Starting phenix.real_space_refine
on Fri Aug 22 17:21:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ygn_33817/08_2025/7ygn_33817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ygn_33817/08_2025/7ygn_33817.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ygn_33817/08_2025/7ygn_33817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ygn_33817/08_2025/7ygn_33817.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ygn_33817/08_2025/7ygn_33817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ygn_33817/08_2025/7ygn_33817.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.200
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      2      5.21       5
     S      43      5.16       5
     C    3896      2.51       5
     N    1057      2.21       5
     O    1126      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6133
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 739, 5945
          Classifications: {'peptide': 739}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 701}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 186
          Classifications: {'RNA': 9}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 3, 'rna3p': 5}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.90, per 1000 atoms: 0.31
  Number of scatterers: 6133
  At special positions: 0
  Unit cell: (76.09, 84.786, 113.048, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      43     16.00
     P       9     15.00
     Mg      2     11.99
     O    1126      8.00
     N    1057      7.00
     C    3896      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 350.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1402

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      39.2% alpha, 24.6% beta
      0 base pairs and 3 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 251 through 262
    Processing helix  chain 'A' and resid 262 through 267
      removed outlier: 3.678A  pdb=" N   THR A 266 " --> pdb=" O   HIS A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 316
      No H-bonds generated for 'chain 'A' and resid 314 through 316'
    Processing helix  chain 'A' and resid 317 through 331
    Processing helix  chain 'A' and resid 344 through 347
      removed outlier: 3.518A  pdb=" N   ALA A 347 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 344 through 347'
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 402 through 414
      removed outlier: 4.603A  pdb=" N   GLY A 413 " --> pdb=" O   LYS A 409 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   SER A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 458
    Processing helix  chain 'A' and resid 502 through 508
      removed outlier: 3.727A  pdb=" N   LYS A 506 " --> pdb=" O   PRO A 502 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LYS A 507 " --> pdb=" O   GLU A 503 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASP A 508 " --> pdb=" O   LYS A 504 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 502 through 508'
    Processing helix  chain 'A' and resid 509 through 520
    Processing helix  chain 'A' and resid 522 through 540
    Processing helix  chain 'A' and resid 540 through 549
    Processing helix  chain 'A' and resid 586 through 593
      removed outlier: 3.579A  pdb=" N   VAL A 590 " --> pdb=" O   TRP A 586 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A 591 " --> pdb=" O   VAL A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 611
      No H-bonds generated for 'chain 'A' and resid 609 through 611'
    Processing helix  chain 'A' and resid 612 through 631
      removed outlier: 4.401A  pdb=" N   GLY A 628 " --> pdb=" O   GLU A 624 " (cutoff:3.500A)
      Proline residue:  A 629  - end of helix
    Processing helix  chain 'A' and resid 646 through 661
    Processing helix  chain 'A' and resid 675 through 688
    Processing helix  chain 'A' and resid 699 through 704
      removed outlier: 3.894A  pdb=" N   GLN A 704 " --> pdb=" O   ARG A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 724
    Processing helix  chain 'A' and resid 781 through 802
      removed outlier: 4.294A  pdb=" N   SER A 785 " --> pdb=" O   GLU A 781 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 788 " --> pdb=" O   ASP A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 818
      No H-bonds generated for 'chain 'A' and resid 816 through 818'
    Processing helix  chain 'A' and resid 819 through 826
    Processing helix  chain 'A' and resid 826 through 833
      removed outlier: 3.512A  pdb=" N   LYS A 833 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 838
    Processing helix  chain 'A' and resid 914 through 926
    Processing helix  chain 'A' and resid 939 through 955
    Processing helix  chain 'A' and resid 961 through 967
      removed outlier: 4.081A  pdb=" N   GLY A 966 " --> pdb=" O   GLN A 963 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 769 through 775
      removed outlier: 3.908A  pdb=" N   ASP A 743 " --> pdb=" O   GLY A 757 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   VAL A 739 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   VAL A 744 " --> pdb=" O   ASP A 813 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ILE A 808 " --> pdb=" O   VAL A 846 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   PHE A 848 " --> pdb=" O   ILE A 808 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 810 " --> pdb=" O   PHE A 848 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   VAL A 850 " --> pdb=" O   VAL A 810 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ARG A 812 " --> pdb=" O   VAL A 850 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 908 " --> pdb=" O   VAL A 847 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   VAL A 849 " --> pdb=" O   CYS A 906 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   CYS A 906 " --> pdb=" O   VAL A 849 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 851 " --> pdb=" O   TYR A 904 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   TYR A 904 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   VAL A 885 " --> pdb=" O   CYS A 906 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   SER A 223 " --> pdb=" O   ALA A 861 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 337
      removed outlier: 3.614A  pdb=" N   ASN A 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337
      removed outlier: 3.614A  pdb=" N   ASN A 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   LEU A 372 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272
      removed outlier: 5.825A  pdb=" N   HIS A 242 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   LEU A 306 " --> pdb=" O   HIS A 242 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   THR A 244 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ILE A 304 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   SER A 246 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   ILE A 302 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 423 through 425
      removed outlier: 3.514A  pdb=" N   ARG A 423 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431
    Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 440
    Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 572
    Processing sheet with id=AA9, first strand: chain 'A' and resid 638 through 641

    289 hydrogen bonds defined for protein.
