Starting phenix.real_space_refine
on Sat May  2 14:44:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v66_64798/05_2026/9v66_64798.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v66_64798/05_2026/9v66_64798.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v66_64798/05_2026/9v66_64798.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v66_64798/05_2026/9v66_64798.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v66_64798/05_2026/9v66_64798.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v66_64798/05_2026/9v66_64798.map"
  }
  resolution = 2.95
  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=  -0.000 sd=   0.043
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: 6
    Type Number    sf(0)   Gaussians
     P      18      5.49       5
     Mg      1      5.21       5
     S      15      5.16       5
     C    4007      2.51       5
     N    1180      2.21       5
     O    1235      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6456
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 760, 6068
          Classifications: {'peptide': 760}
          Link IDs: {'PTRANS': 42, 'TRANS': 717}
    Chain: "B"
      Number of atoms: 379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 379
          Classifications: {'DNA': 18}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 17}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1, 'water': 6}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.74, per 1000 atoms: 0.27
  Number of scatterers: 6456
  At special positions: 0
  Unit cell: (83.398, 94.461, 99.567, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      15     16.00
     P      18     15.00
     Mg      1     11.99
     O    1235      8.00
     N    1180      7.00
     C    4007      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: 0.56
  Conformation dependent library (CDL) restraints added in 392.6 milliseconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1412

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 8 sheets defined
      31.7% alpha, 28.3% beta
      0 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 54
    Processing helix  chain 'A' and resid 104 through 108
      removed outlier: 3.566A  pdb=" N   ALA A 108 " --> pdb=" O   PRO A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'A' and resid 195 through 202
    Processing helix  chain 'A' and resid 254 through 261
    Processing helix  chain 'A' and resid 299 through 304
    Processing helix  chain 'A' and resid 312 through 325
    Processing helix  chain 'A' and resid 360 through 362
      No H-bonds generated for 'chain 'A' and resid 360 through 362'
    Processing helix  chain 'A' and resid 372 through 392
      removed outlier: 3.777A  pdb=" N   LYS A 384 " --> pdb=" O   TYR A 380 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   MET A 385 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   THR A 386 " --> pdb=" O   GLN A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 430
    Processing helix  chain 'A' and resid 451 through 464
    Processing helix  chain 'A' and resid 482 through 491
    Processing helix  chain 'A' and resid 501 through 510
    Processing helix  chain 'A' and resid 516 through 530
    Processing helix  chain 'A' and resid 587 through 605
    Processing helix  chain 'A' and resid 621 through 639
    Processing helix  chain 'A' and resid 697 through 702
      removed outlier: 3.510A  pdb=" N   GLN A 702 " --> pdb=" O   ARG A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 735
    Processing helix  chain 'A' and resid 749 through 753
      removed outlier: 3.531A  pdb=" N   ARG A 753 " --> pdb=" O   VAL A 750 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346
    Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139
      removed outlier: 6.868A  pdb=" N   LEU A 142 " --> pdb=" O   LYS A 138 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   ARG A 162 " --> pdb=" O   ARG A 145 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LYS A 174 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   TYR A 185 " --> pdb=" O   PHE A 295 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   PHE A 232 " --> pdb=" O   ARG A 276 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   ARG A 276 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   ALA A 272 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 139
      removed outlier: 6.868A  pdb=" N   LEU A 142 " --> pdb=" O   LYS A 138 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   ARG A 162 " --> pdb=" O   ARG A 145 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LYS A 174 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   VAL A 330 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 60
      removed outlier: 4.367A  pdb=" N   ALA A  67 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A  26 " --> pdb=" O   PHE A  68 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   LEU A  23 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   GLU A  99 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   VAL A  25 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 246
    Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 365
    Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 442
      removed outlier: 7.159A  pdb=" N   LEU A 402 " --> pdb=" O   ARG A 438 " (cutoff:3.500A)
      removed outlier: 8.357A  pdb=" N   ILE A 440 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LEU A 404 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   TYR A 442 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   TYR A 406 " --> pdb=" O   TYR A 442 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASP A 401 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL A 472 " --> pdb=" O   ASP A 401 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   VAL A 403 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   VAL A 474 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   LEU A 405 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 568 through 575
      removed outlier: 6.369A  pdb=" N   PHE A 545 " --> pdb=" O   VAL A 613 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   HIS A 615 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   MET A 547 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   ASP A 617 " --> pdb=" O   MET A 547 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   VAL A 549 " --> pdb=" O   ASP A 617 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LEU A 612 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   VAL A 650 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL A 614 " --> pdb=" O   VAL A 650 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL A 652 " --> pdb=" O   VAL A 614 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ARG A 616 " --> pdb=" O   VAL A 652 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL A 649 " --> pdb=" O   THR A 714 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   SER A 679 " --> pdb=" O   THR A 691 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    795 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1972
        1.34 -     1.45: 1009
        1.45 -     1.57: 3586
        1.57 -     1.69: 35
        1.69 -     1.81: 23
  Bond restraints: 6625
  Sorted by residual:
  bond pdb=" C3'  DT B  16 "
       pdb=" O3'  DT B  16 "
    ideal  model  delta    sigma   weight residual
    1.422  1.464 -0.042 3.00e-02 1.11e+03 1.95e+00
  bond pdb=" P    DT B   1 "
       pdb=" OP2  DT B   1 "
    ideal  model  delta    sigma   weight residual
    1.480  1.504 -0.024 2.00e-02 2.50e+03 1.40e+00
  bond pdb=" P    DT B   1 "
       pdb=" OP1  DT B   1 "
    ideal  model  delta    sigma   weight residual
    1.480  1.502 -0.022 2.00e-02 2.50e+03 1.21e+00
  bond pdb=" P    DT B   1 "
       pdb=" OP3  DT B   1 "
    ideal  model  delta    sigma   weight residual
    1.480  1.501 -0.021 2.00e-02 2.50e+03 1.08e+00
  bond pdb=" N   ASN A 131 "
       pdb=" CA  ASN A 131 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.53e-01
  ... (remaining 6620 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 8928
        1.51 -     3.02: 121
        3.02 -     4.52: 17
        4.52 -     6.03: 4
        6.03 -     7.54: 3
  Bond angle restraints: 9073
  Sorted by residual:
  angle pdb=" O3'  DT B   1 "
        pdb=" P    DG B   2 "
        pdb=" O5'  DG B   2 "
      ideal   model   delta    sigma   weight residual
     104.00   99.88    4.12 1.50e+00 4.44e-01 7.56e+00
  angle pdb=" C4   DT B   1 "
        pdb=" C5   DT B   1 "
        pdb=" C7   DT B   1 "
      ideal   model   delta    sigma   weight residual
     122.40  118.62    3.78 1.50e+00 4.44e-01 6.36e+00
  angle pdb=" OP1  DT B   1 "
        pdb=" P    DT B   1 "
        pdb=" OP2  DT B   1 "
      ideal   model   delta    sigma   weight residual
     120.00  112.46    7.54 3.00e+00 1.11e-01 6.31e+00
  angle pdb=" O3'  DT B   1 "
        pdb=" C3'  DT B   1 "
        pdb=" C2'  DT B   1 "
      ideal   model   delta    sigma   weight residual
     111.50  108.19    3.31 1.50e+00 4.44e-01 4.88e+00
  angle pdb=" C3'  DT B  16 "
        pdb=" O3'  DT B  16 "
        pdb=" P    DA B  17 "
      ideal   model   delta    sigma   weight residual
     120.20  123.41   -3.21 1.50e+00 4.44e-01 4.57e+00
  ... (remaining 9068 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.97: 3804
       33.97 -    67.93: 131
       67.93 -   101.89: 6
      101.89 -   135.86: 1
      135.86 -   169.82: 1
  Dihedral angle restraints: 3943
    sinusoidal: 1751
      harmonic: 2192
  Sorted by residual:
  dihedral pdb=" C4'  DT B  16 "
           pdb=" C3'  DT B  16 "
           pdb=" O3'  DT B  16 "
           pdb=" P    DA B  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   50.18  169.82     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG B  15 "
           pdb=" C3'  DG B  15 "
           pdb=" O3'  DG B  15 "
           pdb=" P    DT B  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   84.36  135.64     1      3.50e+01 8.16e-04 1.34e+01
  dihedral pdb=" CA  ASP A 329 "
           pdb=" CB  ASP A 329 "
           pdb=" CG  ASP A 329 "
