Starting phenix.real_space_refine
on Wed Aug  5 04:27:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ywm_39638/08_2026/8ywm_39638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ywm_39638/08_2026/8ywm_39638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ywm_39638/08_2026/8ywm_39638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ywm_39638/08_2026/8ywm_39638.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ywm_39638/08_2026/8ywm_39638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ywm_39638/08_2026/8ywm_39638.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.037
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      34      5.49       5
     S      51      5.16       5
     C    5455      2.51       5
     N    1478      2.21       5
     O    1675      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8693
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7980
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 979, 7980
          Classifications: {'peptide': 979}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 934}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 339
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "E"
      Number of atoms: 374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 374
          Classifications: {'DNA': 19}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 18}
  Time building chain proxies: 1.56, per 1000 atoms: 0.18
  Number of scatterers: 8693
  At special positions: 0
  Unit cell: (89.44, 116.48, 110.24, 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      51     16.00
     P      34     15.00
     O    1675      8.00
     N    1478      7.00
     C    5455      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: 0.83
  Conformation dependent library (CDL) restraints added in 259.6 milliseconds
  

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1870

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      48.5% alpha, 16.6% beta
      16 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 15
    Processing helix  chain 'A' and resid 15 through 28
    Processing helix  chain 'A' and resid 79 through 93
      removed outlier: 3.780A  pdb=" N   GLU A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 142
    Processing helix  chain 'A' and resid 154 through 163
      removed outlier: 3.590A  pdb=" N   LYS A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 191
      No H-bonds generated for 'chain 'A' and resid 189 through 191'
    Processing helix  chain 'A' and resid 271 through 287
    Processing helix  chain 'A' and resid 299 through 311
      removed outlier: 3.650A  pdb=" N   PHE A 303 " --> pdb=" O   TYR A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 322
    Processing helix  chain 'A' and resid 328 through 336
      removed outlier: 3.562A  pdb=" N   TYR A 336 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 374
    Processing helix  chain 'A' and resid 381 through 389
    Processing helix  chain 'A' and resid 398 through 409
      removed outlier: 3.550A  pdb=" N   ARG A 409 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 436
      removed outlier: 3.607A  pdb=" N   VAL A 417 " --> pdb=" O   LYS A 413 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   CYS A 428 " --> pdb=" O   ASP A 424 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLN A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
      removed outlier: 3.531A  pdb=" N   ASP A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 458
    Processing helix  chain 'A' and resid 459 through 475
      removed outlier: 4.044A  pdb=" N   LYS A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   HIS A 474 " --> pdb=" O   ALA A 470 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP A 475 " --> pdb=" O   TYR A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 529
    Processing helix  chain 'A' and resid 532 through 534
      No H-bonds generated for 'chain 'A' and resid 532 through 534'
    Processing helix  chain 'A' and resid 539 through 549
    Processing helix  chain 'A' and resid 575 through 579
    Processing helix  chain 'A' and resid 580 through 610
    Processing helix  chain 'A' and resid 616 through 639
    Processing helix  chain 'A' and resid 640 through 647
    Processing helix  chain 'A' and resid 654 through 679
    Processing helix  chain 'A' and resid 697 through 699
      No H-bonds generated for 'chain 'A' and resid 697 through 699'
    Processing helix  chain 'A' and resid 700 through 709
      removed outlier: 3.973A  pdb=" N   TYR A 707 " --> pdb=" O   VAL A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 748
      removed outlier: 3.871A  pdb=" N   THR A 734 " --> pdb=" O   LYS A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 801 through 815
    Processing helix  chain 'A' and resid 826 through 841
    Processing helix  chain 'A' and resid 847 through 851
      removed outlier: 3.710A  pdb=" N   ILE A 851 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 882
    Processing helix  chain 'A' and resid 921 through 923
      No H-bonds generated for 'chain 'A' and resid 921 through 923'
    Processing helix  chain 'A' and resid 928 through 935
    Processing helix  chain 'A' and resid 939 through 953
      removed outlier: 3.616A  pdb=" N   TYR A 943 " --> pdb=" O   ASP A 939 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LEU A 949 " --> pdb=" O   ASN A 945 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   GLY A 950 " --> pdb=" O   ASN A 946 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   LEU A 951 " --> pdb=" O   TYR A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 990
    Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 179
      removed outlier: 6.992A  pdb=" N   PHE A  50 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ILE A  39 " --> pdb=" O   PHE A  50 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   TYR A  52 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A 194 " --> pdb=" O   GLN A 171 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 105
      removed outlier: 4.356A  pdb=" N   VAL A  70 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268
      removed outlier: 3.616A  pdb=" N   ALA A 249 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   VAL A 232 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   TYR A 215 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLY A 293 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344
    Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 508
      removed outlier: 3.502A  pdb=" N   PHE A 765 " --> pdb=" O   GLY A 506 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   TYR A 756 " --> pdb=" O   ASP A 517 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   ASP A 517 " --> pdb=" O   TYR A 756 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   GLU A 758 " --> pdb=" O   GLY A 515 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLY A 515 " --> pdb=" O   GLU A 758 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   SER A 690 " --> pdb=" O   GLY A 686 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLY A 686 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   TYR A 692 " --> pdb=" O   LYS A 684 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508
      removed outlier: 3.502A  pdb=" N   PHE A 765 " --> pdb=" O   GLY A 506 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   LEU A 760 " --> pdb=" O   HIS A 776 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   HIS A 776 " --> pdb=" O   LEU A 760 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   LYS A 770 " --> pdb=" O   THR A 766 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537
    Processing sheet with id=AA8, first strand: chain 'A' and resid 852 through 855

    418 hydrogen bonds defined for protein.
    1200 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      37 hydrogen bonds
      74 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2107
        1.33 -     1.45: 1932
        1.45 -     1.57: 4783
        1.57 -     1.69: 67
        1.69 -     1.81: 81
  Bond restraints: 8970
  Sorted by residual:
  bond pdb=" O3'  DA E  22 "
       pdb=" P    DC E  23 "
    ideal  model  delta    sigma   weight residual
    1.607  1.650 -0.043 1.20e-02 6.94e+03 1.30e+01
  bond pdb=" N   LYS A 712 "
       pdb=" CA  LYS A 712 "
    ideal  model  delta    sigma   weight residual
    1.460  1.512 -0.052 1.45e-02 4.76e+03 1.29e+01
  bond pdb=" C3'  DT E  21 "
       pdb=" C2'  DT E  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  bond pdb=" N   ASP A 822 "
       pdb=" CA  ASP A 822 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.16e-02 7.43e+03 8.45e+00