    801 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      3 stacking parallelities
  Total time for adding SS restraints: 1.14

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 963
        1.30 -     1.43: 1632
        1.43 -     1.56: 3607
        1.56 -     1.69: 16
        1.69 -     1.82: 67
  Bond restraints: 6285
  Sorted by residual:
  bond pdb=" C2  OMC B  26 "
       pdb=" N3  OMC B  26 "
    ideal  model  delta    sigma   weight residual
    1.350  1.491 -0.141 2.00e-02 2.50e+03 4.98e+01
  bond pdb=" C4  OMC B  26 "
       pdb=" N4  OMC B  26 "
    ideal  model  delta    sigma   weight residual
    1.332  1.471 -0.139 2.00e-02 2.50e+03 4.81e+01
  bond pdb=" N3  OMC B  26 "
       pdb=" C4  OMC B  26 "
    ideal  model  delta    sigma   weight residual
    1.317  1.454 -0.137 2.00e-02 2.50e+03 4.66e+01
  bond pdb=" C5  OMC B  26 "
       pdb=" C6  OMC B  26 "
    ideal  model  delta    sigma   weight residual
    1.346  1.481 -0.135 2.00e-02 2.50e+03 4.59e+01
  bond pdb=" O3'   U B   2 "
       pdb=" P     A B   3 "
    ideal  model  delta    sigma   weight residual
    1.607  1.528  0.079 1.50e-02 4.44e+03 2.78e+01
  ... (remaining 6280 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.32: 8507
        4.32 -     8.64: 41
        8.64 -    12.96: 1
       12.96 -    17.28: 2
       17.28 -    21.60: 2
  Bond angle restraints: 8553
  Sorted by residual:
  angle pdb=" O3'   U B  25 "
        pdb=" P   OMC B  26 "
        pdb=" OP1 OMC B  26 "
      ideal   model   delta    sigma   weight residual
     108.00   86.40   21.60 3.00e+00 1.11e-01 5.18e+01
  angle pdb=" O3'   U B  25 "
        pdb=" P   OMC B  26 "
        pdb=" OP2 OMC B  26 "
      ideal   model   delta    sigma   weight residual
     108.00   90.04   17.96 3.00e+00 1.11e-01 3.58e+01
  angle pdb=" N   GLN A 263 "
        pdb=" CA  GLN A 263 "
        pdb=" C   GLN A 263 "
      ideal   model   delta    sigma   weight residual
     111.28  105.23    6.05 1.09e+00 8.42e-01 3.09e+01
  angle pdb=" OP2 OMC B  26 "
        pdb=" P   OMC B  26 "
        pdb=" O5' OMC B  26 "
      ideal   model   delta    sigma   weight residual
     100.81  116.44  -15.63 3.00e+00 1.11e-01 2.71e+01
  angle pdb=" OP1 OMC B  26 "
        pdb=" P   OMC B  26 "
        pdb=" OP2 OMC B  26 "
      ideal   model   delta    sigma   weight residual
     115.29  128.88  -13.59 3.00e+00 1.11e-01 2.05e+01
  ... (remaining 8548 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3353
       17.79 -    35.59: 355
       35.59 -    53.38: 67
       53.38 -    71.17: 20
       71.17 -    88.97: 7
  Dihedral angle restraints: 3802
    sinusoidal: 1637
      harmonic: 2165
  Sorted by residual:
  dihedral pdb=" C4'   U B   2 "
           pdb=" C3'   U B   2 "
           pdb=" C2'   U B   2 "
           pdb=" C1'   U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.00    5.39   30.61     1      8.00e+00 1.56e-02 2.09e+01
  dihedral pdb=" O4'   U B   2 "
           pdb=" C2'   U B   2 "
           pdb=" C1'   U B   2 "
           pdb=" C3'   U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -2.36   27.36     1      8.00e+00 1.56e-02 1.68e+01
  dihedral pdb=" C5'   U B   2 "
           pdb=" C4'   U B   2 "
           pdb=" C3'   U B   2 "
           pdb=" O3'   U B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00  109.29  -27.29     1      8.00e+00 1.56e-02 1.67e+01
  ... (remaining 3799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 837
       0.068 -    0.135: 125
       0.135 -    0.203: 13
       0.203 -    0.271: 1
       0.271 -    0.339: 1
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" P     U B   2 "
            pdb=" OP1   U B   2 "
            pdb=" OP2   U B   2 "
            pdb=" O5'   U B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.07    0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" C3'   U B   2 "
            pdb=" C4'   U B   2 "
            pdb=" O3'   U B   2 "
            pdb=" C2'   U B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.22   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  ILE A 905 "
            pdb=" N   ILE A 905 "
            pdb=" C   ILE A 905 "
            pdb=" CB  ILE A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.73e-01
  ... (remaining 974 not shown)