           pdb=" OD1 ASP A 329 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.63   55.63     1      2.00e+01 2.50e-03 1.05e+01
  ... (remaining 3940 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 970
       0.107 -    0.213: 24
       0.213 -    0.320: 0
       0.320 -    0.427: 1
       0.427 -    0.534: 2
  Chirality restraints: 997
  Sorted by residual:
  chirality pdb=" P    DT B   1 "
            pdb=" OP1  DT B   1 "
            pdb=" OP2  DT B   1 "
            pdb=" O5'  DT B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.88   -0.53 2.00e-01 2.50e+01 7.12e+00
  chirality pdb=" P    DA B   3 "
            pdb=" OP1  DA B   3 "
            pdb=" OP2  DA B   3 "
            pdb=" O5'  DA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.79   -0.44 2.00e-01 2.50e+01 4.94e+00
  chirality pdb=" P    DG B   2 "
            pdb=" OP1  DG B   2 "
            pdb=" OP2  DG B   2 "
            pdb=" O5'  DG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.73   -0.38 2.00e-01 2.50e+01 3.63e+00
  ... (remaining 994 not shown)

  Planarity restraints: 1127
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 533 "    0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO A 534 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 534 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 534 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 607 "   -0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO A 608 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 608 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 608 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG B   2 "    0.018 2.00e-02 2.50e+03   7.18e-03 1.55e+00
        pdb=" N9   DG B   2 "   -0.011 2.00e-02 2.50e+03
        pdb=" C8   DG B   2 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG B   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DG B   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG B   2 "    0.005 2.00e-02 2.50e+03
        pdb=" O6   DG B   2 "    0.002 2.00e-02 2.50e+03
        pdb=" N1   DG B   2 "    0.006 2.00e-02 2.50e+03
        pdb=" C2   DG B   2 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG B   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DG B   2 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4   DG B   2 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1124 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 127
        2.69 -     3.24: 5616
        3.24 -     3.79: 9732
        3.79 -     4.35: 13257
        4.35 -     4.90: 22152
  Nonbonded interactions: 50884
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 497 "
            pdb="MG    MG A 801 "
     model   vdw
     2.136 2.170
  nonbonded pdb=" OG1 THR A 236 "
            pdb=" O   ALA A 272 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OH  TYR A 185 "
            pdb=" O   VAL A 307 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   TYR A 732 "
            pdb=" OG1 THR A 735 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OH  TYR A 257 "
            pdb=" NH1 ARG A 261 "
     model   vdw
     2.309 3.120
  ... (remaining 50879 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     8.820
  Find NCS groups from input model:        0.030
  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:6.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6625  Z= 0.099
  Angle     :  0.466   7.539   9073  Z= 0.237
  Chirality :  0.046   0.534    997
  Planarity :  0.004   0.033   1127
  Dihedral  : 16.072 169.823   2531
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.31 %
    Favored  : 99.54 %
  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 are not related in a simple way.
  whole:  1.38 (0.31), residues: 758
  helix:  2.53 (0.35), residues: 219
  sheet:  0.92 (0.38), residues: 192
  loop : -0.12 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 502 
 TYR   0.009   0.001   TYR A 377 
 PHE   0.016   0.001   PHE A 469 
 TRP   0.008   0.001   TRP A 136 
 HIS   0.002   0.000   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6625)
  covalent geometry    : angle       0.46570 ( 9073)
  hydrogen bonds       : bond        0.18058 (  261)
  hydrogen bonds       : angle       6.49577 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.227 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 75
  average time/residue: 0.6521
  time to fit residues: 51.0561
Evaluate side-chains
  51 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    0.6980
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 420 GLN
A 464 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.178714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.126490 restraints weight = 6694.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.12
r_work: 0.3171 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   6625  Z= 0.260
  Angle     :  0.620   7.830   9073  Z= 0.328
  Chirality :  0.047   0.149    997
  Planarity :  0.005   0.046   1127
  Dihedral  : 15.417 177.305   1045
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  6.92 %
    Favored  : 91.54 %
  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 are not related in a simple way.
