Starting phenix.real_space_refine
on Fri Aug 22 17:51:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j52_61140/08_2025/9j52_61140.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j52_61140/08_2025/9j52_61140.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j52_61140/08_2025/9j52_61140.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j52_61140/08_2025/9j52_61140.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j52_61140/08_2025/9j52_61140.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j52_61140/08_2025/9j52_61140.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.070
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: 5
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     S      30      5.16       5
     C    4462      2.51       5
     N    1024      2.21       5
     O    1072      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6593
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3186
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 14, 'TRANS': 367}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3186
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 14, 'TRANS': 367}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 113
          Unusual residues: {'PC1': 2, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 108
          Unusual residues: {'PC1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.78, per 1000 atoms: 0.27
  Number of scatterers: 6593
  At special positions: 0
  Unit cell: (123.05, 67.41, 75.97, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       5     15.00
     O    1072      8.00
     N    1024      7.00
     C    4462      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 374.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      80.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 258
    Processing helix  chain 'A' and resid 265 through 295
      removed outlier: 4.798A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.564A  pdb=" N   ILE A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 336
    Processing helix  chain 'A' and resid 337 through 340
    Processing helix  chain 'A' and resid 343 through 345
      No H-bonds generated for 'chain 'A' and resid 343 through 345'
    Processing helix  chain 'A' and resid 346 through 360
    Processing helix  chain 'A' and resid 367 through 384
      removed outlier: 4.538A  pdb=" N   ALA A 384 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 402
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 4.324A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 453
      removed outlier: 3.742A  pdb=" N   VAL A 451 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 471
      removed outlier: 3.978A  pdb=" N   ARG A 459 " --> pdb=" O   PRO A 455 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLN A 462 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 503
      removed outlier: 4.247A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ASN A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 532
      removed outlier: 4.179A  pdb=" N   VAL A 509 " --> pdb=" O   SER A 505 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE A 517 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASP A 529 " --> pdb=" O   THR A 525 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   MET A 532 " --> pdb=" O   TRP A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 583
      removed outlier: 3.750A  pdb=" N   TYR A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   VAL A 567 " --> pdb=" O   ILE A 563 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER A 581 " --> pdb=" O   ILE A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 618
      Proline residue:  A 598  - end of helix
      removed outlier: 3.767A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 613 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 258
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.371A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.592A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 361
      removed outlier: 3.930A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 384 through 387
    Processing helix  chain 'B' and resid 390 through 419
      removed outlier: 3.580A  pdb=" N   ASN B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   VAL B 405 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ILE B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 453
    Processing helix  chain 'B' and resid 453 through 462
      removed outlier: 3.816A  pdb=" N   ARG B 459 " --> pdb=" O   PRO B 455 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLN B 462 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 471
    Processing helix  chain 'B' and resid 472 through 503
      removed outlier: 4.193A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ASN B 479 " --> pdb=" O   PRO B 475 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 532
      removed outlier: 3.733A  pdb=" N   LEU B 513 " --> pdb=" O   VAL B 509 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU B 526 " --> pdb=" O   SER B 522 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TRP B 528 " --> pdb=" O   TYR B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 580
      removed outlier: 4.330A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR B 560 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   ALA B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   SER B 578 " --> pdb=" O   THR B 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 618
      Proline residue:  B 598  - end of helix
      removed outlier: 3.805A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 623
      removed outlier: 3.933A  pdb=" N   GLU B 622 " --> pdb=" O   ASN B 619 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   PHE B 623 " --> pdb=" O   CYS B 620 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 619 through 623'

    430 hydrogen bonds defined for protein.