  bond pdb=" C3'  DC E  14 "
       pdb=" C2'  DC E  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 7.92e+00
  ... (remaining 8965 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 11934
        1.99 -     3.99: 290
        3.99 -     5.98: 35
        5.98 -     7.98: 10
        7.98 -     9.97: 5
  Bond angle restraints: 12274
  Sorted by residual:
  angle pdb=" C   VAL A 188 "
        pdb=" N   THR A 189 "
        pdb=" CA  THR A 189 "
      ideal   model   delta    sigma   weight residual
     120.94  130.79   -9.85 1.90e+00 2.77e-01 2.69e+01
  angle pdb=" C   GLU A  93 "
        pdb=" N   ASN A  94 "
        pdb=" CA  ASN A  94 "
      ideal   model   delta    sigma   weight residual
     121.54  130.10   -8.56 1.91e+00 2.74e-01 2.01e+01
  angle pdb=" CB  LYS A 260 "
        pdb=" CG  LYS A 260 "
        pdb=" CD  LYS A 260 "
      ideal   model   delta    sigma   weight residual
     111.30  121.27   -9.97 2.30e+00 1.89e-01 1.88e+01
  angle pdb=" N3   DT E  16 "
        pdb=" C4   DT E  16 "
        pdb=" O4   DT E  16 "
      ideal   model   delta    sigma   weight residual
     119.90  122.44   -2.54 6.00e-01 2.78e+00 1.79e+01
  angle pdb=" N3   DT D  20 "
        pdb=" C4   DT D  20 "
        pdb=" O4   DT D  20 "
      ideal   model   delta    sigma   weight residual
     119.90  122.35   -2.45 6.00e-01 2.78e+00 1.66e+01
  ... (remaining 12269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.12: 4904
       27.12 -    54.24: 365
       54.24 -    81.36: 48
       81.36 -   108.48: 3
      108.48 -   135.61: 1
  Dihedral angle restraints: 5321
    sinusoidal: 2417
      harmonic: 2904
  Sorted by residual:
  dihedral pdb=" CA  PHE A  71 "
           pdb=" C   PHE A  71 "
           pdb=" N   PHE A  72 "
           pdb=" CA  PHE A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.58   19.42     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  TYR A 700 "
           pdb=" C   TYR A 700 "
           pdb=" N   THR A 701 "
           pdb=" CA  THR A 701 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.07  -18.93     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  ILE A 253 "
           pdb=" C   ILE A 253 "
           pdb=" N   THR A 254 "
           pdb=" CA  THR A 254 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.57  -18.43     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 5318 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 885
       0.039 -    0.079: 317
       0.079 -    0.118: 96
       0.118 -    0.157: 29
       0.157 -    0.196: 5
  Chirality restraints: 1332
  Sorted by residual:
  chirality pdb=" CA  ASN A  94 "
            pdb=" N   ASN A  94 "
            pdb=" C   ASN A  94 "
            pdb=" CB  ASN A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.65e-01
  chirality pdb=" CA  LYS A 712 "
            pdb=" N   LYS A 712 "
            pdb=" C   LYS A 712 "
            pdb=" CB  LYS A 712 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" CA  ILE A 693 "
            pdb=" N   ILE A 693 "
            pdb=" C   ILE A 693 "
            pdb=" CB  ILE A 693 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.52e-01
  ... (remaining 1329 not shown)

  Planarity restraints: 1448
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 857 "    0.045 5.00e-02 4.00e+02   6.87e-02 7.54e+00
        pdb=" N   PRO A 858 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 858 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 858 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 287 "   -0.042 5.00e-02 4.00e+02   6.39e-02 6.54e+00
        pdb=" N   PRO A 288 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  99 "    0.176 9.50e-02 1.11e+02   7.96e-02 5.05e+00
        pdb=" NE  ARG A  99 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  99 "    0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  99 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  99 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1445 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1039
        2.75 -     3.29: 8061
        3.29 -     3.83: 14606
        3.83 -     4.36: 16262
        4.36 -     4.90: 28119
  Nonbonded interactions: 68087
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 297 "
            pdb=" OD2 ASP A 365 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OH  TYR A 471 "
            pdb=" OD2 ASP A 588 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   TYR A 406 "
            pdb=" NH1 ARG A 409 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" O   ILE A 636 "
            pdb=" OG1 THR A 640 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" O   THR A 701 "
            pdb=" OG1 THR A 704 "
     model   vdw
     2.360 3.040
  ... (remaining 68082 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:             0.540
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.000
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
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   0.052   8970  Z= 0.283
  Angle     :  0.736   9.974  12274  Z= 0.456
  Chirality :  0.047   0.196   1332
  Planarity :  0.006   0.080   1448
  Dihedral  : 17.374 135.606   3451
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.69 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.21 (0.26), residues: 975
  helix:  0.90 (0.24), residues: 442
  sheet:  0.28 (0.42), residues: 151
  loop : -0.72 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A  99 
 TYR   0.031   0.002   TYR A 177 
 PHE   0.037   0.002   PHE A 303 
 TRP   0.025   0.002   TRP A 325 
 HIS   0.003   0.001   HIS A 326 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00435 /  0.28 ( 8970)
  covalent geometry    : angle       0.73627 /  0.46 (12274)
  hydrogen bonds       : bond        0.15361 / 10.32 (  452)
  hydrogen bonds       : angle       6.55321 /  4.66 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 348
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6535 (mt-10)
REVERT: A   39 ILE cc_start: 0.8175 (mm) cc_final: 0.7801 (mm)
REVERT: A   41 GLU cc_start: 0.7266 (pt0) cc_final: 0.7033 (pt0)
REVERT: A   75 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7540 (tm-30)
REVERT: A  127 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7802 (ttmm)
REVERT: A  134 LYS cc_start: 0.7786 (mmmm) cc_final: 0.7530 (mmmm)
REVERT: A  163 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7947 (mmtp)
REVERT: A  180 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6637 (mtm110)
REVERT: A  191 GLU cc_start: 0.7134 (mp0) cc_final: 0.6889 (mp0)
REVERT: A  206 ILE cc_start: 0.7710 (mt) cc_final: 0.7401 (mm)
REVERT: A  278 SER cc_start: 0.8347 (t) cc_final: 0.8129 (t)
REVERT: A  285 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7121 (mtp85)
REVERT: A  334 LYS cc_start: 0.8333 (tppp) cc_final: 0.8030 (tppp)
REVERT: A  340 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7040 (mt-10)
REVERT: A  349 LYS cc_start: 0.7831 (tttt) cc_final: 0.7544 (mttm)
REVERT: A  399 TYR cc_start: 0.7509 (m-80) cc_final: 0.6604 (m-80)
REVERT: A  474 HIS cc_start: 0.7477 (m90) cc_final: 0.7204 (m170)
REVERT: A  476 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6792 (tm-30)
REVERT: A  513 THR cc_start: 0.6775 (t) cc_final: 0.6496 (p)
REVERT: A  517 ASP cc_start: 0.6609 (t70) cc_final: 0.6254 (t70)
REVERT: A  593 ARG cc_start: 0.7998 (ttt90) cc_final: 0.7774 (ttt180)
REVERT: A  630 LYS cc_start: 0.8035 (mttt) cc_final: 0.7756 (mtpp)
REVERT: A  632 LYS cc_start: 0.8017 (tptt) cc_final: 0.7751 (ttmm)
REVERT: A  636 ILE cc_start: 0.8157 (tt) cc_final: 0.7946 (tt)
REVERT: A  687 ASP cc_start: 0.6487 (t0) cc_final: 0.5806 (t0)
REVERT: A  738 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7271 (mt-10)
REVERT: A  824 ARG cc_start: 0.6503 (mtt-85) cc_final: 0.6177 (mtt-85)
REVERT: A  846 ASN cc_start: 0.6664 (p0) cc_final: 0.6117 (p0)
REVERT: A  863 LYS cc_start: 0.7210 (mmmm) cc_final: 0.6961 (mmmm)
REVERT: A  924 LYS cc_start: 0.7449 (mttp) cc_final: 0.6785 (mttm)
REVERT: A  937 PRO cc_start: 0.7002 (Cg_endo) cc_final: 0.5930 (Cg_exo)
REVERT: A  947 TYR cc_start: 0.7645 (m-80) cc_final: 0.7428 (m-10)
  outliers start: 2
  outliers final: 2
  residues processed: 350
  average time/residue: 0.0905
  time to fit residues: 41.9027
Evaluate side-chains
  302 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 300
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  712 LYS
Chi-restraints excluded: chain A residue  938 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  40 HIS
A 319 ASN
** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN
A 963 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.151858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.125516 restraints weight = 13042.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.56