  Planarity restraints: 1051
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   2 "   -0.044 2.00e-02 2.50e+03   2.47e-02 1.38e+01
        pdb=" N1    U B   2 "    0.056 2.00e-02 2.50e+03
        pdb=" C2    U B   2 "    0.014 2.00e-02 2.50e+03
        pdb=" O2    U B   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    U B   2 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4    U B   2 "   -0.013 2.00e-02 2.50e+03
        pdb=" O4    U B   2 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    U B   2 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U B   2 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 220 "   -0.038 5.00e-02 4.00e+02   5.66e-02 5.12e+00
        pdb=" N   PRO A 221 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 221 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 221 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 246 "   -0.037 5.00e-02 4.00e+02   5.65e-02 5.10e+00
        pdb=" N   PRO A 247 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 247 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 247 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1048 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 29
        2.49 -     3.10: 4032
        3.10 -     3.70: 8648
        3.70 -     4.30: 12746
        4.30 -     4.90: 21940
  Nonbonded interactions: 47395
  Sorted by model distance:
  nonbonded pdb=" OP1   U B   1 "
            pdb="MG    MG A1001 "
     model   vdw
     1.892 2.170
  nonbonded pdb=" O   LEU A 971 "
            pdb="MG    MG A1001 "
     model   vdw
     1.900 2.170
  nonbonded pdb=" OD2 ASP A 743 "
            pdb="MG    MG A1002 "
     model   vdw
     2.039 2.170
  nonbonded pdb=" OP1   A B   3 "
            pdb="MG    MG A1001 "
     model   vdw
     2.114 2.170
  nonbonded pdb=" OG  SER A 439 "
            pdb=" OE2 GLU A 447 "
     model   vdw
     2.209 3.040
  ... (remaining 47390 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:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     8.780
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.141   6285  Z= 0.291
  Angle     :  0.854  21.598   8553  Z= 0.441
  Chirality :  0.049   0.339    977
  Planarity :  0.006   0.058   1051
  Dihedral  : 15.418  88.968   2400
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.31), residues: 733
  helix:  1.28 (0.36), residues: 234
  sheet:  0.54 (0.36), residues: 198
  loop : -1.22 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 570 
 TYR   0.013   0.002   TYR A 239 
 PHE   0.017   0.002   PHE A 578 
 TRP   0.007   0.001   TRP A 728 
 HIS   0.010   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 ( 6285)
  covalent geometry    : angle       0.85402 ( 8553)
  hydrogen bonds       : bond        0.15886 (  284)
  hydrogen bonds       : angle       6.85611 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.255 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.5993
  time to fit residues: 48.4327
Evaluate side-chains
  63 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0000
   overall best weight:    0.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
A 535 GLN
A 746 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.192187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.142750 restraints weight = 6748.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 3.31
r_work: 0.3444 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6285  Z= 0.139
  Angle     :  0.548   5.168   8553  Z= 0.284
  Chirality :  0.045   0.152    977
  Planarity :  0.005   0.058   1051
  Dihedral  :  9.413  79.366    918
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.22 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.31), residues: 733
  helix:  1.66 (0.35), residues: 239
  sheet:  0.83 (0.37), residues: 191
  loop : -0.96 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 570 
 TYR   0.015   0.001   TYR A 239 
 PHE   0.023   0.002   PHE A 320 
 TRP   0.007   0.001   TRP A 884 
 HIS   0.005   0.001   HIS A 927 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6285)
  covalent geometry    : angle       0.54785 ( 8553)
  hydrogen bonds       : bond        0.03706 (  284)
  hydrogen bonds       : angle       5.20262 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6587 (mmp) cc_final: 0.6143 (mtm)