    1284 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 992
        1.32 -     1.44: 2062
        1.44 -     1.57: 3694
        1.57 -     1.69: 10
        1.69 -     1.81: 42
  Bond restraints: 6800
  Sorted by residual:
  bond pdb=" C   ILE A 454 "
       pdb=" N   PRO A 455 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.014 1.19e-02 7.06e+03 1.33e+00
  bond pdb=" C   ALA A 337 "
       pdb=" N   PRO A 338 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 9.86e-01
  bond pdb=" CA  ILE B 342 "
       pdb=" C   ILE B 342 "
    ideal  model  delta    sigma   weight residual
    1.526  1.519  0.007 7.90e-03 1.60e+04 8.82e-01
  bond pdb=" CA  LEU B 259 "
       pdb=" C   LEU B 259 "
    ideal  model  delta    sigma   weight residual
    1.532  1.524  0.009 9.60e-03 1.09e+04 8.53e-01
  bond pdb=" CG  GLN B 399 "
       pdb=" CD  GLN B 399 "
    ideal  model  delta    sigma   weight residual
    1.516  1.495  0.021 2.50e-02 1.60e+03 7.00e-01
  ... (remaining 6795 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 8908
        1.29 -     2.59: 244
        2.59 -     3.88: 35
        3.88 -     5.18: 14
        5.18 -     6.47: 7
  Bond angle restraints: 9208
  Sorted by residual:
  angle pdb=" C   LYS A 422 "
        pdb=" N   TRP A 423 "
        pdb=" CA  TRP A 423 "
      ideal   model   delta    sigma   weight residual
     121.54  127.40   -5.86 1.91e+00 2.74e-01 9.41e+00
  angle pdb=" C   CYS B 453 "
        pdb=" N   ILE B 454 "
        pdb=" CA  ILE B 454 "
      ideal   model   delta    sigma   weight residual
     120.33  122.47   -2.14 8.00e-01 1.56e+00 7.17e+00
  angle pdb=" C   VAL B 447 "
        pdb=" N   ARG B 448 "
        pdb=" CA  ARG B 448 "
      ideal   model   delta    sigma   weight residual
     120.38  124.01   -3.63 1.37e+00 5.33e-01 7.01e+00
  angle pdb=" N   LEU B 464 "
        pdb=" CA  LEU B 464 "
        pdb=" C   LEU B 464 "
      ideal   model   delta    sigma   weight residual
     113.12  109.83    3.29 1.25e+00 6.40e-01 6.91e+00
  angle pdb=" C   ILE B 454 "
        pdb=" CA  ILE B 454 "
        pdb=" CB  ILE B 454 "
      ideal   model   delta    sigma   weight residual
     114.00  110.92    3.08 1.31e+00 5.83e-01 5.54e+00
  ... (remaining 9203 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 3600
       17.43 -    34.86: 244
       34.86 -    52.30: 58
       52.30 -    69.73: 13
       69.73 -    87.16: 3
  Dihedral angle restraints: 3918
    sinusoidal: 1668
      harmonic: 2250
  Sorted by residual:
  dihedral pdb=" CA  CYS B 463 "
           pdb=" C   CYS B 463 "
           pdb=" N   LEU B 464 "
           pdb=" CA  LEU B 464 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.68   19.32     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  GLU B 260 "
           pdb=" C   GLU B 260 "
           pdb=" N   THR B 261 "
           pdb=" CA  THR B 261 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.96  -18.04     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  SER A 578 "
           pdb=" C   SER A 578 "
           pdb=" N   ILE A 579 "
           pdb=" CA  ILE A 579 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.24  -16.76     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 3915 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 500
       0.025 -    0.050: 307
       0.050 -    0.075: 119
       0.075 -    0.099: 40
       0.099 -    0.124: 20
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" CA  ILE B 342 "
            pdb=" N   ILE B 342 "
            pdb=" C   ILE B 342 "
            pdb=" CB  ILE B 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  TRP B 266 "
            pdb=" N   TRP B 266 "
            pdb=" C   TRP B 266 "
            pdb=" CB  TRP B 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.80e-01
  chirality pdb=" CA  PRO B 554 "
            pdb=" N   PRO B 554 "
            pdb=" C   PRO B 554 "
            pdb=" CB  PRO B 554 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.76e-01
  ... (remaining 983 not shown)

  Planarity restraints: 1098
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 337 "   -0.035 5.00e-02 4.00e+02   5.23e-02 4.38e+00