r_work: 0.3456 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   8970  Z= 0.196
  Angle     :  0.682   8.196  12274  Z= 0.362
  Chirality :  0.048   0.210   1332
  Planarity :  0.005   0.053   1448
  Dihedral  : 18.697 137.518   1464
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.18 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 13.42 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.61 (0.27), residues: 975
  helix:  1.34 (0.24), residues: 445
  sheet:  0.26 (0.39), residues: 164
  loop : -0.61 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  13 
 TYR   0.025   0.002   TYR A 772 
 PHE   0.030   0.002   PHE A 294 
 TRP   0.023   0.002   TRP A 325 
 HIS   0.004   0.001   HIS A 722 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00427 /  0.20 ( 8970)
  covalent geometry    : angle       0.68213 /  0.36 (12274)
  hydrogen bonds       : bond        0.06676 /  4.17 (  452)
  hydrogen bonds       : angle       4.52722 /  3.19 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  333 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 309
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLN cc_start: 0.8634 (tp40) cc_final: 0.8269 (tp-100)
REVERT: A   41 GLU cc_start: 0.8166 (pt0) cc_final: 0.7659 (pt0)
REVERT: A   54 SER cc_start: 0.8289 (m) cc_final: 0.7931 (p)
REVERT: A   75 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: A  127 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8228 (ttmm)
REVERT: A  134 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7843 (mmmm)
REVERT: A  149 ASP cc_start: 0.7536 (p0) cc_final: 0.7154 (p0)
REVERT: A  163 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8158 (tppt)
REVERT: A  180 ARG cc_start: 0.7870 (mtm110) cc_final: 0.7200 (mtt90)
REVERT: A  191 GLU cc_start: 0.7678 (mp0) cc_final: 0.7338 (mp0)
REVERT: A  285 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.7964 (mmm-85)
REVERT: A  313 ILE cc_start: 0.8575 (pt) cc_final: 0.8321 (pt)
REVERT: A  334 LYS cc_start: 0.8517 (tppp) cc_final: 0.8145 (tppp)
REVERT: A  349 LYS cc_start: 0.8217 (tttt) cc_final: 0.7969 (mttm)
REVERT: A  376 LYS cc_start: 0.8273 (mmtt) cc_final: 0.8013 (mmtm)
REVERT: A  399 TYR cc_start: 0.7865 (m-80) cc_final: 0.6848 (m-80)
REVERT: A  469 ILE cc_start: 0.8458 (mt) cc_final: 0.8089 (tt)
REVERT: A  474 HIS cc_start: 0.7740 (m90) cc_final: 0.7508 (m170)
REVERT: A  476 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7227 (tm-30)
REVERT: A  513 THR cc_start: 0.7282 (t) cc_final: 0.6982 (p)
REVERT: A  517 ASP cc_start: 0.7305 (t70) cc_final: 0.6902 (t70)
REVERT: A  549 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8131 (ptmt)
REVERT: A  579 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7416 (ttm)
REVERT: A  593 ARG cc_start: 0.8205 (ttt90) cc_final: 0.7969 (ttt90)
REVERT: A  630 LYS cc_start: 0.8222 (mttt) cc_final: 0.7995 (mtpp)
REVERT: A  632 LYS cc_start: 0.8170 (tptt) cc_final: 0.7852 (ttmm)
REVERT: A  635 LYS cc_start: 0.8361 (tttt) cc_final: 0.8109 (ttpt)
REVERT: A  647 ASN cc_start: 0.8070 (t0) cc_final: 0.7803 (t0)
REVERT: A  738 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8177 (mt-10)
REVERT: A  839 VAL cc_start: 0.8460 (t) cc_final: 0.8254 (m)
REVERT: A  842 MET cc_start: 0.7375 (ttt) cc_final: 0.7037 (tpp)
REVERT: A  846 ASN cc_start: 0.7406 (p0) cc_final: 0.6984 (p0)
REVERT: A  848 GLU cc_start: 0.7840 (mp0) cc_final: 0.7518 (mp0)
REVERT: A  849 ASP cc_start: 0.7676 (m-30) cc_final: 0.7469 (m-30)
REVERT: A  863 LYS cc_start: 0.7710 (mmmm) cc_final: 0.7357 (mmmm)
REVERT: A  900 TYR cc_start: 0.7848 (p90) cc_final: 0.7199 (p90)
REVERT: A  924 LYS cc_start: 0.8010 (mttp) cc_final: 0.6985 (mttm)
REVERT: A  947 TYR cc_start: 0.8119 (m-80) cc_final: 0.7869 (m-10)
  outliers start: 24
  outliers final: 13
  residues processed: 318
  average time/residue: 0.1049
  time to fit residues: 43.8745
Evaluate side-chains
  314 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 300
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 GLU
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  489 LYS
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  694 THR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  938 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0470
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6278

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 227 GLN
A 319 ASN
** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.151540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.125005 restraints weight = 12825.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.57
r_work: 0.3487 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8970  Z= 0.141
  Angle     :  0.603   9.045  12274  Z= 0.322
  Chirality :  0.044   0.197   1332
  Planarity :  0.005   0.042   1448
  Dihedral  : 18.668 135.202   1460
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.08 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.84 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.76 (0.27), residues: 975
  helix:  1.55 (0.24), residues: 444
  sheet:  0.14 (0.38), residues: 164
  loop : -0.55 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 824 
 TYR   0.020   0.002   TYR A 772 
 PHE   0.016   0.002   PHE A 294 
 TRP   0.014   0.001   TRP A 325 
 HIS   0.004   0.001   HIS A 722 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 ( 8970)
  covalent geometry    : angle       0.60344 /  0.32 (12274)
  hydrogen bonds       : bond        0.05692 /  3.59 (  452)
  hydrogen bonds       : angle       4.27983 /  3.02 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 313
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLN cc_start: 0.8619 (tp40) cc_final: 0.8253 (tp-100)
REVERT: A   41 GLU cc_start: 0.8035 (pt0) cc_final: 0.7556 (pt0)
REVERT: A   54 SER cc_start: 0.8331 (m) cc_final: 0.7994 (p)
REVERT: A   59 TYR cc_start: 0.8139 (m-10) cc_final: 0.7620 (m-80)
REVERT: A   62 GLU cc_start: 0.7595 (tt0) cc_final: 0.7333 (tt0)
REVERT: A   75 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8176 (tm-30)
REVERT: A   85 PHE cc_start: 0.8926 (t80) cc_final: 0.8505 (t80)
REVERT: A  116 LYS cc_start: 0.8420 (mttm) cc_final: 0.7987 (mtmm)
REVERT: A  127 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8199 (ttmm)
REVERT: A  134 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7828 (mmmm)
REVERT: A  142 MET cc_start: 0.7901 (mmm) cc_final: 0.7628 (tmm)
REVERT: A  149 ASP cc_start: 0.7570 (p0) cc_final: 0.6923 (p0)
REVERT: A  180 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7313 (mtm110)
REVERT: A  191 GLU cc_start: 0.7709 (mp0) cc_final: 0.7388 (mp0)
REVERT: A  334 LYS cc_start: 0.8482 (tppp) cc_final: 0.8109 (tppp)
REVERT: A  349 LYS cc_start: 0.8243 (tttt) cc_final: 0.7994 (mttm)
REVERT: A  376 LYS cc_start: 0.8283 (mmtt) cc_final: 0.8015 (mmtm)
REVERT: A  399 TYR cc_start: 0.7860 (m-80) cc_final: 0.6910 (m-80)
REVERT: A  424 ASP cc_start: 0.8091 (t0) cc_final: 0.7656 (t0)
REVERT: A  467 MET cc_start: 0.8056 (ttp) cc_final: 0.7697 (ttt)
REVERT: A  469 ILE cc_start: 0.8523 (mt) cc_final: 0.8159 (tt)
REVERT: A  476 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7396 (tm-30)
REVERT: A  484 THR cc_start: 0.7703 (m) cc_final: 0.7390 (p)
REVERT: A  513 THR cc_start: 0.7339 (t) cc_final: 0.7038 (p)
REVERT: A  517 ASP cc_start: 0.7375 (t70) cc_final: 0.6955 (t70)
REVERT: A  527 MET cc_start: 0.8081 (mtm) cc_final: 0.7843 (mtp)
REVERT: A  549 LYS cc_start: 0.8560 (ptmt) cc_final: 0.8208 (ptmt)
REVERT: A  570 VAL cc_start: 0.8041 (t) cc_final: 0.7839 (t)
REVERT: A  579 MET cc_start: 0.7772 (ttm) cc_final: 0.7456 (ttm)
REVERT: A  593 ARG cc_start: 0.8254 (ttt90) cc_final: 0.7984 (ttt90)
REVERT: A  630 LYS cc_start: 0.8294 (mttt) cc_final: 0.8047 (mtpp)
REVERT: A  632 LYS cc_start: 0.8218 (tptt) cc_final: 0.7776 (ttmm)
REVERT: A  635 LYS cc_start: 0.8424 (tttt) cc_final: 0.7846 (ttmm)
REVERT: A  636 ILE cc_start: 0.8391 (tt) cc_final: 0.8159 (tt)
REVERT: A  647 ASN cc_start: 0.8161 (t0) cc_final: 0.7885 (t0)
REVERT: A  718 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6559 (mp0)
REVERT: A  792 ILE cc_start: 0.8167 (mt) cc_final: 0.7957 (mm)
REVERT: A  810 ILE cc_start: 0.8632 (mt) cc_final: 0.8262 (tp)
REVERT: A  839 VAL cc_start: 0.8622 (t) cc_final: 0.8369 (m)
REVERT: A  842 MET cc_start: 0.7447 (ttt) cc_final: 0.7183 (ttt)
REVERT: A  848 GLU cc_start: 0.7724 (mp0) cc_final: 0.7341 (mp0)
REVERT: A  849 ASP cc_start: 0.7651 (m-30) cc_final: 0.7344 (m-30)
REVERT: A  863 LYS cc_start: 0.7774 (mmmm) cc_final: 0.7397 (mmmm)
REVERT: A  900 TYR cc_start: 0.7836 (p90) cc_final: 0.7109 (p90)
