Starting phenix.real_space_refine
on Tue Jan 14 09:16:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zbq_39907/01_2025/8zbq_39907_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zbq_39907/01_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_39907/01_2025/8zbq_39907.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zbq_39907/01_2025/8zbq_39907.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zbq_39907/01_2025/8zbq_39907_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zbq_39907/01_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-5571/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: 4.48, per 1000 atoms: 0.71
  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: 1.78
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.65
  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: 1.85

  Time building geometry restraints manager: 1.90 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:             1.680
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     18.540
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:2.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.180
-------------------------------------------------------------------------------
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  : 0.774 
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: 0.2043
  time to fit residues: 43.6117
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  : 0.732 
-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.163230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.132478 restraints weight = 7387.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.41
r_work: 0.3307 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
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   6.248   8875  Z= 0.347
  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  : 0.700 
Fit side-chains
REVERT: D   62 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7281 (ttt)
REVERT: D   63 ASN cc_start: 0.7377 (m110) cc_final: 0.6758 (m110)
REVERT: D  120 LEU cc_start: 0.8754 (mt) cc_final: 0.8550 (mt)
REVERT: D  228 HIS cc_start: 0.8021 (m170) cc_final: 0.7758 (m-70)
REVERT: D  306 ARG cc_start: 0.7470 (ttt180) cc_final: 0.7147 (ttt180)
REVERT: D  307 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7936 (mt)
REVERT: D  483 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8247 (pp20)
REVERT: F  346 ARG cc_start: 0.5604 (OUTLIER) cc_final: 0.4884 (tmm160)
  outliers start: 24
  outliers final: 12
  residues processed: 121
  average time/residue: 0.2078
  time to fit residues: 32.9796
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  : 0.901 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 56 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 52 optimal weight:    0.3980
   chunk 64 optimal weight:    8.9990
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0670
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.161250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.130226 restraints weight = 7520.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.45
r_work: 0.3288 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6532  Z= 0.233
  Angle     :  0.586   5.947   8875  Z= 0.310
  Chirality :  0.043   0.143    918
  Planarity :  0.005   0.052   1150
  Dihedral  :  5.634  45.104    850
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 13.99 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.35 (0.30), residues: 775
  helix: -0.25 (0.27), residues: 357
  sheet: -1.58 (0.86), residues: 36
  loop : -1.42 (0.33), residues: 382

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   0.018   0.001   PHE D 523 
 TYR   0.022   0.001   TYR D 385 
 ARG   0.004   0.000   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: 24
    poor density    : 114
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7541 (mm-30)
REVERT: D   62 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7123 (ttt)
REVERT: D   63 ASN cc_start: 0.7294 (m110) cc_final: 0.6742 (m110)
REVERT: D  306 ARG cc_start: 0.7458 (ttt180) cc_final: 0.7051 (ttt180)
REVERT: D  307 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7927 (mt)
REVERT: D  323 MET cc_start: 0.8083 (mmm) cc_final: 0.7792 (mmt)
REVERT: D  472 GLN cc_start: 0.8635 (mt0) cc_final: 0.8410 (mt0)
REVERT: D  474 MET cc_start: 0.8884 (mmp) cc_final: 0.8643 (mmp)
REVERT: D  483 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8252 (pp20)
REVERT: D  518 ARG cc_start: 0.8311 (tmm160) cc_final: 0.8072 (tmm160)
  outliers start: 24
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1857
  time to fit residues: 31.8102
Evaluate side-chains
  122 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
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  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:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3742 r_free = 0.3742 target = 0.160063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.128337 restraints weight = 7547.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.52
r_work: 0.3215 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2872

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= 0.289
  Angle     :  0.608   6.080   8875  Z= 0.321
  Chirality :  0.045   0.144    918
  Planarity :  0.005   0.051   1150
  Dihedral  :  5.652  45.564    850
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 15.60 %
    Favored  : 80.32 %
  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: -1.35 (0.30), residues: 775
  helix: -0.29 (0.27), residues: 362
  sheet: -1.43 (0.87), residues: 36
  loop : -1.39 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   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   0.005   0.001   ARG F 454 