        pdb=" N   PRO A 338 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 338 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 338 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 266 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO A 267 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 567 "   -0.007 2.00e-02 2.50e+03   1.38e-02 1.90e+00
        pdb=" C   VAL A 567 "    0.024 2.00e-02 2.50e+03
        pdb=" O   VAL A 567 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ILE A 568 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1095 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 110
        2.66 -     3.22: 6718
        3.22 -     3.78: 10471
        3.78 -     4.34: 14351
        4.34 -     4.90: 23284
  Nonbonded interactions: 54934
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 271 "
            pdb=" OH  TYR B 352 "
     model   vdw
     2.100 3.040
  nonbonded pdb=" O   LYS B 482 "
            pdb=" OG1 THR B 485 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" N   ASN A 479 "
            pdb=" OD1 ASN A 479 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" NH1 ARG A 570 "
            pdb=" O2  PO4 A 803 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OD2 ASP A 529 "
            pdb=" NH2 ARG A 570 "
     model   vdw
     2.217 3.120
  ... (remaining 54929 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 229 through 802)
  selection = chain 'B'
}

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:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.220
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
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      :  0.004   0.028   6800  Z= 0.170
  Angle     :  0.554   6.471   9208  Z= 0.307
  Chirality :  0.038   0.124    986
  Planarity :  0.005   0.052   1098
  Dihedral  : 12.860  87.159   2466
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.48 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  6.19 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.31), residues: 756
  helix:  1.11 (0.22), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.95 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 459 
 TYR   0.011   0.001   TYR B 367 
 PHE   0.016   0.001   PHE A 517 
 TRP   0.011   0.001   TRP B 607 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 6800)
  covalent geometry    : angle       0.55351 ( 9208)
  hydrogen bonds       : bond        0.17111 (  430)
  hydrogen bonds       : angle       6.53942 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  258 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7054 (mmtm)
REVERT: A  270 ARG cc_start: 0.7674 (mtm180) cc_final: 0.6105 (mtp-110)
REVERT: A  398 ASP cc_start: 0.8567 (m-30) cc_final: 0.8275 (m-30)
REVERT: A  399 GLN cc_start: 0.8609 (mm110) cc_final: 0.8331 (mm110)
REVERT: A  590 ASP cc_start: 0.8269 (m-30) cc_final: 0.7757 (m-30)
REVERT: B  290 TYR cc_start: 0.8325 (t80) cc_final: 0.7902 (t80)
REVERT: B  357 PHE cc_start: 0.8228 (t80) cc_final: 0.7203 (m-10)
REVERT: B  364 LYS cc_start: 0.8201 (mttt) cc_final: 0.7904 (mtpt)
REVERT: B  416 PHE cc_start: 0.8667 (t80) cc_final: 0.8369 (t80)
REVERT: B  487 PHE cc_start: 0.7327 (m-10) cc_final: 0.6400 (t80)
REVERT: B  538 ASP cc_start: 0.8741 (t70) cc_final: 0.8461 (t0)
REVERT: B  555 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7261 (mm-40)
  outliers start: 16
  outliers final: 7
  residues processed: 179
  average time/residue: 0.0602
  time to fit residues: 15.3838
Evaluate side-chains
  135 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  393 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.1980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 315 HIS
A 387 HIS
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 499 HIS
A 587 HIS
B 288 ASN
B 387 HIS
B 399 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.186812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.157727 restraints weight = 9341.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.39
r_work: 0.3777 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6800  Z= 0.139
  Angle     :  0.554   6.839   9208  Z= 0.295
  Chirality :  0.040   0.142    986
  Planarity :  0.005   0.054   1098
  Dihedral  : 11.816  75.405   1047
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 10.62 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.31), residues: 756