REVERT: A  924 LYS cc_start: 0.7739 (mttp) cc_final: 0.7250 (mttm)
REVERT: A  925 MET cc_start: 0.7165 (mmm) cc_final: 0.6556 (mmm)
REVERT: A  947 TYR cc_start: 0.8256 (m-80) cc_final: 0.7974 (m-10)
  outliers start: 25
  outliers final: 15
  residues processed: 321
  average time/residue: 0.1074
  time to fit residues: 45.4784
Evaluate side-chains
  319 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 303
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  178 GLU
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  489 LYS
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  694 THR
Chi-restraints excluded: chain A residue  718 GLU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  844 GLN
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  938 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 26 optimal weight:    8.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 GLN
A 509 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.147335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.120704 restraints weight = 12999.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.49
r_work: 0.3433 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   8970  Z= 0.203
  Angle     :  0.636   9.573  12274  Z= 0.339
  Chirality :  0.045   0.205   1332
  Planarity :  0.005   0.041   1448
  Dihedral  : 18.680 136.252   1460
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.28 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.20 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.80 (0.27), residues: 975
  helix:  1.68 (0.24), residues: 444
  sheet:  0.22 (0.39), residues: 156
  loop : -0.71 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  99 
 TYR   0.020   0.002   TYR A 405 
 PHE   0.033   0.003   PHE A  72 
 TRP   0.014   0.002   TRP A 325 
 HIS   0.004   0.001   HIS A 722 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00454 /  0.20 ( 8970)
  covalent geometry    : angle       0.63598 /  0.34 (12274)
  hydrogen bonds       : bond        0.05474 /  3.50 (  452)
  hydrogen bonds       : angle       4.24668 /  3.00 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 327
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A    5 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6845 (ttp)
REVERT: A   27 GLN cc_start: 0.8641 (tp40) cc_final: 0.8337 (tp-100)
REVERT: A   41 GLU cc_start: 0.8063 (pt0) cc_final: 0.7676 (pt0)
REVERT: A   54 SER cc_start: 0.8407 (m) cc_final: 0.8038 (t)
REVERT: A   56 GLU cc_start: 0.7639 (pt0) cc_final: 0.7176 (pt0)
REVERT: A   59 TYR cc_start: 0.8325 (m-10) cc_final: 0.7860 (m-80)
REVERT: A   62 GLU cc_start: 0.7606 (tt0) cc_final: 0.7397 (tt0)
REVERT: A   75 GLN cc_start: 0.8503 (tm-30) cc_final: 0.7840 (tm-30)
REVERT: A   85 PHE cc_start: 0.8954 (t80) cc_final: 0.8536 (t80)
REVERT: A  127 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8104 (ttmm)
REVERT: A  134 LYS cc_start: 0.8193 (mmmm) cc_final: 0.7915 (mmmm)
REVERT: A  142 MET cc_start: 0.8019 (mmm) cc_final: 0.7716 (tmm)
REVERT: A  149 ASP cc_start: 0.7598 (p0) cc_final: 0.6968 (p0)
REVERT: A  180 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7356 (mtm110)
REVERT: A  191 GLU cc_start: 0.7743 (mp0) cc_final: 0.7460 (mp0)
REVERT: A  260 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8172 (mmmt)
REVERT: A  285 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8042 (mmm-85)
REVERT: A  307 LYS cc_start: 0.8415 (mmtt) cc_final: 0.7756 (mmmt)
REVERT: A  320 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8247 (ttpp)
REVERT: A  334 LYS cc_start: 0.8452 (tppp) cc_final: 0.8050 (tppp)
REVERT: A  349 LYS cc_start: 0.8378 (tttt) cc_final: 0.8123 (tttm)
REVERT: A  376 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8092 (mmtm)
REVERT: A  399 TYR cc_start: 0.7935 (m-80) cc_final: 0.7051 (m-80)
REVERT: A  404 LYS cc_start: 0.8229 (tttm) cc_final: 0.7947 (tttm)
REVERT: A  424 ASP cc_start: 0.8111 (t0) cc_final: 0.7675 (t0)
REVERT: A  475 ASP cc_start: 0.7251 (t0) cc_final: 0.7013 (t0)
REVERT: A  476 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7332 (tm-30)
REVERT: A  484 THR cc_start: 0.7881 (m) cc_final: 0.7578 (p)
REVERT: A  511 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7967 (ptpp)
REVERT: A  513 THR cc_start: 0.7842 (t) cc_final: 0.7608 (p)
REVERT: A  549 LYS cc_start: 0.8561 (ptmt) cc_final: 0.8249 (ptmt)
REVERT: A  579 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7609 (ttm)
REVERT: A  597 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7722 (tppp)
REVERT: A  630 LYS cc_start: 0.8357 (mttt) cc_final: 0.8083 (mttp)
REVERT: A  632 LYS cc_start: 0.8232 (tptt) cc_final: 0.7786 (ttmm)
REVERT: A  635 LYS cc_start: 0.8434 (tttt) cc_final: 0.7868 (ttmm)
REVERT: A  636 ILE cc_start: 0.8479 (tt) cc_final: 0.8093 (tp)
REVERT: A  644 GLU cc_start: 0.7477 (tp30) cc_final: 0.7056 (tp30)
REVERT: A  647 ASN cc_start: 0.8312 (t0) cc_final: 0.8013 (t0)
REVERT: A  687 ASP cc_start: 0.7371 (t0) cc_final: 0.7024 (t0)
REVERT: A  721 CYS cc_start: 0.7791 (m) cc_final: 0.7328 (m)
REVERT: A  747 ASN cc_start: 0.8116 (p0) cc_final: 0.7841 (p0)
REVERT: A  778 ASN cc_start: 0.8727 (m-40) cc_final: 0.8347 (m-40)
REVERT: A  810 ILE cc_start: 0.8720 (mt) cc_final: 0.8415 (tp)
REVERT: A  816 LYS cc_start: 0.8465 (ptpp) cc_final: 0.8246 (ptpp)
REVERT: A  846 ASN cc_start: 0.7751 (p0) cc_final: 0.7425 (p0)
REVERT: A  863 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7509 (mmmm)
REVERT: A  900 TYR cc_start: 0.8004 (p90) cc_final: 0.7261 (p90)
REVERT: A  924 LYS cc_start: 0.7977 (mttp) cc_final: 0.7317 (mttm)
REVERT: A  946 ASN cc_start: 0.8488 (m110) cc_final: 0.7969 (m110)
REVERT: A  947 TYR cc_start: 0.8323 (m-80) cc_final: 0.8115 (m-80)
  outliers start: 28
  outliers final: 15
  residues processed: 333
  average time/residue: 0.1136
  time to fit residues: 49.4845
Evaluate side-chains
  347 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 330
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  694 THR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  836 LYS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  938 ILE
Chi-restraints excluded: chain A residue  958 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0770
   chunk 50 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 82 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.7740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.148642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.122499 restraints weight = 12940.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.44
r_work: 0.3422 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8970  Z= 0.142
  Angle     :  0.590  10.470  12274  Z= 0.312
  Chirality :  0.043   0.214   1332
  Planarity :  0.005   0.046   1448
  Dihedral  : 18.639 134.876   1460
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.05 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.84 (0.27), residues: 975
  helix:  1.76 (0.24), residues: 444
  sheet:  0.07 (0.37), residues: 164
  loop : -0.66 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  99 
 TYR   0.017   0.001   TYR A 138 
 PHE   0.027   0.002   PHE A 986 
 TRP   0.012   0.001   TRP A 325 
 HIS   0.005   0.001   HIS A 474 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 ( 8970)
  covalent geometry    : angle       0.59003 /  0.31 (12274)
  hydrogen bonds       : bond        0.04868 /  3.10 (  452)
  hydrogen bonds       : angle       4.14356 /  2.94 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 325
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.5260 (ttt)
REVERT: A    9 GLU cc_start: 0.7581 (tt0) cc_final: 0.6773 (tt0)
REVERT: A   27 GLN cc_start: 0.8644 (tp40) cc_final: 0.8376 (tp-100)
REVERT: A   41 GLU cc_start: 0.8103 (pt0) cc_final: 0.7651 (pt0)
REVERT: A   54 SER cc_start: 0.8386 (m) cc_final: 0.8017 (t)
REVERT: A   56 GLU cc_start: 0.7636 (pt0) cc_final: 0.7137 (pt0)
REVERT: A   59 TYR cc_start: 0.8280 (m-10) cc_final: 0.8025 (m-80)
REVERT: A   62 GLU cc_start: 0.7675 (tt0) cc_final: 0.7468 (tt0)
REVERT: A   75 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: A   85 PHE cc_start: 0.8980 (t80) cc_final: 0.8565 (t80)
REVERT: A  127 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8149 (ttmm)
REVERT: A  134 LYS cc_start: 0.8154 (mmmm) cc_final: 0.7876 (mmmm)
REVERT: A  142 MET cc_start: 0.8041 (mmm) cc_final: 0.7736 (tmm)
REVERT: A  149 ASP cc_start: 0.7634 (p0) cc_final: 0.7013 (p0)
REVERT: A  180 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7327 (mtm110)
REVERT: A  191 GLU cc_start: 0.7759 (mp0) cc_final: 0.7450 (mp0)
REVERT: A  211 ASP cc_start: 0.7664 (t70) cc_final: 0.7237 (t70)
REVERT: A  285 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.7972 (mmm-85)
