.71), residues: 48
  loop : -1.35 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP F 353 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.018   0.001   PHE D 523 
 TYR   0.017   0.001   TYR D 385 
 ARG   0.004   0.000   ARG D 192 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7572 (mm-30)
REVERT: D   63 ASN cc_start: 0.7402 (m110) cc_final: 0.6808 (m110)
REVERT: D  150 GLU cc_start: 0.7715 (mp0) cc_final: 0.7241 (mp0)
REVERT: D  306 ARG cc_start: 0.7427 (ttt180) cc_final: 0.7072 (ttt180)
REVERT: D  307 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7953 (mt)
REVERT: D  474 MET cc_start: 0.9010 (mmp) cc_final: 0.8552 (mmp)
REVERT: D  483 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8221 (pp20)
REVERT: D  531 GLN cc_start: 0.8085 (mt0) cc_final: 0.7861 (mt0)
REVERT: F  439 ASN cc_start: 0.8338 (t0) cc_final: 0.7999 (t0)
  outliers start: 28
  outliers final: 25
  residues processed: 128
  average time/residue: 0.1814
  time to fit residues: 31.7163
Evaluate side-chains
  130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  325 GLN
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  483 GLU
Chi-restraints excluded: chain D residue  485 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  527 GLU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  611 SER
Chi-restraints excluded: chain F residue  339 HIS
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  501 TYR
Chi-restraints excluded: chain F residue  503 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 50 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   chunk 39 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.158942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.127806 restraints weight = 7496.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.46
r_work: 0.3268 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6532  Z= 0.220
  Angle     :  0.563   6.393   8875  Z= 0.298
  Chirality :  0.043   0.156    918
  Planarity :  0.005   0.052   1150
  Dihedral  :  5.435  47.765    850
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 17.93 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.30), residues: 775
  helix:  0.27 (0.28), residues: 344
  sheet: -1.65 (0.72), residues: 48
  loop : -1.34 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP F 353 
 HIS   0.006   0.001   HIS D 374 
 PHE   0.019   0.001   PHE D 523 
 TYR   0.025   0.001   TYR D 497 
 ARG   0.005   0.001   ARG D 582 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7582 (mm-30)
REVERT: D   63 ASN cc_start: 0.7404 (m110) cc_final: 0.6807 (m110)
REVERT: D  150 GLU cc_start: 0.7721 (mp0) cc_final: 0.7222 (mp0)
REVERT: D  307 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7954 (mt)
REVERT: D  474 MET cc_start: 0.9030 (mmp) cc_final: 0.8513 (mmp)
REVERT: D  483 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8232 (pp20)
REVERT: D  531 GLN cc_start: 0.8082 (mt0) cc_final: 0.7849 (mt0)
REVERT: D  578 ASN cc_start: 0.7331 (t0) cc_final: 0.7018 (p0)
REVERT: F  439 ASN cc_start: 0.8319 (t0) cc_final: 0.7989 (t0)
  outliers start: 31
  outliers final: 28
  residues processed: 124
  average time/residue: 0.1671
  time to fit residues: 28.3702
Evaluate side-chains
  132 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  325 GLN
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  483 GLU
Chi-restraints excluded: chain D residue  485 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  527 GLU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  611 SER
Chi-restraints excluded: chain F residue  339 HIS
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  458 LYS
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  471 GLU
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  501 TYR
Chi-restraints excluded: chain F residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0970
   chunk 5 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 40 optimal weight:    0.2980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.159087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.127771 restraints weight = 7517.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.49
r_work: 0.3270 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6532  Z= 0.220
  Angle     :  0.566   6.347   8875  Z= 0.299
  Chirality :  0.043   0.148    918
  Planarity :  0.005   0.052   1150
  Dihedral  :  5.415  48.191    850
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 17.93 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.30), residues: 775
  helix:  0.30 (0.28), residues: 343
  sheet: -1.49 (0.73), residues: 48
  loop : -1.30 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP F 353 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.019   0.001   PHE D 523 
 TYR   0.024   0.001   TYR D 497 
 ARG   0.005   0.001   ARG D 582 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7593 (mm-30)
REVERT: D   63 ASN cc_start: 0.7399 (m110) cc_final: 0.6781 (m110)
REVERT: D  150 GLU cc_start: 0.7665 (mp0) cc_final: 0.7211 (mp0)
REVERT: D  307 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7946 (mt)
REVERT: D  474 MET cc_start: 0.9013 (mmp) cc_final: 0.8494 (mmp)
REVERT: D  483 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8233 (pp20)
REVERT: D  531 GLN cc_start: 0.8087 (mt0) cc_final: 0.7854 (mt0)
REVERT: D  578 ASN cc_start: 0.7230 (t0) cc_final: 0.6921 (p0)
REVERT: F  439 ASN cc_start: 0.8334 (t0) cc_final: 0.7992 (t0)
  outliers start: 30
  outliers final: 27
  residues processed: 123
  average time/residue: 0.1620
  time to fit residues: 27.6703
Evaluate side-chains
  132 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  134 ASN
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  325 GLN
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  483 GLU
Chi-restraints excluded: chain D residue  485 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  527 GLU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  611 SER
Chi-restraints excluded: chain F residue  339 HIS
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  345 THR
Chi-restraints excluded: chain F residue  346 ARG
Chi-restraints excluded: chain F residue  347 PHE
Chi-restraints excluded: chain F residue  458 LYS
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  471 GLU
Chi-restraints excluded: chain F residue  500 THR
Chi-restraints excluded: chain F residue  501 TYR
Chi-restraints excluded: chain F residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 76 optimal weight:    0.3980
   chunk 54 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3709 r_free = 0.3709 target = 0.157148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.125742 restraints weight = 7689.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.48
r_work: 0.3230 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6532  Z= 0.259
  Angle     :  0.588   7.130   8875  Z= 0.310
  Chirality :  0.044   0.144    918
  Planarity :  0.005   0.053   1150
  Dihedral  :  5.506  48.230    850
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 17.49 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.30), residues: 775
  helix:  0.11 (0.28), residues: 353
  sheet: -1.47 (0.74), residues: 46
  loop : -1.23 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP F 353 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.021   0.002   PHE D 523 
 TYR   0.025   0.002   TYR D 497 
 ARG   0.006   0.001   ARG D 582 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4165.06 seconds
wall clock time: 72 minutes 3.35 seconds (4323.35 seconds total)