REVERT: A  423 ARG cc_start: 0.7391 (ttm110) cc_final: 0.7186 (mtp-110)
REVERT: A  505 MET cc_start: 0.6105 (mmt) cc_final: 0.5834 (mmt)
REVERT: A  520 ASN cc_start: 0.7812 (m110) cc_final: 0.7541 (m110)
REVERT: A  613 MET cc_start: 0.6939 (ttm) cc_final: 0.6641 (ttm)
REVERT: A  624 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7564 (mt-10)
REVERT: A  763 ASN cc_start: 0.8303 (t0) cc_final: 0.8064 (t0)
REVERT: A  827 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6712 (mp0)
REVERT: A  845 MET cc_start: 0.8156 (ttm) cc_final: 0.7857 (ttt)
REVERT: A  895 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6011 (ptp90)
  outliers start: 12
  outliers final: 2
  residues processed: 84
  average time/residue: 0.6709
  time to fit residues: 58.9011
Evaluate side-chains
  66 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN
A 539 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.175490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.128873 restraints weight = 6744.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.57
r_work: 0.3167 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6285  Z= 0.121
  Angle     :  0.502   4.845   8553  Z= 0.261
  Chirality :  0.043   0.149    977
  Planarity :  0.005   0.056   1051
  Dihedral  :  9.022  80.761    918
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 13.11 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.31), residues: 733
  helix:  1.91 (0.35), residues: 241
  sheet:  0.83 (0.37), residues: 191
  loop : -0.89 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 570 
 TYR   0.012   0.001   TYR A 239 
 PHE   0.021   0.002   PHE A 950 
 TRP   0.010   0.001   TRP A 604 
 HIS   0.004   0.001   HIS A 927 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6285)
  covalent geometry    : angle       0.50165 ( 8553)
  hydrogen bonds       : bond        0.03639 (  284)
  hydrogen bonds       : angle       4.94522 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  258 MET cc_start: 0.6656 (mmp) cc_final: 0.6080 (mmp)
REVERT: A  423 ARG cc_start: 0.7507 (ttm110) cc_final: 0.7297 (mtp-110)
REVERT: A  505 MET cc_start: 0.5744 (mmt) cc_final: 0.5462 (mmt)
REVERT: A  520 ASN cc_start: 0.7642 (m110) cc_final: 0.7135 (m-40)
REVERT: A  618 GLU cc_start: 0.7934 (tt0) cc_final: 0.7017 (mm-30)
REVERT: A  624 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7721 (mt-10)
REVERT: A  643 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7557 (mmtt)
REVERT: A  700 ARG cc_start: 0.8038 (ttp-110) cc_final: 0.7200 (ttp80)
REVERT: A  707 ARG cc_start: 0.7397 (mtm110) cc_final: 0.7012 (ptm-80)
REVERT: A  827 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6438 (mp0)
REVERT: A  845 MET cc_start: 0.8238 (ttm) cc_final: 0.8028 (ttt)
REVERT: A  895 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6056 (ptp90)
  outliers start: 18
  outliers final: 5
  residues processed: 85
  average time/residue: 0.7312
  time to fit residues: 64.7525
Evaluate side-chains
  69 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 52 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 263 GLN
A 535 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.177444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.131586 restraints weight = 6777.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 3.14
r_work: 0.3152 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6285  Z= 0.132
  Angle     :  0.518   5.923   8553  Z= 0.266
  Chirality :  0.044   0.156    977
  Planarity :  0.005   0.055   1051
  Dihedral  :  8.955  79.469    918
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.65 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.31), residues: 733
  helix:  2.01 (0.35), residues: 241
  sheet:  0.71 (0.36), residues: 196
  loop : -0.91 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 646 
 TYR   0.012   0.001   TYR A 239 
 PHE   0.021   0.002   PHE A 320 
 TRP   0.009   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6285)
  covalent geometry    : angle       0.51795 ( 8553)
  hydrogen bonds       : bond        0.03592 (  284)
  hydrogen bonds       : angle       4.87980 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8175 (tttt) cc_final: 0.7386 (tptt)
REVERT: A  258 MET cc_start: 0.6721 (mmp) cc_final: 0.6172 (mmp)