  helix:  1.58 (0.22), residues: 560
  sheet:  None (None), residues: 0
  loop : -1.90 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 293 
 TYR   0.017   0.001   TYR B 496 
 PHE   0.025   0.002   PHE A 517 
 TRP   0.014   0.001   TRP B 528 
 HIS   0.004   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6800)
  covalent geometry    : angle       0.55390 ( 9208)
  hydrogen bonds       : bond        0.05151 (  430)
  hydrogen bonds       : angle       4.57321 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  258 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7240 (mmtm)
REVERT: A  270 ARG cc_start: 0.7709 (mtm180) cc_final: 0.6804 (mtp-110)
REVERT: A  301 LEU cc_start: 0.8396 (mt) cc_final: 0.8018 (tp)
REVERT: A  323 LEU cc_start: 0.8116 (mt) cc_final: 0.7734 (mt)
REVERT: A  398 ASP cc_start: 0.8581 (m-30) cc_final: 0.8190 (m-30)
REVERT: A  590 ASP cc_start: 0.8298 (m-30) cc_final: 0.8061 (m-30)
REVERT: B  290 TYR cc_start: 0.8302 (t80) cc_final: 0.8031 (t80)
REVERT: B  352 TYR cc_start: 0.7877 (m-80) cc_final: 0.7246 (m-80)
REVERT: B  357 PHE cc_start: 0.8257 (t80) cc_final: 0.7545 (m-10)
REVERT: B  364 LYS cc_start: 0.8182 (mttt) cc_final: 0.7902 (mtpt)
REVERT: B  408 MET cc_start: 0.8352 (mmm) cc_final: 0.8068 (mmm)
REVERT: B  487 PHE cc_start: 0.7331 (m-10) cc_final: 0.6467 (t80)
REVERT: B  538 ASP cc_start: 0.8869 (t70) cc_final: 0.8468 (t0)
REVERT: B  549 GLU cc_start: 0.6985 (mp0) cc_final: 0.6689 (mm-30)
REVERT: B  555 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7287 (mm-40)
  outliers start: 21
  outliers final: 10
  residues processed: 162
  average time/residue: 0.0572
  time to fit residues: 13.2053
Evaluate side-chains
  145 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  564 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0870
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.8360

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 499 HIS
A 587 HIS
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 619 ASN
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.184994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.155844 restraints weight = 9224.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 2.37
r_work: 0.3760 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6800  Z= 0.167
  Angle     :  0.566   7.191   9208  Z= 0.296
  Chirality :  0.041   0.138    986
  Planarity :  0.005   0.053   1098
  Dihedral  : 11.647  74.207   1038
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 12.09 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.31), residues: 756
  helix:  1.55 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop : -1.96 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 604 
 TYR   0.016   0.001   TYR B 496 
 PHE   0.024   0.002   PHE A 517 
 TRP   0.010   0.001   TRP B 528 
 HIS   0.005   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6800)
  covalent geometry    : angle       0.56591 ( 9208)
  hydrogen bonds       : bond        0.04995 (  430)
  hydrogen bonds       : angle       4.52866 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  258 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7275 (mmtm)
REVERT: A  270 ARG cc_start: 0.7760 (mtm180) cc_final: 0.6781 (mtp-110)
REVERT: A  301 LEU cc_start: 0.8396 (mt) cc_final: 0.8138 (tp)
REVERT: A  323 LEU cc_start: 0.8189 (mt) cc_final: 0.7854 (mt)
REVERT: A  398 ASP cc_start: 0.8625 (m-30) cc_final: 0.8349 (m-30)
REVERT: A  590 ASP cc_start: 0.8168 (m-30) cc_final: 0.7962 (m-30)
REVERT: B  290 TYR cc_start: 0.8406 (t80) cc_final: 0.8084 (t80)
REVERT: B  357 PHE cc_start: 0.8243 (t80) cc_final: 0.7508 (m-10)
REVERT: B  364 LYS cc_start: 0.8176 (mttt) cc_final: 0.7921 (mtpt)
REVERT: B  408 MET cc_start: 0.8304 (mmm) cc_final: 0.7963 (mmm)
REVERT: B  487 PHE cc_start: 0.7368 (m-10) cc_final: 0.6505 (t80)
REVERT: B  538 ASP cc_start: 0.8838 (t70) cc_final: 0.8473 (t0)
REVERT: B  549 GLU cc_start: 0.7090 (mp0) cc_final: 0.6447 (mm-30)
REVERT: B  555 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7375 (mm-40)
  outliers start: 20
  outliers final: 10
  residues processed: 153
  average time/residue: 0.0590
  time to fit residues: 12.8465
Evaluate side-chains