REVERT: A  307 LYS cc_start: 0.8471 (mmtt) cc_final: 0.7774 (mmmt)
REVERT: A  320 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8463 (ttmm)
REVERT: A  334 LYS cc_start: 0.8516 (tppp) cc_final: 0.8094 (tppp)
REVERT: A  349 LYS cc_start: 0.8356 (tttt) cc_final: 0.8130 (tttm)
REVERT: A  365 ASP cc_start: 0.6950 (t0) cc_final: 0.6731 (t0)
REVERT: A  369 MET cc_start: 0.8039 (mmp) cc_final: 0.7758 (mmt)
REVERT: A  376 LYS cc_start: 0.8325 (mmtt) cc_final: 0.8050 (mmtm)
REVERT: A  395 VAL cc_start: 0.7528 (m) cc_final: 0.7174 (p)
REVERT: A  399 TYR cc_start: 0.7966 (m-80) cc_final: 0.6972 (m-80)
REVERT: A  404 LYS cc_start: 0.8230 (tttm) cc_final: 0.7965 (tttm)
REVERT: A  424 ASP cc_start: 0.8184 (t0) cc_final: 0.7725 (t0)
REVERT: A  434 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7983 (tpt90)
REVERT: A  476 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7235 (tm-30)
REVERT: A  484 THR cc_start: 0.7733 (m) cc_final: 0.7447 (p)
REVERT: A  511 LYS cc_start: 0.8391 (ptpp) cc_final: 0.8084 (ptpt)
REVERT: A  513 THR cc_start: 0.7858 (t) cc_final: 0.7635 (p)
REVERT: A  579 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7578 (ttm)
REVERT: A  597 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7737 (tppp)
REVERT: A  630 LYS cc_start: 0.8320 (mttt) cc_final: 0.8055 (mttp)
REVERT: A  632 LYS cc_start: 0.8217 (tptt) cc_final: 0.7728 (ttmm)
REVERT: A  636 ILE cc_start: 0.8437 (tt) cc_final: 0.7964 (tp)
REVERT: A  644 GLU cc_start: 0.7457 (tp30) cc_final: 0.7086 (tp30)
REVERT: A  647 ASN cc_start: 0.8255 (t0) cc_final: 0.7929 (t0)
REVERT: A  676 VAL cc_start: 0.8404 (t) cc_final: 0.8080 (m)
REVERT: A  687 ASP cc_start: 0.7464 (t0) cc_final: 0.7113 (t0)
REVERT: A  690 SER cc_start: 0.8233 (t) cc_final: 0.7812 (m)
REVERT: A  721 CYS cc_start: 0.7837 (m) cc_final: 0.7351 (m)
REVERT: A  744 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7890 (tmm-80)
REVERT: A  747 ASN cc_start: 0.8090 (p0) cc_final: 0.7870 (p0)
REVERT: A  778 ASN cc_start: 0.8841 (m-40) cc_final: 0.8388 (m-40)
REVERT: A  804 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7924 (mmtt)
REVERT: A  810 ILE cc_start: 0.8625 (mt) cc_final: 0.8292 (tp)
REVERT: A  819 ARG cc_start: 0.6521 (ttm-80) cc_final: 0.6223 (ttm-80)
REVERT: A  863 LYS cc_start: 0.8022 (mmmm) cc_final: 0.7623 (mmmm)
REVERT: A  900 TYR cc_start: 0.7935 (p90) cc_final: 0.7216 (p90)
REVERT: A  924 LYS cc_start: 0.8007 (mttp) cc_final: 0.7350 (mttm)
REVERT: A  925 MET cc_start: 0.7621 (mmm) cc_final: 0.7048 (mmm)
REVERT: A  932 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8279 (mtmm)
REVERT: A  946 ASN cc_start: 0.8483 (m110) cc_final: 0.7900 (m110)
REVERT: A  947 TYR cc_start: 0.8239 (m-80) cc_final: 0.8023 (m-10)
  outliers start: 23
  outliers final: 15
  residues processed: 332
  average time/residue: 0.1045
  time to fit residues: 45.6161
Evaluate side-chains
  339 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 322
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  178 GLU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  694 THR
Chi-restraints excluded: chain A residue  712 LYS
Chi-restraints excluded: chain A residue  718 GLU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  836 LYS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  938 ILE
Chi-restraints excluded: chain A residue  958 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0980
   chunk 75 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 105 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.148259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.122182 restraints weight = 12870.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.43
r_work: 0.3431 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8970  Z= 0.137
  Angle     :  0.576  10.851  12274  Z= 0.304
  Chirality :  0.043   0.212   1332
  Planarity :  0.004   0.047   1448
  Dihedral  : 18.575 135.352   1460
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.27 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.96 (0.27), residues: 975
  helix:  1.91 (0.25), residues: 444
  sheet:  0.07 (0.38), residues: 164
  loop : -0.66 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 593 
 TYR   0.018   0.001   TYR A 138 
 PHE   0.035   0.002   PHE A 294 
 TRP   0.009   0.001   TRP A 325 
 HIS   0.004   0.001   HIS A 722 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 ( 8970)
  covalent geometry    : angle       0.57616 /  0.30 (12274)
  hydrogen bonds       : bond        0.04652 /  2.98 (  452)
  hydrogen bonds       : angle       4.09277 /  2.90 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 328
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.5694 (ttp)
REVERT: A    9 GLU cc_start: 0.7578 (tt0) cc_final: 0.7133 (tt0)
REVERT: A   27 GLN cc_start: 0.8615 (tp40) cc_final: 0.8346 (tp-100)
REVERT: A   41 GLU cc_start: 0.8049 (pt0) cc_final: 0.7626 (pt0)
REVERT: A   54 SER cc_start: 0.8397 (m) cc_final: 0.8008 (t)
REVERT: A   56 GLU cc_start: 0.7636 (pt0) cc_final: 0.7127 (pt0)
REVERT: A   75 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8030 (tm-30)
REVERT: A   85 PHE cc_start: 0.8977 (t80) cc_final: 0.8584 (t80)
REVERT: A  126 PHE cc_start: 0.8296 (m-10) cc_final: 0.8036 (m-10)
REVERT: A  127 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8141 (ttmm)
REVERT: A  134 LYS cc_start: 0.8177 (mmmm) cc_final: 0.7893 (mmmm)
REVERT: A  142 MET cc_start: 0.8026 (mmm) cc_final: 0.7707 (tmm)
REVERT: A  149 ASP cc_start: 0.7606 (p0) cc_final: 0.7152 (p0)
REVERT: A  163 LYS cc_start: 0.8491 (tptt) cc_final: 0.8119 (tptt)
REVERT: A  180 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7267 (mtm110)
REVERT: A  191 GLU cc_start: 0.7748 (mp0) cc_final: 0.7422 (mp0)
REVERT: A  211 ASP cc_start: 0.7664 (t70) cc_final: 0.7257 (t70)
REVERT: A  285 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7928 (mmm-85)
REVERT: A  307 LYS cc_start: 0.8539 (mmtt) cc_final: 0.7893 (mmmt)
REVERT: A  334 LYS cc_start: 0.8508 (tppp) cc_final: 0.8075 (tppp)
REVERT: A  349 LYS cc_start: 0.8329 (tttt) cc_final: 0.8116 (tttm)
REVERT: A  376 LYS cc_start: 0.8325 (mmtt) cc_final: 0.8058 (mmtm)
REVERT: A  387 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7681 (mm-30)
REVERT: A  395 VAL cc_start: 0.7572 (m) cc_final: 0.7224 (p)
REVERT: A  399 TYR cc_start: 0.7976 (m-80) cc_final: 0.7062 (m-80)
REVERT: A  404 LYS cc_start: 0.8257 (tttm) cc_final: 0.7994 (tttm)
REVERT: A  424 ASP cc_start: 0.8186 (t0) cc_final: 0.7743 (t0)
REVERT: A  434 ARG cc_start: 0.8275 (mmm160) cc_final: 0.8007 (tpt90)
REVERT: A  476 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7209 (tm-30)
REVERT: A  511 LYS cc_start: 0.8608 (ptpp) cc_final: 0.7854 (ptpp)
REVERT: A  547 MET cc_start: 0.7963 (tpp) cc_final: 0.7752 (tpp)
REVERT: A  579 MET cc_start: 0.7931 (ttm) cc_final: 0.7606 (ttm)
REVERT: A  597 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7746 (tppp)
REVERT: A  630 LYS cc_start: 0.8358 (mttt) cc_final: 0.8078 (mttp)
REVERT: A  632 LYS cc_start: 0.8225 (tptt) cc_final: 0.7741 (ttmm)
REVERT: A  635 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7810 (ttmm)
REVERT: A  636 ILE cc_start: 0.8433 (tt) cc_final: 0.8063 (tp)
REVERT: A  644 GLU cc_start: 0.7547 (tp30) cc_final: 0.6920 (tp30)
REVERT: A  647 ASN cc_start: 0.8302 (t0) cc_final: 0.7966 (t0)
REVERT: A  676 VAL cc_start: 0.8408 (t) cc_final: 0.8099 (m)
REVERT: A  687 ASP cc_start: 0.7504 (t0) cc_final: 0.7230 (t0)
REVERT: A  690 SER cc_start: 0.8236 (t) cc_final: 0.7857 (m)
REVERT: A  721 CYS cc_start: 0.7897 (m) cc_final: 0.7396 (m)
REVERT: A  778 ASN cc_start: 0.8832 (m-40) cc_final: 0.8390 (m-40)
REVERT: A  793 ASP cc_start: 0.7672 (t0) cc_final: 0.7332 (t0)
REVERT: A  804 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7932 (mmtt)
REVERT: A  810 ILE cc_start: 0.8668 (mt) cc_final: 0.8375 (tp)
REVERT: A  819 ARG cc_start: 0.6574 (ttm-80) cc_final: 0.6138 (ttm110)
REVERT: A  842 MET cc_start: 0.7621 (ttt) cc_final: 0.7295 (tpp)
REVERT: A  863 LYS cc_start: 0.8071 (mmmm) cc_final: 0.7735 (mmmm)
REVERT: A  893 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6805 (mm-30)
REVERT: A  900 TYR cc_start: 0.7982 (p90) cc_final: 0.7215 (p90)
REVERT: A  924 LYS cc_start: 0.7912 (mttp) cc_final: 0.7275 (mttm)
REVERT: A  932 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8275 (mtmm)
REVERT: A  946 ASN cc_start: 0.8521 (m110) cc_final: 0.7897 (m110)
REVERT: A  947 TYR cc_start: 0.8254 (m-80) cc_final: 0.8035 (m-10)
  outliers start: 21
  outliers final: 17
  residues processed: 333
  average time/residue: 0.1102
  time to fit residues: 47.8927
Evaluate side-chains
  339 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 320