*********************** 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
  137 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7378 (m110) cc_final: 0.6838 (m110)
REVERT: D   81 GLN cc_start: 0.7640 (mm110) cc_final: 0.7415 (mm-40)
REVERT: D  302 TRP cc_start: 0.8559 (m-10) cc_final: 0.8334 (m-10)
REVERT: D  306 ARG cc_start: 0.7424 (ttt180) cc_final: 0.6985 (ttt180)
REVERT: D  307 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7973 (mt)
REVERT: D  472 GLN cc_start: 0.8748 (mt0) cc_final: 0.8520 (mt0)
REVERT: D  474 MET cc_start: 0.9054 (mmp) cc_final: 0.8462 (mmp)
REVERT: D  483 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8255 (pp20)
REVERT: D  518 ARG cc_start: 0.8422 (tmm160) cc_final: 0.8160 (tmm160)
REVERT: D  531 GLN cc_start: 0.8175 (mt0) cc_final: 0.7854 (mt0)
REVERT: F  346 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.3452 (tmm160)
REVERT: F  439 ASN cc_start: 0.8342 (t0) cc_final: 0.7940 (t0)
  outliers start: 28
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1906
  time to fit residues: 32.6170
Evaluate side-chains
  127 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
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  363 LYS
Chi-restraints excluded: chain D residue  401 HIS
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:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 75 optimal weight:    0.4980
   chunk 72 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.155028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.123440 restraints weight = 7534.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.46
r_work: 0.3252 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6532  Z= 0.271
  Angle     :  0.585   6.747   8875  Z= 0.309
  Chirality :  0.044   0.145    918
  Planarity :  0.004   0.051   1150
  Dihedral  :  5.628  46.201    850
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  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: -1.34 (0.30), residues: 775
  helix: -0.20 (0.27), residues: 362
  sheet: -1.40 (0.87), residues: 36
  loop : -1.50 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 478 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.019   0.002   PHE D 523 
 TYR   0.021   0.002   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
  139 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7429 (m110) cc_final: 0.6851 (m110)
REVERT: D  189 GLU cc_start: 0.7586 (mp0) cc_final: 0.6991 (mt-10)
REVERT: D  307 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7991 (mt)
REVERT: D  472 GLN cc_start: 0.8721 (mt0) cc_final: 0.8483 (mt0)
REVERT: D  474 MET cc_start: 0.9039 (mmp) cc_final: 0.8450 (mmp)
REVERT: D  483 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8225 (pp20)
REVERT: D  531 GLN cc_start: 0.8176 (mt0) cc_final: 0.7894 (mt0)
REVERT: F  346 ARG cc_start: 0.5575 (OUTLIER) cc_final: 0.3532 (tmm160)
REVERT: F  439 ASN cc_start: 0.8327 (t0) cc_final: 0.7918 (t0)
  outliers start: 31
  outliers final: 25
  residues processed: 131
  average time/residue: 0.1773
  time to fit residues: 31.2814
Evaluate side-chains
  131 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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  299 ASP
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  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  495 TYR
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:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.157731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.126706 restraints weight = 7376.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.44
r_work: 0.3239 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3159

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= 0.281
  Angle     :  0.590   6.880   8875  Z= 0.311
  Chirality :  0.044   0.140    918
  Planarity :  0.004   0.052   1150
  Dihedral  :  5.624  46.441    850
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 15.60 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.23 (0.27), residues: 366
  sheet: -1.20 (0.87), residues: 36
  loop : -1.47 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP F 353 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.021   0.002   PHE D 523 
 TYR   0.020   0.002   TYR D 385 
 ARG   0.003   0.000   ARG D 482 