  whole:  0.89 (0.31), residues: 758
  helix:  2.00 (0.34), residues: 227
  sheet:  0.56 (0.37), residues: 206
  loop : -0.34 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 157 
 TYR   0.021   0.002   TYR A 377 
 PHE   0.011   0.002   PHE A 545 
 TRP   0.013   0.002   TRP A 136 
 HIS   0.012   0.002   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 ( 6625)
  covalent geometry    : angle       0.61987 ( 9073)
  hydrogen bonds       : bond        0.05504 (  261)
  hydrogen bonds       : angle       4.89700 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  174 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7926 (mptp)
  outliers start: 10
  outliers final: 5
  residues processed: 65
  average time/residue: 0.6411
  time to fit residues: 43.6307
Evaluate side-chains
  59 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  657 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 9 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
A 420 GLN
A 685 ASN
A 702 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.186535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.133516 restraints weight = 6727.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.20
r_work: 0.3209 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6625  Z= 0.115
  Angle     :  0.481   4.938   9073  Z= 0.260
  Chirality :  0.041   0.136    997
  Planarity :  0.004   0.038   1127
  Dihedral  : 15.339 179.566   1045
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.38 %
    Favored  : 86.92 %
  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 are not related in a simple way.
  whole:  1.04 (0.31), residues: 758
  helix:  2.28 (0.34), residues: 227
  sheet:  0.61 (0.37), residues: 206
  loop : -0.36 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 157 
 TYR   0.012   0.001   TYR A 377 
 PHE   0.009   0.001   PHE A 545 
 TRP   0.011   0.001   TRP A 136 
 HIS   0.007   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6625)
  covalent geometry    : angle       0.48081 ( 9073)
  hydrogen bonds       : bond        0.03510 (  261)
  hydrogen bonds       : angle       4.44572 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  121 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8121 (ttpt)
REVERT: A  147 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7716 (tt0)
REVERT: A  174 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7873 (mptp)
REVERT: A  490 ARG cc_start: 0.6706 (tpp80) cc_final: 0.6435 (tpt-90)
  outliers start: 11
  outliers final: 2
  residues processed: 63
  average time/residue: 0.5966
  time to fit residues: 39.5628
Evaluate side-chains
  59 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  398 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 1 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 66 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
A 420 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.180543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.127231 restraints weight = 6770.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.19
r_work: 0.3102 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050   6625  Z= 0.312
  Angle     :  0.674  10.343   9073  Z= 0.351
  Chirality :  0.049   0.161    997
  Planarity :  0.005   0.050   1127
  Dihedral  : 15.509 178.814   1045
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.62 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.30), residues: 758
  helix:  1.78 (0.34), residues: 226
  sheet:  0.48 (0.38), residues: 195
  loop : -0.63 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 157 
 TYR   0.022   0.002   TYR A 377 
 PHE   0.013   0.002   PHE A 545 
 TRP   0.014   0.002   TRP A 136 
 HIS   0.012   0.002   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00776 ( 6625)
  covalent geometry    : angle       0.67354 ( 9073)
  hydrogen bonds       : bond        0.05692 (  261)
  hydrogen bonds       : angle       4.77828 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  147 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7723 (tt0)
REVERT: A  150 ASN cc_start: 0.8175 (t0) cc_final: 0.7911 (t0)
REVERT: A  174 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7904 (mptp)
REVERT: A  698 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7528 (ttp80)
  outliers start: 17
  outliers final: 6
  residues processed: 68
  average time/residue: 0.6489
  time to fit residues: 46.2797
Evaluate side-chains
  64 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  698 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
A 685 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.181606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.130388 restraints weight = 6727.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.02
r_work: 0.3243 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6625  Z= 0.121
  Angle     :  0.500   8.544   9073  Z= 0.267
  Chirality :  0.042   0.136    997
  Planarity :  0.004   0.042   1127