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue  105 GLN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  694 THR
Chi-restraints excluded: chain A residue  718 GLU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  836 LYS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  938 ILE
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  958 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0770
   chunk 84 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 105 GLN
A 204 HIS
A 945 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.148337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.122029 restraints weight = 12932.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.43
r_work: 0.3442 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8970  Z= 0.126
  Angle     :  0.578  10.869  12274  Z= 0.303
  Chirality :  0.043   0.222   1332
  Planarity :  0.004   0.045   1448
  Dihedral  : 18.515 135.149   1460
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 22.53 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.99 (0.27), residues: 975
  helix:  1.96 (0.25), residues: 443
  sheet: -0.04 (0.37), residues: 169
  loop : -0.59 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  13 
 TYR   0.019   0.001   TYR A  59 
 PHE   0.024   0.002   PHE A 986 
 TRP   0.008   0.001   TRP A 325 
 HIS   0.005   0.001   HIS A 722 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.13 ( 8970)
  covalent geometry    : angle       0.57843 /  0.30 (12274)
  hydrogen bonds       : bond        0.04445 /  2.84 (  452)
  hydrogen bonds       : angle       4.07579 /  2.89 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 327
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.5553 (ttp)
REVERT: A    9 GLU cc_start: 0.7610 (tt0) cc_final: 0.7156 (tt0)
REVERT: A   27 GLN cc_start: 0.8610 (tp40) cc_final: 0.8335 (tp-100)
REVERT: A   41 GLU cc_start: 0.8007 (pt0) cc_final: 0.7606 (pt0)
REVERT: A   54 SER cc_start: 0.8386 (m) cc_final: 0.8003 (t)
REVERT: A   59 TYR cc_start: 0.8206 (m-80) cc_final: 0.7796 (m-80)
REVERT: A   62 GLU cc_start: 0.7700 (tt0) cc_final: 0.6704 (tt0)
REVERT: A   75 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: A   85 PHE cc_start: 0.8973 (t80) cc_final: 0.8598 (t80)
REVERT: A  126 PHE cc_start: 0.8299 (m-10) cc_final: 0.8026 (m-10)
REVERT: A  127 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8171 (ttmm)
REVERT: A  134 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7875 (mmmm)
REVERT: A  142 MET cc_start: 0.8015 (mmm) cc_final: 0.7691 (tmm)
REVERT: A  149 ASP cc_start: 0.7615 (p0) cc_final: 0.7165 (p0)
REVERT: A  163 LYS cc_start: 0.8488 (tptt) cc_final: 0.8080 (tptt)
REVERT: A  180 ARG cc_start: 0.7803 (mtm110) cc_final: 0.5762 (mtm110)
REVERT: A  191 GLU cc_start: 0.7758 (mp0) cc_final: 0.7437 (mp0)
REVERT: A  211 ASP cc_start: 0.7636 (t70) cc_final: 0.7244 (t70)
REVERT: A  285 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.7881 (mmm-85)
REVERT: A  307 LYS cc_start: 0.8507 (mmtt) cc_final: 0.7889 (mmmt)
REVERT: A  321 MET cc_start: 0.8316 (ttp) cc_final: 0.8089 (ttm)
REVERT: A  334 LYS cc_start: 0.8483 (tppp) cc_final: 0.8055 (tppp)
REVERT: A  349 LYS cc_start: 0.8311 (tttt) cc_final: 0.8103 (tttm)
REVERT: A  369 MET cc_start: 0.7914 (mmp) cc_final: 0.7664 (mmt)
REVERT: A  376 LYS cc_start: 0.8326 (mmtt) cc_final: 0.8058 (mmtm)
REVERT: A  387 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7641 (mm-30)
REVERT: A  395 VAL cc_start: 0.7584 (m) cc_final: 0.7250 (p)
REVERT: A  399 TYR cc_start: 0.8021 (m-80) cc_final: 0.7050 (m-80)
REVERT: A  404 LYS cc_start: 0.8272 (tttm) cc_final: 0.8008 (tttm)
REVERT: A  424 ASP cc_start: 0.8138 (t0) cc_final: 0.7699 (t0)
REVERT: A  433 VAL cc_start: 0.8438 (t) cc_final: 0.8230 (p)
REVERT: A  434 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7950 (tpt90)
REVERT: A  476 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7205 (tm-30)
REVERT: A  511 LYS cc_start: 0.8592 (ptpp) cc_final: 0.8330 (ptpp)
REVERT: A  547 MET cc_start: 0.7965 (tpp) cc_final: 0.7750 (tpp)
REVERT: A  579 MET cc_start: 0.7952 (ttm) cc_final: 0.7508 (mtp)
REVERT: A  597 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7725 (tppp)
REVERT: A  630 LYS cc_start: 0.8364 (mttt) cc_final: 0.8087 (mttp)
REVERT: A  632 LYS cc_start: 0.8237 (tptt) cc_final: 0.7747 (ttmm)
REVERT: A  636 ILE cc_start: 0.8449 (tt) cc_final: 0.8089 (tp)
REVERT: A  644 GLU cc_start: 0.7575 (tp30) cc_final: 0.6980 (tp30)
REVERT: A  647 ASN cc_start: 0.8299 (t0) cc_final: 0.7961 (t0)
REVERT: A  676 VAL cc_start: 0.8410 (t) cc_final: 0.8098 (m)
REVERT: A  687 ASP cc_start: 0.7530 (t0) cc_final: 0.7295 (t0)
REVERT: A  690 SER cc_start: 0.8239 (t) cc_final: 0.7788 (m)
REVERT: A  715 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7901 (mmtm)
REVERT: A  721 CYS cc_start: 0.7865 (m) cc_final: 0.7400 (m)
REVERT: A  738 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8315 (tt0)
REVERT: A  747 ASN cc_start: 0.8106 (p0) cc_final: 0.7794 (p0)
REVERT: A  778 ASN cc_start: 0.8828 (m-40) cc_final: 0.8407 (m-40)
REVERT: A  793 ASP cc_start: 0.7695 (t0) cc_final: 0.7355 (t0)
REVERT: A  804 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7899 (mmtt)
REVERT: A  810 ILE cc_start: 0.8670 (mt) cc_final: 0.8356 (tp)
REVERT: A  819 ARG cc_start: 0.6615 (ttm-80) cc_final: 0.6179 (ttm110)
REVERT: A  828 ILE cc_start: 0.8353 (pt) cc_final: 0.8003 (mt)
REVERT: A  842 MET cc_start: 0.7614 (ttt) cc_final: 0.7304 (tpp)
REVERT: A  900 TYR cc_start: 0.7870 (p90) cc_final: 0.7253 (p90)
REVERT: A  924 LYS cc_start: 0.7907 (mttp) cc_final: 0.7372 (mttm)
REVERT: A  932 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8260 (mtmm)
REVERT: A  946 ASN cc_start: 0.8530 (m110) cc_final: 0.7889 (m110)
  outliers start: 20
  outliers final: 15
  residues processed: 330
  average time/residue: 0.1184
  time to fit residues: 50.9934
Evaluate side-chains
  340 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 324
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  694 THR
Chi-restraints excluded: chain A residue  712 LYS
Chi-restraints excluded: chain A residue  718 GLU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  836 LYS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  938 ILE
Chi-restraints excluded: chain A residue  958 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0870
   chunk 62 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0980
   chunk 94 optimal weight:    0.3980
   chunk 93 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.3758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 945 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.149029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.122851 restraints weight = 12869.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.41
r_work: 0.3451 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8970  Z= 0.120
  Angle     :  0.574  10.964  12274  Z= 0.303
  Chirality :  0.042   0.225   1332
  Planarity :  0.005   0.071   1448
  Dihedral  : 18.419 135.281   1460
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 22.64 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  1.03 (0.27), residues: 975
  helix:  2.01 (0.25), residues: 442
  sheet: -0.09 (0.38), residues: 167
  loop : -0.55 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 180 
 TYR   0.019   0.001   TYR A 138 
 PHE   0.026   0.002   PHE A 986 
 TRP   0.008   0.001   TRP A 845 
 HIS   0.005   0.001   HIS A 722 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 8970)
  covalent geometry    : angle       0.57373 /  0.30 (12274)
  hydrogen bonds       : bond        0.04258 /  2.72 (  452)
  hydrogen bonds       : angle       4.05071 /  2.88 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 327
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.5212 (ttp)
REVERT: A    9 GLU cc_start: 0.7582 (tt0) cc_final: 0.7115 (tt0)
REVERT: A   27 GLN cc_start: 0.8601 (tp40) cc_final: 0.8282 (tp-100)
REVERT: A   41 GLU cc_start: 0.7993 (pt0) cc_final: 0.7583 (pt0)
REVERT: A   54 SER cc_start: 0.8367 (m) cc_final: 0.7960 (p)
REVERT: A   59 TYR cc_start: 0.8165 (m-80) cc_final: 0.7765 (m-80)
REVERT: A   75 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8017 (tm-30)
REVERT: A   85 PHE cc_start: 0.8963 (t80) cc_final: 0.8579 (t80)
REVERT: A  126 PHE cc_start: 0.8299 (m-10) cc_final: 0.8076 (m-10)
REVERT: A  127 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8160 (ttmm)
REVERT: A  134 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7855 (mmmm)
REVERT: A  142 MET cc_start: 0.8001 (mmm) cc_final: 0.7663 (tmm)
REVERT: A  149 ASP cc_start: 0.7592 (p0) cc_final: 0.7171 (p0)