*********************** 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
  139 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
REVERT: D   63 ASN cc_start: 0.7430 (m110) cc_final: 0.6846 (m110)
REVERT: D  306 ARG cc_start: 0.7472 (ttt180) cc_final: 0.7012 (ttt180)
REVERT: D  307 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8014 (mt)
REVERT: D  472 GLN cc_start: 0.8738 (mt0) cc_final: 0.8495 (mt0)
REVERT: D  474 MET cc_start: 0.9047 (mmp) cc_final: 0.8767 (mmp)
REVERT: D  531 GLN cc_start: 0.8167 (mt0) cc_final: 0.7886 (mt0)
REVERT: F  346 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.3824 (tmm160)
REVERT: F  439 ASN cc_start: 0.8376 (t0) cc_final: 0.7987 (t0)
  outliers start: 33
  outliers final: 27
  residues processed: 131
  average time/residue: 0.1814
  time to fit residues: 32.0396
Evaluate side-chains
  126 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
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  299 ASP
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  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  495 TYR
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:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0670
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 69 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0000
   overall best weight:    0.2722

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.160977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.130508 restraints weight = 7501.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.46
r_work: 0.3287 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6532  Z= 0.187
  Angle     :  0.549   7.340   8875  Z= 0.289
  Chirality :  0.042   0.138    918
  Planarity :  0.004   0.052   1150
  Dihedral  :  5.424  46.263    850
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.47 %
    Favored  : 79.01 %
  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: -1.07 (0.30), residues: 775
  helix:  0.06 (0.28), residues: 357
  sheet: -1.55 (0.73), residues: 48
  loop : -1.33 (0.32), residues: 370

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   0.017   0.001   TYR D 385 
 ARG   0.004   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
  149 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7575 (mm-30)
REVERT: D   63 ASN cc_start: 0.7400 (m110) cc_final: 0.6810 (m110)
REVERT: D  189 GLU cc_start: 0.7317 (mp0) cc_final: 0.6888 (tt0)
REVERT: D  306 ARG cc_start: 0.7380 (ttt180) cc_final: 0.7039 (ttt180)
REVERT: D  307 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7958 (mt)
REVERT: D  472 GLN cc_start: 0.8759 (mt0) cc_final: 0.8530 (mt0)
REVERT: D  474 MET cc_start: 0.9005 (mmp) cc_final: 0.8429 (mmp)
REVERT: D  483 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8212 (pp20)
REVERT: D  531 GLN cc_start: 0.8078 (mt0) cc_final: 0.7852 (mt0)
REVERT: D  578 ASN cc_start: 0.7199 (t0) cc_final: 0.6895 (p0)
REVERT: F  439 ASN cc_start: 0.8287 (t0) cc_final: 0.7920 (t0)
  outliers start: 31
  outliers final: 25
  residues processed: 141
  average time/residue: 0.1819
  time to fit residues: 35.0115
Evaluate side-chains
  131 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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  299 ASP
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  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  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:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 42 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.156883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.124792 restraints weight = 7480.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.54
r_work: 0.3225 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6532  Z= 0.285
  Angle     :  0.597   7.463   8875  Z= 0.314
  Chirality :  0.044   0.166    918
  Planarity :  0.004   0.053   1150
  Dihedral  :  5.550  47.203    850
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 16.18 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.03 (0.28), residues: 353
  sheet: -1.49 (0.73), residues: 49
  loop : -1.30 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 302 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.022   0.002   PHE D 523 
 TYR   0.017   0.002   TYR D 497 
 ARG   0.005   0.001   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
  134 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7589 (mm-30)
REVERT: D   63 ASN cc_start: 0.7409 (m110) cc_final: 0.6812 (m110)
REVERT: D  307 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7981 (mt)
REVERT: D  472 GLN cc_start: 0.8793 (mt0) cc_final: 0.8557 (mt0)
REVERT: D  474 MET cc_start: 0.9044 (mmp) cc_final: 0.8514 (mmp)
REVERT: D  483 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8266 (pp20)
REVERT: D  531 GLN cc_start: 0.8199 (mt0) cc_final: 0.7904 (mt0)
REVERT: F  439 ASN cc_start: 0.8398 (t0) cc_final: 0.8069 (t0)
  outliers start: 30
  outliers final: 28
  residues processed: 126
  average time/residue: 0.1673
  time to fit residues: 28.7816
Evaluate side-chains
  129 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 99
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
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  549 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  495 TYR
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:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.157362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.126405 restraints weight = 7462.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.43
r_work: 0.3239 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6532  Z= 0.282
  Angle     :  0.599   6.885   8875  Z= 0.317
  Chirality :  0.044   0.173    918
  Planarity :  0.004   0.052   1150
  Dihedral  :  5.606  47.815    850
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 16.76 %
    Favored  : 78.57 %
  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: -1.10 (0.30), residues: 775
  helix: -0.07 (0.27), residues: 359
  sheet: -1.38 (0.76), residues: 47
  loop : -1.25 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP F 353 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.021   0.002   PHE D 523 
 TYR   0.016   0.002   TYR D 385 
 ARG   0.005   0.001   ARG D 192 