REVERT: A  313 CYS cc_start: 0.8304 (p) cc_final: 0.8058 (p)
REVERT: A  419 ARG cc_start: 0.7683 (tpp80) cc_final: 0.7446 (mmm160)
REVERT: A  520 ASN cc_start: 0.7591 (m110) cc_final: 0.7296 (m110)
REVERT: A  532 CYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7507 (p)
REVERT: A  593 ASP cc_start: 0.7520 (m-30) cc_final: 0.6956 (t70)
REVERT: A  618 GLU cc_start: 0.7859 (tt0) cc_final: 0.7061 (mm-30)
REVERT: A  624 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7505 (mt-10)
REVERT: A  700 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7311 (ttp80)
REVERT: A  707 ARG cc_start: 0.7309 (mtm110) cc_final: 0.7105 (ptm-80)
REVERT: A  827 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6675 (mp0)
REVERT: A  845 MET cc_start: 0.8163 (ttm) cc_final: 0.7883 (ttt)
REVERT: A  895 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6029 (ptp90)
  outliers start: 16
  outliers final: 4
  residues processed: 83
  average time/residue: 0.6837
  time to fit residues: 59.3212
Evaluate side-chains
  70 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0570
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0370
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
A 262 HIS
A 263 GLN
A 535 GLN
A 539 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.177575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.131727 restraints weight = 6876.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 3.21
r_work: 0.3148 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6285  Z= 0.095
  Angle     :  0.474   6.424   8553  Z= 0.243
  Chirality :  0.042   0.141    977
  Planarity :  0.004   0.053   1051
  Dihedral  :  8.854  78.586    918
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.54 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.32), residues: 733
  helix:  2.42 (0.35), residues: 235
  sheet:  0.83 (0.37), residues: 191
  loop : -0.72 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 423 
 TYR   0.010   0.001   TYR A 239 
 PHE   0.023   0.001   PHE A 272 
 TRP   0.009   0.001   TRP A 604 
 HIS   0.004   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 6285)
  covalent geometry    : angle       0.47424 ( 8553)
  hydrogen bonds       : bond        0.02904 (  284)
  hydrogen bonds       : angle       4.72987 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8152 (tttt) cc_final: 0.7343 (tptp)
REVERT: A  258 MET cc_start: 0.6705 (mmp) cc_final: 0.6436 (mtm)
REVERT: A  313 CYS cc_start: 0.8323 (p) cc_final: 0.8061 (p)
REVERT: A  419 ARG cc_start: 0.7706 (tpp80) cc_final: 0.7475 (mmm160)
REVERT: A  520 ASN cc_start: 0.7555 (m110) cc_final: 0.6938 (m110)
REVERT: A  532 CYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7515 (p)
REVERT: A  593 ASP cc_start: 0.7256 (m-30) cc_final: 0.6744 (t70)
REVERT: A  610 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7808 (mptt)
REVERT: A  611 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7522 (pmm-80)
REVERT: A  618 GLU cc_start: 0.7810 (tt0) cc_final: 0.6964 (mm-30)
REVERT: A  624 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7459 (mt-10)
REVERT: A  700 ARG cc_start: 0.8014 (ttp-110) cc_final: 0.7286 (ttp80)
REVERT: A  763 ASN cc_start: 0.8340 (t0) cc_final: 0.7851 (t0)
REVERT: A  827 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6660 (mp0)
REVERT: A  845 MET cc_start: 0.8201 (ttm) cc_final: 0.7937 (ttt)
REVERT: A  853 LYS cc_start: 0.7989 (pmtt) cc_final: 0.7600 (mptt)
  outliers start: 15
  outliers final: 6
  residues processed: 77
  average time/residue: 0.7143
  time to fit residues: 57.4529
Evaluate side-chains
  71 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  868 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.169497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.123001 restraints weight = 6820.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 3.01
r_work: 0.3053 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6285  Z= 0.196
  Angle     :  0.563   6.810   8553  Z= 0.289
  Chirality :  0.046   0.175    977
  Planarity :  0.005   0.053   1051
  Dihedral  :  8.877  78.588    918
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.84 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.31), residues: 733
  helix:  1.95 (0.35), residues: 241
  sheet:  0.56 (0.36), residues: 196