REVERT: A  163 LYS cc_start: 0.8481 (tptt) cc_final: 0.8085 (tptt)
REVERT: A  191 GLU cc_start: 0.7754 (mp0) cc_final: 0.7433 (mp0)
REVERT: A  255 MET cc_start: 0.8198 (mmt) cc_final: 0.7843 (mmt)
REVERT: A  277 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8138 (mm)
REVERT: A  285 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.7872 (mmm-85)
REVERT: A  307 LYS cc_start: 0.8484 (mmtt) cc_final: 0.7905 (mmmt)
REVERT: A  334 LYS cc_start: 0.8482 (tppp) cc_final: 0.8055 (tppp)
REVERT: A  349 LYS cc_start: 0.8287 (tttt) cc_final: 0.8064 (mttm)
REVERT: A  369 MET cc_start: 0.7908 (mmp) cc_final: 0.7651 (mmt)
REVERT: A  376 LYS cc_start: 0.8315 (mmtt) cc_final: 0.8045 (mmtm)
REVERT: A  387 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7638 (mm-30)
REVERT: A  395 VAL cc_start: 0.7569 (m) cc_final: 0.7217 (p)
REVERT: A  399 TYR cc_start: 0.8009 (m-80) cc_final: 0.7020 (m-80)
REVERT: A  404 LYS cc_start: 0.8276 (tttm) cc_final: 0.7995 (tttm)
REVERT: A  424 ASP cc_start: 0.8123 (t0) cc_final: 0.7705 (t0)
REVERT: A  433 VAL cc_start: 0.8429 (t) cc_final: 0.8227 (p)
REVERT: A  434 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7940 (tpt90)
REVERT: A  476 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7199 (tm-30)
REVERT: A  511 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8110 (ptpp)
REVERT: A  547 MET cc_start: 0.7954 (tpp) cc_final: 0.7733 (tpp)
REVERT: A  579 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7559 (ttm)
REVERT: A  593 ARG cc_start: 0.8277 (ttt90) cc_final: 0.7875 (ttt90)
REVERT: A  597 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7739 (tppp)
REVERT: A  630 LYS cc_start: 0.8359 (mttt) cc_final: 0.8048 (mttp)
REVERT: A  632 LYS cc_start: 0.8237 (tptt) cc_final: 0.7739 (ttmm)
REVERT: A  635 LYS cc_start: 0.8348 (ttpp) cc_final: 0.7777 (ttmm)
REVERT: A  636 ILE cc_start: 0.8400 (tt) cc_final: 0.8063 (tp)
REVERT: A  644 GLU cc_start: 0.7588 (tp30) cc_final: 0.7043 (tp30)
REVERT: A  647 ASN cc_start: 0.8323 (t0) cc_final: 0.8006 (t0)
REVERT: A  676 VAL cc_start: 0.8379 (t) cc_final: 0.8131 (m)
REVERT: A  679 LYS cc_start: 0.8696 (tptt) cc_final: 0.8460 (tptt)
REVERT: A  687 ASP cc_start: 0.7549 (t0) cc_final: 0.7323 (t0)
REVERT: A  690 SER cc_start: 0.8192 (t) cc_final: 0.7758 (m)
REVERT: A  693 ILE cc_start: 0.8440 (mm) cc_final: 0.8208 (mm)
REVERT: A  711 GLN cc_start: 0.8138 (tp40) cc_final: 0.7733 (tp40)
REVERT: A  715 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7842 (mmtm)
REVERT: A  721 CYS cc_start: 0.7880 (m) cc_final: 0.7433 (m)
REVERT: A  738 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8196 (tt0)
REVERT: A  747 ASN cc_start: 0.8163 (p0) cc_final: 0.7820 (p0)
REVERT: A  778 ASN cc_start: 0.8834 (m-40) cc_final: 0.8393 (m-40)
REVERT: A  793 ASP cc_start: 0.7697 (t0) cc_final: 0.7355 (t0)
REVERT: A  804 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7886 (mmtt)
REVERT: A  819 ARG cc_start: 0.6605 (ttm-80) cc_final: 0.6161 (ttm110)
REVERT: A  828 ILE cc_start: 0.8366 (pt) cc_final: 0.8033 (mt)
REVERT: A  842 MET cc_start: 0.7508 (ttt) cc_final: 0.7265 (tpp)
REVERT: A  897 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7834 (ttm-80)
REVERT: A  900 TYR cc_start: 0.7853 (p90) cc_final: 0.7187 (p90)
REVERT: A  924 LYS cc_start: 0.7888 (mttp) cc_final: 0.7316 (mttm)
REVERT: A  927 TYR cc_start: 0.8761 (m-10) cc_final: 0.8519 (m-10)
REVERT: A  946 ASN cc_start: 0.8372 (m110) cc_final: 0.8005 (m110)
  outliers start: 22
  outliers final: 14
  residues processed: 331
  average time/residue: 0.1146
  time to fit residues: 49.7399
Evaluate side-chains
  336 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 319
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  494 LYS
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  694 THR
Chi-restraints excluded: chain A residue  712 LYS
Chi-restraints excluded: chain A residue  718 GLU
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  836 LYS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  958 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.147212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.120460 restraints weight = 12839.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.46
r_work: 0.3418 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.4461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8970  Z= 0.155
  Angle     :  0.600  10.982  12274  Z= 0.314
  Chirality :  0.043   0.227   1332
  Planarity :  0.005   0.097   1448
  Dihedral  : 18.328 135.487   1458
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 23.89 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  1.08 (0.27), residues: 975
  helix:  2.05 (0.25), residues: 442
  sheet:  0.08 (0.39), residues: 159
  loop : -0.60 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 593 
 TYR   0.018   0.001   TYR A 138 
 PHE   0.026   0.002   PHE A 986 
 TRP   0.006   0.001   TRP A 169 
 HIS   0.005   0.001   HIS A 722 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 8970)
  covalent geometry    : angle       0.60030 /  0.31 (12274)
  hydrogen bonds       : bond        0.04401 /  2.83 (  452)
  hydrogen bonds       : angle       4.09800 /  2.92 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 329
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.5470 (ttp)
REVERT: A    9 GLU cc_start: 0.7621 (tt0) cc_final: 0.7189 (tt0)
REVERT: A   27 GLN cc_start: 0.8599 (tp40) cc_final: 0.8224 (tp-100)
REVERT: A   41 GLU cc_start: 0.7930 (pt0) cc_final: 0.7527 (pt0)
REVERT: A   54 SER cc_start: 0.8463 (m) cc_final: 0.8052 (p)
REVERT: A   56 GLU cc_start: 0.7602 (pt0) cc_final: 0.7094 (pt0)
REVERT: A   75 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8047 (tm-30)
REVERT: A   85 PHE cc_start: 0.9007 (t80) cc_final: 0.8633 (t80)
REVERT: A  127 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8172 (ttmm)
REVERT: A  134 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7882 (mmmm)
REVERT: A  142 MET cc_start: 0.8063 (mmm) cc_final: 0.7740 (tmm)
REVERT: A  149 ASP cc_start: 0.7594 (p0) cc_final: 0.7164 (p0)
REVERT: A  163 LYS cc_start: 0.8539 (tptt) cc_final: 0.8154 (tptt)
REVERT: A  174 HIS cc_start: 0.7500 (t-90) cc_final: 0.7192 (t-90)
REVERT: A  191 GLU cc_start: 0.7785 (mp0) cc_final: 0.7444 (mp0)
REVERT: A  277 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8141 (mm)
REVERT: A  285 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.7891 (mmm-85)
REVERT: A  307 LYS cc_start: 0.8505 (mmtt) cc_final: 0.7882 (mmmt)
REVERT: A  334 LYS cc_start: 0.8523 (tppp) cc_final: 0.8112 (tppp)
REVERT: A  349 LYS cc_start: 0.8334 (tttt) cc_final: 0.8133 (tttm)
REVERT: A  376 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8060 (mmtm)
REVERT: A  387 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7665 (mm-30)
REVERT: A  395 VAL cc_start: 0.7683 (m) cc_final: 0.7342 (p)
REVERT: A  399 TYR cc_start: 0.8031 (m-80) cc_final: 0.7041 (m-80)
REVERT: A  404 LYS cc_start: 0.8310 (tttm) cc_final: 0.8038 (tttm)
REVERT: A  424 ASP cc_start: 0.8201 (t0) cc_final: 0.7703 (t0)
REVERT: A  433 VAL cc_start: 0.8441 (t) cc_final: 0.8240 (p)
REVERT: A  434 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7969 (tpt90)
REVERT: A  467 MET cc_start: 0.8116 (ttp) cc_final: 0.7715 (ttm)
REVERT: A  476 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7221 (tm-30)
REVERT: A  511 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8168 (ptpp)
REVERT: A  547 MET cc_start: 0.7998 (tpp) cc_final: 0.7768 (tpp)
REVERT: A  558 PHE cc_start: 0.7805 (p90) cc_final: 0.7582 (p90)
REVERT: A  579 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7505 (mtp)
REVERT: A  630 LYS cc_start: 0.8374 (mttt) cc_final: 0.8068 (mttp)
REVERT: A  632 LYS cc_start: 0.8276 (tptt) cc_final: 0.7772 (ttmm)
REVERT: A  635 LYS cc_start: 0.8374 (ttpp) cc_final: 0.7812 (ttmm)
REVERT: A  636 ILE cc_start: 0.8467 (tt) cc_final: 0.8113 (tp)
REVERT: A  644 GLU cc_start: 0.7606 (tp30) cc_final: 0.7078 (tp30)
REVERT: A  647 ASN cc_start: 0.8348 (t0) cc_final: 0.8008 (t0)
REVERT: A  676 VAL cc_start: 0.8389 (t) cc_final: 0.8125 (m)
REVERT: A  679 LYS cc_start: 0.8751 (tptt) cc_final: 0.8494 (tptt)
REVERT: A  687 ASP cc_start: 0.7522 (t0) cc_final: 0.7304 (t0)
REVERT: A  690 SER cc_start: 0.8196 (t) cc_final: 0.7804 (m)
REVERT: A  711 GLN cc_start: 0.8218 (tp40) cc_final: 0.7777 (tp40)
REVERT: A  721 CYS cc_start: 0.8017 (m) cc_final: 0.7493 (m)
REVERT: A  738 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8170 (tt0)
REVERT: A  747 ASN cc_start: 0.8176 (p0) cc_final: 0.7854 (p0)
REVERT: A  770 LYS cc_start: 0.7902 (mttp) cc_final: 0.7682 (mttp)
REVERT: A  778 ASN cc_start: 0.8851 (m-40) cc_final: 0.8429 (m-40)
REVERT: A  793 ASP cc_start: 0.7741 (t0) cc_final: 0.7399 (t0)