  144 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  574 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 499 HIS
A 587 HIS
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 ASN
B 387 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.185128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.156001 restraints weight = 9316.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.33
r_work: 0.3769 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6800  Z= 0.159
  Angle     :  0.560   6.593   9208  Z= 0.294
  Chirality :  0.040   0.139    986
  Planarity :  0.005   0.054   1098
  Dihedral  : 11.507  74.475   1036
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.75 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.31), residues: 756
  helix:  1.53 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -2.05 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 293 
 TYR   0.016   0.001   TYR B 496 
 PHE   0.021   0.002   PHE A 517 
 TRP   0.013   0.001   TRP B 528 
 HIS   0.005   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6800)
  covalent geometry    : angle       0.55997 ( 9208)
  hydrogen bonds       : bond        0.04852 (  430)
  hydrogen bonds       : angle       4.49324 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  258 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7319 (mmtm)
REVERT: A  270 ARG cc_start: 0.7741 (mtm180) cc_final: 0.6859 (mtp-110)
REVERT: A  398 ASP cc_start: 0.8588 (m-30) cc_final: 0.8341 (m-30)
REVERT: A  590 ASP cc_start: 0.8164 (m-30) cc_final: 0.7937 (m-30)
REVERT: B  357 PHE cc_start: 0.8211 (t80) cc_final: 0.7517 (m-10)
REVERT: B  364 LYS cc_start: 0.8161 (mttt) cc_final: 0.7924 (mtpt)
REVERT: B  408 MET cc_start: 0.8420 (mmm) cc_final: 0.8004 (mmm)
REVERT: B  487 PHE cc_start: 0.7359 (m-10) cc_final: 0.6511 (t80)
REVERT: B  538 ASP cc_start: 0.8769 (t70) cc_final: 0.8537 (t0)
REVERT: B  555 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7490 (mm-40)
  outliers start: 17
  outliers final: 12
  residues processed: 151
  average time/residue: 0.0551
  time to fit residues: 11.7729
Evaluate side-chains
  146 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  574 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 54 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 387 HIS
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 499 HIS
A 587 HIS
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.185107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.155892 restraints weight = 9353.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 2.34
r_work: 0.3762 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6800  Z= 0.160
  Angle     :  0.562   7.231   9208  Z= 0.295
  Chirality :  0.040   0.146    986
  Planarity :  0.005   0.054   1098
  Dihedral  : 11.443  74.404   1034
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.11 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.31), residues: 756
  helix:  1.67 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop : -1.92 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 603 
 TYR   0.016   0.001   TYR B 496 
 PHE   0.019   0.001   PHE A 517 
 TRP   0.013   0.001   TRP B 528 
 HIS   0.005   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6800)
  covalent geometry    : angle       0.56162 ( 9208)
  hydrogen bonds       : bond        0.04770 (  430)
  hydrogen bonds       : angle       4.46976 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  258 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7286 (mmtm)
REVERT: A  270 ARG cc_start: 0.7729 (mtm180) cc_final: 0.6854 (mtp-110)
REVERT: A  398 ASP cc_start: 0.8586 (m-30) cc_final: 0.8371 (m-30)
REVERT: A  590 ASP cc_start: 0.8141 (m-30) cc_final: 0.7927 (m-30)
REVERT: B  357 PHE cc_start: 0.8207 (t80) cc_final: 0.7520 (m-10)
REVERT: B  364 LYS cc_start: 0.8151 (mttt) cc_final: 0.7927 (mtpt)
REVERT: B  408 MET cc_start: 0.8386 (mmm) cc_final: 0.8050 (mmm)
REVERT: B  487 PHE cc_start: 0.7354 (m-10) cc_final: 0.6509 (t80)
REVERT: B  538 ASP cc_start: 0.8768 (t70) cc_final: 0.8367 (t0)
REVERT: B  549 GLU cc_start: 0.6990 (mp0) cc_final: 0.6513 (mm-30)
REVERT: B  555 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7480 (mm-40)
  outliers start: 16
  outliers final: 13