  loop : -0.95 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 423 
 TYR   0.013   0.002   TYR A 239 
 PHE   0.025   0.002   PHE A 272 
 TRP   0.009   0.001   TRP A 604 
 HIS   0.005   0.001   HIS A 927 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 6285)
  covalent geometry    : angle       0.56319 ( 8553)
  hydrogen bonds       : bond        0.04409 (  284)
  hydrogen bonds       : angle       4.99546 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LYS cc_start: 0.8194 (tttt) cc_final: 0.7286 (tptp)
REVERT: A  423 ARG cc_start: 0.7426 (mtp-110) cc_final: 0.7095 (mtp-110)
REVERT: A  505 MET cc_start: 0.6050 (mmt) cc_final: 0.5563 (mmt)
REVERT: A  508 ASP cc_start: 0.7165 (m-30) cc_final: 0.6303 (t0)
REVERT: A  520 ASN cc_start: 0.7294 (m110) cc_final: 0.6857 (m110)
REVERT: A  532 CYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7430 (p)
REVERT: A  593 ASP cc_start: 0.7531 (m-30) cc_final: 0.6951 (t70)
REVERT: A  610 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7936 (mptt)
REVERT: A  624 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7541 (mt-10)
REVERT: A  700 ARG cc_start: 0.7970 (ttp-110) cc_final: 0.7255 (ttp80)
REVERT: A  827 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6767 (mp0)
REVERT: A  845 MET cc_start: 0.8175 (ttm) cc_final: 0.7964 (ttt)
REVERT: A  895 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.5853 (ptp90)
  outliers start: 18
  outliers final: 5
  residues processed: 80
  average time/residue: 0.6792
  time to fit residues: 56.8279
Evaluate side-chains
  72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 18 optimal weight:    0.0070
   chunk 28 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 59 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A 763 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.173082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.127507 restraints weight = 6798.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.86
r_work: 0.3217 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6285  Z= 0.099
  Angle     :  0.478   7.211   8553  Z= 0.245
  Chirality :  0.042   0.141    977
  Planarity :  0.004   0.053   1051
  Dihedral  :  8.781  77.146    918
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.18 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.31), residues: 733
  helix:  2.45 (0.35), residues: 235
  sheet:  0.80 (0.36), residues: 189
  loop : -0.84 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 423 
 TYR   0.010   0.001   TYR A 239 
 PHE   0.017   0.001   PHE A 320 
 TRP   0.009   0.001   TRP A 604 
 HIS   0.004   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6285)
  covalent geometry    : angle       0.47811 ( 8553)
  hydrogen bonds       : bond        0.02931 (  284)
  hydrogen bonds       : angle       4.75844 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8183 (tttt) cc_final: 0.7353 (tptp)
REVERT: A  258 MET cc_start: 0.6736 (mmp) cc_final: 0.6522 (mtm)
REVERT: A  348 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6792 (ppp)
REVERT: A  505 MET cc_start: 0.6070 (mmt) cc_final: 0.5615 (mmt)
REVERT: A  508 ASP cc_start: 0.7067 (m-30) cc_final: 0.6260 (t0)
REVERT: A  520 ASN cc_start: 0.7317 (m110) cc_final: 0.7045 (m110)
REVERT: A  532 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7677 (p)
REVERT: A  610 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7974 (mptt)
REVERT: A  618 GLU cc_start: 0.7845 (tt0) cc_final: 0.7095 (mm-30)
REVERT: A  624 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7441 (mt-10)
REVERT: A  700 ARG cc_start: 0.8032 (ttp-110) cc_final: 0.7404 (ttp80)
REVERT: A  827 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6784 (mp0)
REVERT: A  895 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6001 (ptp90)
  outliers start: 16
  outliers final: 6
  residues processed: 80
  average time/residue: 0.6742
  time to fit residues: 56.4177
Evaluate side-chains
  72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 25 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 896 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.171906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.126001 restraints weight = 6892.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.83
r_work: 0.3107 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6285  Z= 0.118