  Dihedral  : 15.424 178.711   1045
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.62 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.31), residues: 758
  helix:  2.14 (0.34), residues: 228
  sheet:  0.54 (0.37), residues: 206
  loop : -0.47 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 157 
 TYR   0.012   0.001   TYR A 377 
 PHE   0.014   0.001   PHE A 469 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.007   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6625)
  covalent geometry    : angle       0.50040 ( 9073)
  hydrogen bonds       : bond        0.03459 (  261)
  hydrogen bonds       : angle       4.33722 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.166 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 62
  average time/residue: 0.6532
  time to fit residues: 42.4576
Evaluate side-chains
  57 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  493 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 35 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 58 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.183621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.130974 restraints weight = 6802.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.14
r_work: 0.3171 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6625  Z= 0.157
  Angle     :  0.525   5.703   9073  Z= 0.279
  Chirality :  0.042   0.138    997
  Planarity :  0.004   0.042   1127
  Dihedral  : 15.392 177.986   1045
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.92 %
    Favored  : 83.08 %
  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 are not related in a simple way.
  whole:  0.87 (0.31), residues: 758
  helix:  2.12 (0.34), residues: 229
  sheet:  0.52 (0.37), residues: 206
  loop : -0.48 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 490 
 TYR   0.017   0.001   TYR A 377 
 PHE   0.017   0.001   PHE A 469 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 6625)
  covalent geometry    : angle       0.52498 ( 9073)
  hydrogen bonds       : bond        0.03938 (  261)
  hydrogen bonds       : angle       4.34529 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  698 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7518 (ttp80)
  outliers start: 13
  outliers final: 4
  residues processed: 64
  average time/residue: 0.6494
  time to fit residues: 43.5982
Evaluate side-chains
  56 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  698 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 3 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN
A 420 GLN
A 439 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.184428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.130831 restraints weight = 6757.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.22
r_work: 0.3198 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6625  Z= 0.146
  Angle     :  0.514   6.308   9073  Z= 0.273
  Chirality :  0.042   0.137    997
  Planarity :  0.004   0.041   1127
  Dihedral  : 15.397 176.421   1045
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.92 %
    Favored  : 82.92 %
  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 are not related in a simple way.
  whole:  0.91 (0.31), residues: 758
  helix:  2.17 (0.34), residues: 229
  sheet:  0.53 (0.37), residues: 206
  loop : -0.47 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 255 
 TYR   0.015   0.001   TYR A 377 
 PHE   0.018   0.001   PHE A 469 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6625)
  covalent geometry    : angle       0.51420 ( 9073)
  hydrogen bonds       : bond        0.03741 (  261)
  hydrogen bonds       : angle       4.30853 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  121 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8129 (ttpt)
REVERT: A  698 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7513 (ttp80)
  outliers start: 14
  outliers final: 7
  residues processed: 65
  average time/residue: 0.6287
  time to fit residues: 42.8460
Evaluate side-chains
  61 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  590 GLN
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  698 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0870
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.9364

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
A 439 GLN
A 685 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.185415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.133744 restraints weight = 6748.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.04
r_work: 0.3219 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6625  Z= 0.125
  Angle     :  0.498   6.595   9073  Z= 0.264
  Chirality :  0.041   0.135    997
  Planarity :  0.004   0.040   1127
  Dihedral  : 15.409 174.654   1045
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.54 %
    Favored  : 82.31 %
  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 are not related in a simple way.