REVERT: A  804 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7909 (mmtt)
REVERT: A  819 ARG cc_start: 0.6822 (ttm-80) cc_final: 0.6354 (ttm110)
REVERT: A  828 ILE cc_start: 0.8490 (pt) cc_final: 0.8205 (mt)
REVERT: A  842 MET cc_start: 0.7618 (ttt) cc_final: 0.7326 (tpp)
REVERT: A  897 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7851 (ttm-80)
REVERT: A  900 TYR cc_start: 0.7859 (p90) cc_final: 0.7210 (p90)
REVERT: A  924 LYS cc_start: 0.7916 (mttp) cc_final: 0.7326 (mttm)
REVERT: A  927 TYR cc_start: 0.8750 (m-10) cc_final: 0.8474 (m-10)
REVERT: A  946 ASN cc_start: 0.8450 (m110) cc_final: 0.8182 (m110)
  outliers start: 15
  outliers final: 12
  residues processed: 330
  average time/residue: 0.1178
  time to fit residues: 50.8519
Evaluate side-chains
  344 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 329
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  694 THR
Chi-restraints excluded: chain A residue  712 LYS
Chi-restraints excluded: chain A residue  718 GLU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  836 LYS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  958 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.147934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.121188 restraints weight = 12828.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.44
r_work: 0.3426 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8970  Z= 0.140
  Angle     :  0.616  10.677  12274  Z= 0.321
  Chirality :  0.043   0.237   1332
  Planarity :  0.005   0.100   1448
  Dihedral  : 18.293 135.601   1458
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 24.69 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  1.06 (0.27), residues: 975
  helix:  2.00 (0.24), residues: 443
  sheet:  0.20 (0.40), residues: 157
  loop : -0.62 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 185 
 TYR   0.023   0.001   TYR A 772 
 PHE   0.027   0.002   PHE A 986 
 TRP   0.006   0.001   TRP A 264 
 HIS   0.005   0.001   HIS A 722 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 ( 8970)
  covalent geometry    : angle       0.61602 /  0.32 (12274)
  hydrogen bonds       : bond        0.04206 /  2.70 (  452)
  hydrogen bonds       : angle       4.10941 /  2.93 ( 1274)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 331
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.5253 (ttp)
REVERT: A    9 GLU cc_start: 0.7611 (tt0) cc_final: 0.7127 (tt0)
REVERT: A   22 VAL cc_start: 0.8598 (t) cc_final: 0.8386 (t)
REVERT: A   23 THR cc_start: 0.8735 (t) cc_final: 0.8432 (p)
REVERT: A   27 GLN cc_start: 0.8592 (tp40) cc_final: 0.8189 (tp-100)
REVERT: A   41 GLU cc_start: 0.7938 (pt0) cc_final: 0.7550 (pt0)
REVERT: A   54 SER cc_start: 0.8451 (m) cc_final: 0.8131 (p)
REVERT: A   75 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8046 (tm-30)
REVERT: A   85 PHE cc_start: 0.8995 (t80) cc_final: 0.8630 (t80)
REVERT: A  127 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8144 (ttmm)
REVERT: A  134 LYS cc_start: 0.8160 (mmmm) cc_final: 0.7811 (mmmm)
REVERT: A  137 THR cc_start: 0.8381 (m) cc_final: 0.8180 (m)
REVERT: A  142 MET cc_start: 0.8042 (mmm) cc_final: 0.7690 (tmm)
REVERT: A  149 ASP cc_start: 0.7592 (p0) cc_final: 0.7159 (p0)
REVERT: A  163 LYS cc_start: 0.8548 (tptt) cc_final: 0.8180 (tptt)
REVERT: A  180 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.7158 (mtm180)
REVERT: A  185 ARG cc_start: 0.7366 (ttm170) cc_final: 0.7092 (ttm170)
REVERT: A  191 GLU cc_start: 0.7791 (mp0) cc_final: 0.7442 (mp0)
REVERT: A  255 MET cc_start: 0.8260 (mmt) cc_final: 0.7665 (mmt)
REVERT: A  277 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8108 (mm)
REVERT: A  285 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.7898 (mmm-85)
REVERT: A  289 ASP cc_start: 0.7943 (m-30) cc_final: 0.7483 (m-30)
REVERT: A  307 LYS cc_start: 0.8486 (mmtt) cc_final: 0.7914 (mmmt)
REVERT: A  334 LYS cc_start: 0.8505 (tppp) cc_final: 0.8099 (tppp)
REVERT: A  349 LYS cc_start: 0.8329 (tttt) cc_final: 0.8123 (tttm)
REVERT: A  376 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8055 (mmtm)
REVERT: A  387 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7689 (mm-30)
REVERT: A  395 VAL cc_start: 0.7689 (m) cc_final: 0.7343 (p)
REVERT: A  399 TYR cc_start: 0.7943 (m-80) cc_final: 0.6983 (m-80)
REVERT: A  404 LYS cc_start: 0.8315 (tttm) cc_final: 0.8043 (tttm)
REVERT: A  424 ASP cc_start: 0.8141 (t0) cc_final: 0.7730 (t0)
REVERT: A  433 VAL cc_start: 0.8463 (t) cc_final: 0.8260 (p)
REVERT: A  434 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7974 (tpt90)
REVERT: A  467 MET cc_start: 0.8111 (ttp) cc_final: 0.7708 (ttm)
REVERT: A  476 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7165 (tm-30)
REVERT: A  511 LYS cc_start: 0.8664 (ptpp) cc_final: 0.8187 (ptpp)
REVERT: A  547 MET cc_start: 0.7936 (tpp) cc_final: 0.7706 (tpp)
REVERT: A  579 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7628 (ttm)
REVERT: A  630 LYS cc_start: 0.8392 (mttt) cc_final: 0.8084 (mttp)
REVERT: A  632 LYS cc_start: 0.8296 (tptt) cc_final: 0.7788 (ttmm)
REVERT: A  636 ILE cc_start: 0.8502 (tt) cc_final: 0.8118 (tp)
REVERT: A  644 GLU cc_start: 0.7629 (tp30) cc_final: 0.7123 (tp30)
REVERT: A  647 ASN cc_start: 0.8351 (t0) cc_final: 0.8015 (t0)
REVERT: A  676 VAL cc_start: 0.8373 (t) cc_final: 0.8068 (m)
REVERT: A  679 LYS cc_start: 0.8738 (tptt) cc_final: 0.8481 (tptt)
REVERT: A  687 ASP cc_start: 0.7544 (t0) cc_final: 0.7343 (t0)
REVERT: A  690 SER cc_start: 0.8198 (t) cc_final: 0.7803 (m)
REVERT: A  711 GLN cc_start: 0.8220 (tp40) cc_final: 0.7783 (tp40)
REVERT: A  721 CYS cc_start: 0.8017 (m) cc_final: 0.7514 (m)
REVERT: A  738 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8143 (tt0)
REVERT: A  747 ASN cc_start: 0.8108 (p0) cc_final: 0.7792 (p0)
REVERT: A  770 LYS cc_start: 0.7896 (mttp) cc_final: 0.7691 (mttp)
REVERT: A  778 ASN cc_start: 0.8855 (m-40) cc_final: 0.8427 (m-40)
REVERT: A  793 ASP cc_start: 0.7729 (t0) cc_final: 0.7384 (t0)
REVERT: A  804 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7940 (mmtt)
REVERT: A  819 ARG cc_start: 0.6821 (ttm-80) cc_final: 0.6318 (ttm110)
REVERT: A  828 ILE cc_start: 0.8488 (pt) cc_final: 0.8203 (mt)
REVERT: A  842 MET cc_start: 0.7607 (ttt) cc_final: 0.7323 (tpp)
REVERT: A  897 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.7857 (ttm-80)
REVERT: A  900 TYR cc_start: 0.7844 (p90) cc_final: 0.7194 (p90)
REVERT: A  924 LYS cc_start: 0.7921 (mttp) cc_final: 0.7123 (mtpp)
REVERT: A  927 TYR cc_start: 0.8722 (m-10) cc_final: 0.8444 (m-10)
REVERT: A  946 ASN cc_start: 0.8525 (m110) cc_final: 0.8012 (m110)
  outliers start: 16
  outliers final: 12
  residues processed: 332
  average time/residue: 0.1197
  time to fit residues: 52.0207
Evaluate side-chains
  345 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 330
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 MET
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  637 PHE
Chi-restraints excluded: chain A residue  694 THR
Chi-restraints excluded: chain A residue  712 LYS
Chi-restraints excluded: chain A residue  718 GLU
Chi-restraints excluded: chain A residue  830 ILE
Chi-restraints excluded: chain A residue  836 LYS
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  958 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 96 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    1.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.144562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.118373 restraints weight = 12626.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.35
r_work: 0.3377 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.4927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   8970  Z= 0.237
  Angle     :  0.668  10.846  12274  Z= 0.352
  Chirality :  0.045   0.241   1332
  Planarity :  0.006   0.077   1448
  Dihedral  : 18.313 135.940   1458
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 24.91 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.99 (0.27), residues: 975
  helix:  1.98 (0.25), residues: 442
  sheet:  0.11 (0.39), residues: 159
  loop : -0.70 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 185 
 TYR   0.032   0.002   TYR A 772 
 PHE   0.037   0.003   PHE A 558 
 TRP   0.015   0.002   TRP A 169 
 HIS   0.006   0.001   HIS A 722 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00521 /  0.24 ( 8970)
  covalent geometry    : angle       0.66824 /  0.35 (12274)
  hydrogen bonds       : bond        0.04915 /  3.18 (  452)
  hydrogen bonds       : angle       4.27060 /  3.04 ( 1274)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2228.96 seconds
wall clock time: 38 minutes 57.56 seconds (2337.56 seconds total)