  Angle     :  0.498   7.370   8553  Z= 0.256
  Chirality :  0.043   0.170    977
  Planarity :  0.004   0.053   1051
  Dihedral  :  8.756  76.642    918
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.63 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.32), residues: 733
  helix:  2.45 (0.35), residues: 236
  sheet:  0.70 (0.36), residues: 191
  loop : -0.80 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 423 
 TYR   0.011   0.001   TYR A 239 
 PHE   0.021   0.002   PHE A 950 
 TRP   0.009   0.001   TRP A 604 
 HIS   0.004   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6285)
  covalent geometry    : angle       0.49810 ( 8553)
  hydrogen bonds       : bond        0.03282 (  284)
  hydrogen bonds       : angle       4.79278 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8141 (tttt) cc_final: 0.7248 (tptp)
REVERT: A  258 MET cc_start: 0.6583 (mmp) cc_final: 0.6076 (mmp)
REVERT: A  348 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6735 (ppp)
REVERT: A  423 ARG cc_start: 0.7482 (mtp-110) cc_final: 0.6799 (ttm110)
REVERT: A  508 ASP cc_start: 0.7076 (m-30) cc_final: 0.6307 (t0)
REVERT: A  520 ASN cc_start: 0.7271 (m110) cc_final: 0.7020 (m110)
REVERT: A  532 CYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7553 (p)
REVERT: A  610 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7954 (mptt)
REVERT: A  618 GLU cc_start: 0.7828 (tt0) cc_final: 0.7009 (mm-30)
REVERT: A  624 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7460 (mt-10)
REVERT: A  820 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7671 (tp)
REVERT: A  827 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6681 (mp0)
REVERT: A  895 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5916 (ptp90)
  outliers start: 17
  outliers final: 8
  residues processed: 75
  average time/residue: 0.7027
  time to fit residues: 55.0965
Evaluate side-chains
  74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 42 optimal weight:    0.0470
   chunk 25 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6680

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.173083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.127025 restraints weight = 6799.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.85
r_work: 0.3124 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6285  Z= 0.105
  Angle     :  0.496   7.519   8553  Z= 0.256
  Chirality :  0.043   0.146    977
  Planarity :  0.004   0.054   1051
  Dihedral  :  8.761  75.732    918
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.82 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.32), residues: 733
  helix:  2.54 (0.35), residues: 236
  sheet:  0.76 (0.36), residues: 189
  loop : -0.77 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 423 
 TYR   0.010   0.001   TYR A 239 
 PHE   0.017   0.001   PHE A 320 
 TRP   0.009   0.001   TRP A 604 
 HIS   0.004   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6285)
  covalent geometry    : angle       0.49607 ( 8553)
  hydrogen bonds       : bond        0.02977 (  284)
  hydrogen bonds       : angle       4.72834 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8119 (tttt) cc_final: 0.7242 (tptp)
REVERT: A  258 MET cc_start: 0.6546 (mmp) cc_final: 0.5989 (mmp)
REVERT: A  423 ARG cc_start: 0.7029 (mtp-110) cc_final: 0.6480 (ttm110)
REVERT: A  508 ASP cc_start: 0.7148 (m-30) cc_final: 0.6368 (t0)
REVERT: A  520 ASN cc_start: 0.7551 (m110) cc_final: 0.7157 (m110)
REVERT: A  532 CYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7603 (p)
REVERT: A  610 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7971 (mptt)
REVERT: A  618 GLU cc_start: 0.7833 (tt0) cc_final: 0.7013 (mm-30)
REVERT: A  624 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7451 (mt-10)
REVERT: A  700 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7511 (ttp80)
REVERT: A  820 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7678 (tp)
REVERT: A  827 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6681 (mp0)
REVERT: A  853 LYS cc_start: 0.8078 (pmtt) cc_final: 0.7642 (mptt)
REVERT: A  895 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.5957 (ptp90)
  outliers start: 15
  outliers final: 8
  residues processed: 75
  average time/residue: 0.7013