  residues processed: 145
  average time/residue: 0.0638
  time to fit residues: 13.2136
Evaluate side-chains
  146 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  574 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0270
   chunk 60 optimal weight:    0.0570
   chunk 37 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 499 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.186911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.158197 restraints weight = 9312.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 2.32
r_work: 0.3788 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6800  Z= 0.134
  Angle     :  0.539   6.506   9208  Z= 0.285
  Chirality :  0.040   0.163    986
  Planarity :  0.005   0.054   1098
  Dihedral  : 11.265  74.896   1034
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.52 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.31), residues: 756
  helix:  1.81 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop : -1.91 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 603 
 TYR   0.016   0.001   TYR B 496 
 PHE   0.017   0.001   PHE B 610 
 TRP   0.014   0.001   TRP B 528 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6800)
  covalent geometry    : angle       0.53893 ( 9208)
  hydrogen bonds       : bond        0.04573 (  430)
  hydrogen bonds       : angle       4.41018 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  258 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7318 (mmtm)
REVERT: A  270 ARG cc_start: 0.7654 (mtm180) cc_final: 0.6811 (mtp-110)
REVERT: A  298 ASN cc_start: 0.7668 (t0) cc_final: 0.7374 (t0)
REVERT: A  622 GLU cc_start: 0.7268 (pt0) cc_final: 0.7014 (pp20)
REVERT: B  301 LEU cc_start: 0.8507 (tt) cc_final: 0.8209 (tt)
REVERT: B  357 PHE cc_start: 0.8163 (t80) cc_final: 0.7527 (m-10)
REVERT: B  364 LYS cc_start: 0.8137 (mttt) cc_final: 0.7906 (mtpt)
REVERT: B  408 MET cc_start: 0.8392 (mmm) cc_final: 0.8027 (mmm)
REVERT: B  487 PHE cc_start: 0.7254 (m-10) cc_final: 0.6503 (t80)
REVERT: B  508 MET cc_start: 0.6858 (mmt) cc_final: 0.6538 (mmt)
REVERT: B  549 GLU cc_start: 0.7059 (mp0) cc_final: 0.6746 (mm-30)
REVERT: B  555 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7398 (mm-40)
  outliers start: 18
  outliers final: 14
  residues processed: 149
  average time/residue: 0.0644
  time to fit residues: 13.6484
Evaluate side-chains
  150 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  574 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0970
   chunk 69 optimal weight:    0.1980
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 499 HIS
A 587 HIS
B 399 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.187164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.158641 restraints weight = 9242.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 2.30
r_work: 0.3790 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6800  Z= 0.136
  Angle     :  0.552   7.729   9208  Z= 0.291
  Chirality :  0.040   0.169    986
  Planarity :  0.005   0.054   1098
  Dihedral  : 11.182  74.903   1034
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.44 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.31), residues: 756
  helix:  1.79 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.88 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 603 
 TYR   0.014   0.001   TYR B 496 
 PHE   0.020   0.001   PHE A 596 
 TRP   0.013   0.001   TRP B 528 
 HIS   0.006   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6800)
  covalent geometry    : angle       0.55209 ( 9208)
  hydrogen bonds       : bond        0.04551 (  430)
  hydrogen bonds       : angle       4.38095 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 147
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  258 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7259 (mmtm)
REVERT: A  270 ARG cc_start: 0.7652 (mtm180) cc_final: 0.6805 (mtp-110)
REVERT: A  298 ASN cc_start: 0.7588 (t0) cc_final: 0.7316 (t0)
REVERT: A  622 GLU cc_start: 0.7296 (pt0) cc_final: 0.7049 (pp20)
REVERT: B  301 LEU cc_start: 0.8497 (tt) cc_final: 0.8217 (tt)
REVERT: B  357 PHE cc_start: 0.8118 (t80) cc_final: 0.7529 (m-10)
REVERT: B  364 LYS cc_start: 0.8136 (mttt) cc_final: 0.7902 (mtpt)