*********************** 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: 32
    poor density    : 104
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7561 (mm-30)
REVERT: D   63 ASN cc_start: 0.7428 (m110) cc_final: 0.6844 (m110)
REVERT: D  307 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8015 (mt)
REVERT: D  472 GLN cc_start: 0.8735 (mt0) cc_final: 0.8528 (mt0)
REVERT: D  474 MET cc_start: 0.9007 (mmp) cc_final: 0.8160 (mmp)
REVERT: D  531 GLN cc_start: 0.8160 (mt0) cc_final: 0.7860 (mt0)
REVERT: F  439 ASN cc_start: 0.8384 (t0) cc_final: 0.8073 (t0)
  outliers start: 32
  outliers final: 30
  residues processed: 126
  average time/residue: 0.1675
  time to fit residues: 28.8716
Evaluate side-chains
  130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 99
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
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  491 VAL
Chi-restraints excluded: chain D residue  527 GLU
Chi-restraints excluded: chain D residue  549 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  495 TYR
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:    0.0020
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 54 optimal weight:    0.1980
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.3388

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.161098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.130375 restraints weight = 7488.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.46
r_work: 0.3275 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3401

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= 0.194
  Angle     :  0.554   6.679   8875  Z= 0.293
  Chirality :  0.042   0.158    918
  Planarity :  0.004   0.052   1150
  Dihedral  :  5.436  47.835    850
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 17.49 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.30), residues: 775
  helix:  0.22 (0.28), residues: 350
  sheet: -1.31 (0.75), residues: 49
  loop : -1.27 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP F 353 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.019   0.001   PHE D 523 
 TYR   0.015   0.001   TYR D 385 
 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  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7571 (mm-30)
REVERT: D   63 ASN cc_start: 0.7413 (m110) cc_final: 0.6804 (m110)
REVERT: D  150 GLU cc_start: 0.7671 (mp0) cc_final: 0.7215 (mp0)
REVERT: D  307 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7948 (mt)
REVERT: D  472 GLN cc_start: 0.8724 (mt0) cc_final: 0.8506 (mt0)
REVERT: D  474 MET cc_start: 0.8997 (mmp) cc_final: 0.8454 (mmp)
REVERT: D  483 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8225 (pp20)
REVERT: D  578 ASN cc_start: 0.6943 (t0) cc_final: 0.6461 (p0)
REVERT: F  439 ASN cc_start: 0.8338 (t0) cc_final: 0.8008 (t0)
  outliers start: 30
  outliers final: 26
  residues processed: 125
  average time/residue: 0.1713
  time to fit residues: 29.2509
Evaluate side-chains
  130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
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  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  549 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  458 LYS
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=1.00
-------------------------------------------------------------------------------
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:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 67 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0060
   chunk 60 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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 = 0.158803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.127625 restraints weight = 7652.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.48
r_work: 0.3245 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6532  Z= 0.225
  Angle     :  0.569   6.596   8875  Z= 0.301
  Chirality :  0.043   0.149    918
  Planarity :  0.004   0.052   1150
  Dihedral  :  5.428  48.039    850
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 17.06 %
    Favored  : 78.57 %
  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: -0.87 (0.30), residues: 775
  helix:  0.20 (0.28), residues: 351
  sheet: -1.19 (0.76), residues: 49
  loop : -1.21 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP F 353 
 HIS   0.007   0.001   HIS D 374 
 PHE   0.020   0.002   PHE D 523 
 TYR   0.017   0.001   TYR D 385 
 ARG   0.007   0.001   ARG D 582 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3713.90 seconds
wall clock time: 66 minutes 43.23 seconds (4003.23 seconds total)