  time to fit residues: 54.9682
Evaluate side-chains
  73 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  895 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 8 optimal weight:   20.0000
   chunk 72 optimal weight:    0.1980
   chunk 64 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 39 optimal weight:    0.4980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.187825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.141912 restraints weight = 6664.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.35
r_work: 0.3134 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6285  Z= 0.106
  Angle     :  0.519   7.684   8553  Z= 0.264
  Chirality :  0.042   0.146    977
  Planarity :  0.004   0.054   1051
  Dihedral  :  8.749  75.063    918
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 20.27 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.32), residues: 733
  helix:  2.58 (0.35), residues: 236
  sheet:  0.78 (0.37), residues: 189
  loop : -0.73 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 423 
 TYR   0.010   0.001   TYR A 239 
 PHE   0.021   0.002   PHE A 950 
 TRP   0.009   0.001   TRP A 604 
 HIS   0.004   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6285)
  covalent geometry    : angle       0.51925 ( 8553)
  hydrogen bonds       : bond        0.02922 (  284)
  hydrogen bonds       : angle       4.71736 (  801)

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  218 LYS cc_start: 0.8044 (tttt) cc_final: 0.7058 (tptp)
REVERT: A  258 MET cc_start: 0.6399 (mmp) cc_final: 0.5898 (mmp)
REVERT: A  348 MET cc_start: 0.7465 (ppp) cc_final: 0.6950 (ptt)
REVERT: A  423 ARG cc_start: 0.7135 (mtp-110) cc_final: 0.6465 (ttm110)
REVERT: A  505 MET cc_start: 0.5578 (mmt) cc_final: 0.5252 (mmt)
REVERT: A  508 ASP cc_start: 0.6958 (m-30) cc_final: 0.6222 (t0)
REVERT: A  520 ASN cc_start: 0.7415 (m110) cc_final: 0.7118 (m110)
REVERT: A  532 CYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7539 (p)
REVERT: A  610 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7882 (mptt)
REVERT: A  618 GLU cc_start: 0.7856 (tt0) cc_final: 0.6960 (mm-30)
REVERT: A  624 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7497 (mt-10)
REVERT: A  700 ARG cc_start: 0.8106 (ttp-110) cc_final: 0.7426 (ttp80)
REVERT: A  798 TYR cc_start: 0.7075 (t80) cc_final: 0.6563 (t80)
REVERT: A  820 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7618 (tp)
REVERT: A  827 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6586 (mp0)
REVERT: A  853 LYS cc_start: 0.8117 (pmtt) cc_final: 0.7625 (mptt)
  outliers start: 12
  outliers final: 8
  residues processed: 71
  average time/residue: 0.7021
  time to fit residues: 52.1084
Evaluate side-chains
  71 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  532 CYS
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  610 LYS
Chi-restraints excluded: chain A residue  672 MET
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  820 LEU
Chi-restraints excluded: chain A residue  868 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0070
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN
A 285 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.173407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.127148 restraints weight = 6844.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.90
r_work: 0.3172 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6285  Z= 0.108
  Angle     :  0.523   7.654   8553  Z= 0.266
  Chirality :  0.043   0.169    977
  Planarity :  0.004   0.054   1051
  Dihedral  :  8.744  74.284    918
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.52 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.32), residues: 733
  helix:  2.63 (0.35), residues: 236
  sheet:  0.71 (0.36), residues: 189
  loop : -0.72 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 423 
 TYR   0.011   0.001   TYR A 239 
 PHE   0.018   0.001   PHE A 320 
 TRP   0.009   0.001   TRP A 604 
 HIS   0.004   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6285)
  covalent geometry    : angle       0.52303 ( 8553)
  hydrogen bonds       : bond        0.02995 (  284)
  hydrogen bonds       : angle       4.75578 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2380.26 seconds
wall clock time: 41 minutes 27.59 seconds (2487.59 seconds total)