REVERT: B  408 MET cc_start: 0.8371 (mmm) cc_final: 0.7988 (mmm)
REVERT: B  452 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7765 (tm-30)
REVERT: B  487 PHE cc_start: 0.7247 (m-10) cc_final: 0.6503 (t80)
REVERT: B  549 GLU cc_start: 0.7034 (mp0) cc_final: 0.6691 (mm-30)
REVERT: B  555 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7416 (mm-40)
  outliers start: 13
  outliers final: 12
  residues processed: 150
  average time/residue: 0.0619
  time to fit residues: 13.2366
Evaluate side-chains
  148 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  574 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 54 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 499 HIS
B 387 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.186199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.157351 restraints weight = 9313.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.32
r_work: 0.3776 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6800  Z= 0.155
  Angle     :  0.568   8.164   9208  Z= 0.299
  Chirality :  0.041   0.180    986
  Planarity :  0.005   0.054   1098
  Dihedral  : 11.179  74.577   1034
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.73 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.31), residues: 756
  helix:  1.78 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.90 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 603 
 TYR   0.014   0.001   TYR B 496 
 PHE   0.017   0.001   PHE B 354 
 TRP   0.013   0.001   TRP B 528 
 HIS   0.004   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6800)
  covalent geometry    : angle       0.56798 ( 9208)
  hydrogen bonds       : bond        0.04653 (  430)
  hydrogen bonds       : angle       4.41874 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  258 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7261 (mmtm)
REVERT: A  270 ARG cc_start: 0.7634 (mtm180) cc_final: 0.6810 (mtp-110)
REVERT: A  298 ASN cc_start: 0.7605 (t0) cc_final: 0.7359 (t0)
REVERT: A  622 GLU cc_start: 0.7318 (pt0) cc_final: 0.7115 (pp20)
REVERT: B  357 PHE cc_start: 0.8144 (t80) cc_final: 0.7516 (m-10)
REVERT: B  364 LYS cc_start: 0.8153 (mttt) cc_final: 0.7920 (mtpt)
REVERT: B  408 MET cc_start: 0.8326 (mmm) cc_final: 0.8005 (mmm)
REVERT: B  487 PHE cc_start: 0.7298 (m-10) cc_final: 0.6503 (t80)
REVERT: B  549 GLU cc_start: 0.7045 (mp0) cc_final: 0.6697 (mm-30)
  outliers start: 15
  outliers final: 15
  residues processed: 145
  average time/residue: 0.0655
  time to fit residues: 13.4708
Evaluate side-chains
  153 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  574 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0570
   chunk 56 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 499 HIS
B 555 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.186524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.157684 restraints weight = 9420.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.34
r_work: 0.3775 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6800  Z= 0.148
  Angle     :  0.575   8.162   9208  Z= 0.301
  Chirality :  0.042   0.303    986
  Planarity :  0.005   0.054   1098
  Dihedral  : 11.165  74.624   1034
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.58 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.31), residues: 756
  helix:  1.76 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.88 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 603 
 TYR   0.014   0.001   TYR B 496 
 PHE   0.028   0.001   PHE A 596 
 TRP   0.015   0.001   TRP B 528 
 HIS   0.004   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6800)
  covalent geometry    : angle       0.57498 ( 9208)
  hydrogen bonds       : bond        0.04640 (  430)
  hydrogen bonds       : angle       4.42983 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  248 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7811 (m-40)
REVERT: A  258 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7263 (mmtm)
REVERT: A  270 ARG cc_start: 0.7640 (mtm180) cc_final: 0.6807 (mtp-110)
REVERT: A  298 ASN cc_start: 0.7753 (t0) cc_final: 0.7463 (t0)
REVERT: B  357 PHE cc_start: 0.8144 (t80) cc_final: 0.7517 (m-10)
REVERT: B  364 LYS cc_start: 0.8155 (mttt) cc_final: 0.7921 (mtpt)