  whole:  0.98 (0.31), residues: 758
  helix:  2.26 (0.34), residues: 229
  sheet:  0.57 (0.37), residues: 206
  loop : -0.44 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 490 
 TYR   0.014   0.001   TYR A 377 
 PHE   0.017   0.001   PHE A 469 
 TRP   0.011   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6625)
  covalent geometry    : angle       0.49778 ( 9073)
  hydrogen bonds       : bond        0.03393 (  261)
  hydrogen bonds       : angle       4.21611 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  121 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8166 (ttpt)
REVERT: A  490 ARG cc_start: 0.6677 (tpt-90) cc_final: 0.6426 (tpt90)
  outliers start: 14
  outliers final: 6
  residues processed: 65
  average time/residue: 0.6923
  time to fit residues: 47.0161
Evaluate side-chains
  58 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  590 GLN
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  657 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.184899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.131310 restraints weight = 6841.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.23
r_work: 0.3203 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6625  Z= 0.140
  Angle     :  0.514   6.759   9073  Z= 0.271
  Chirality :  0.042   0.137    997
  Planarity :  0.004   0.040   1127
  Dihedral  : 15.435 173.371   1045
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.85 %
    Favored  : 82.15 %
  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 are not related in a simple way.
  whole:  0.94 (0.31), residues: 758
  helix:  2.23 (0.34), residues: 229
  sheet:  0.55 (0.37), residues: 206
  loop : -0.48 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 490 
 TYR   0.016   0.001   TYR A 377 
 PHE   0.017   0.001   PHE A 469 
 TRP   0.011   0.001   TRP A 136 
 HIS   0.007   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6625)
  covalent geometry    : angle       0.51378 ( 9073)
  hydrogen bonds       : bond        0.03624 (  261)
  hydrogen bonds       : angle       4.23730 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  121 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8139 (ttpt)
REVERT: A  698 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7460 (ttp80)
  outliers start: 13
  outliers final: 6
  residues processed: 61
  average time/residue: 0.5842
  time to fit residues: 37.5356
Evaluate side-chains
  58 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  590 GLN
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  698 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 41 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.184235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.131760 restraints weight = 6747.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.13
r_work: 0.3189 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6625  Z= 0.160
  Angle     :  0.534   6.955   9073  Z= 0.281
  Chirality :  0.043   0.139    997
  Planarity :  0.004   0.041   1127
  Dihedral  : 15.473 172.526   1045
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.77 %
    Favored  : 81.69 %
  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 are not related in a simple way.
  whole:  0.87 (0.31), residues: 758
  helix:  2.16 (0.34), residues: 229
  sheet:  0.54 (0.37), residues: 206
  loop : -0.52 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 157 
 TYR   0.017   0.001   TYR A 377 
 PHE   0.017   0.001   PHE A 469 
 TRP   0.011   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6625)
  covalent geometry    : angle       0.53438 ( 9073)
  hydrogen bonds       : bond        0.03896 (  261)
  hydrogen bonds       : angle       4.30702 (  795)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  121 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8194 (ttpt)
REVERT: A  490 ARG cc_start: 0.6596 (tpt-90) cc_final: 0.6358 (tpt90)
REVERT: A  698 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7479 (ttp80)
  outliers start: 10
  outliers final: 7
  residues processed: 61
  average time/residue: 0.6377
  time to fit residues: 40.9196
Evaluate side-chains
  61 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  590 GLN
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  698 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.183248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.131712 restraints weight = 6687.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.15
r_work: 0.3233 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6625  Z= 0.116
  Angle     :  0.491   6.827   9073  Z= 0.260
  Chirality :  0.041   0.133    997
  Planarity :  0.004   0.039   1127
  Dihedral  : 15.632 170.856   1045
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.92 %
    Favored  : 81.38 %
  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 are not related in a simple way.
  whole:  1.00 (0.31), residues: 758
  helix:  2.28 (0.34), residues: 229
  sheet:  0.74 (0.39), residues: 189
  loop : -0.49 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 157 
 TYR   0.013   0.001   TYR A 377 
 PHE   0.018   0.001   PHE A 469 
 TRP   0.012   0.001   TRP A 570 
 HIS   0.006   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6625)
  covalent geometry    : angle       0.49066 ( 9073)
  hydrogen bonds       : bond        0.03187 (  261)
  hydrogen bonds       : angle       4.13333 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1925.09 seconds
wall clock time: 33 minutes 41.02 seconds (2021.02 seconds total)