REVERT: B  408 MET cc_start: 0.8396 (mmm) cc_final: 0.8039 (mmm)
REVERT: B  487 PHE cc_start: 0.7297 (m-10) cc_final: 0.6496 (t80)
REVERT: B  549 GLU cc_start: 0.7012 (mp0) cc_final: 0.6652 (mm-30)
REVERT: B  555 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7515 (mm-40)
  outliers start: 15
  outliers final: 14
  residues processed: 146
  average time/residue: 0.0653
  time to fit residues: 13.4511
Evaluate side-chains
  152 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  574 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0170
   chunk 20 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 69 optimal weight:    0.4980
   chunk 64 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 499 HIS
B 310 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.187542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.158805 restraints weight = 9260.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 2.31
r_work: 0.3789 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6800  Z= 0.139
  Angle     :  0.580   8.251   9208  Z= 0.305
  Chirality :  0.042   0.209    986
  Planarity :  0.005   0.054   1098
  Dihedral  : 11.082  74.847   1034
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.44 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.31), residues: 756
  helix:  1.77 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.82 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 603 
 TYR   0.014   0.001   TYR B 496 
 PHE   0.028   0.001   PHE A 596 
 TRP   0.015   0.001   TRP B 528 
 HIS   0.005   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6800)
  covalent geometry    : angle       0.58007 ( 9208)
  hydrogen bonds       : bond        0.04574 (  430)
  hydrogen bonds       : angle       4.43226 ( 1284)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  248 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7843 (m-40)
REVERT: A  258 LYS cc_start: 0.7696 (mmtt) cc_final: 0.6608 (tttm)
REVERT: A  270 ARG cc_start: 0.7612 (mtm180) cc_final: 0.6752 (mtp-110)
REVERT: A  298 ASN cc_start: 0.7668 (t0) cc_final: 0.7390 (t0)
REVERT: B  357 PHE cc_start: 0.8146 (t80) cc_final: 0.7522 (m-10)
REVERT: B  364 LYS cc_start: 0.8142 (mttt) cc_final: 0.7908 (mtpt)
REVERT: B  408 MET cc_start: 0.8357 (mmm) cc_final: 0.7998 (mmm)
REVERT: B  487 PHE cc_start: 0.7269 (m-10) cc_final: 0.6490 (t80)
REVERT: B  549 GLU cc_start: 0.6961 (mp0) cc_final: 0.6574 (mm-30)
REVERT: B  555 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7418 (mm-40)
REVERT: B  573 TRP cc_start: 0.7696 (t60) cc_final: 0.7466 (t60)
  outliers start: 16
  outliers final: 15
  residues processed: 148
  average time/residue: 0.0642
  time to fit residues: 13.5172
Evaluate side-chains
  157 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  491 THR
Chi-restraints excluded: chain B residue  574 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0770
   chunk 75 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0770
   chunk 46 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.5096

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 288 ASN
A 499 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.187641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.158769 restraints weight = 9238.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 2.31
r_work: 0.3790 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6800  Z= 0.140
  Angle     :  0.582   8.216   9208  Z= 0.305
  Chirality :  0.042   0.230    986
  Planarity :  0.005   0.054   1098
  Dihedral  : 11.034  74.859   1034
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.73 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.31), residues: 756
  helix:  1.80 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.81 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 603 
 TYR   0.014   0.001   TYR B 496 
 PHE   0.034   0.001   PHE A 596 
 TRP   0.015   0.001   TRP B 528 
 HIS   0.004   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6800)
  covalent geometry    : angle       0.58177 ( 9208)
  hydrogen bonds       : bond        0.04558 (  430)
  hydrogen bonds       : angle       4.44986 ( 1284)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1527.80 seconds
wall clock time: 27 minutes 5.11 seconds (1625.11 seconds total)