Starting phenix.real_space_refine
on Thu Jul  2 05:18:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iw3_60944/07_2026/9iw3_60944_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iw3_60944/07_2026/9iw3_60944.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iw3_60944/07_2026/9iw3_60944_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iw3_60944/07_2026/9iw3_60944_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iw3_60944/07_2026/9iw3_60944.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iw3_60944/07_2026/9iw3_60944.map"
  }
  resolution = 3.58
  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=   0.015
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      51      5.49       5
     Mg      1      5.21       5
     S      22      5.16       5
     C    4226      2.51       5
     N    1211      2.21       5
     O    1368      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6879
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 515
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "B"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 305
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "D"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 224
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "A"
      Number of atoms: 5834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 712, 5834
          Classifications: {'peptide': 712}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 681}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.60, per 1000 atoms: 0.23
  Number of scatterers: 6879
  At special positions: 0
  Unit cell: (78.288, 96.928, 116.5, 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      22     16.00
     P      51     15.00
     Mg      1     11.99
     O    1368      8.00
     N    1211      7.00
     C    4226      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: 0.59
  Conformation dependent library (CDL) restraints added in 286.9 milliseconds
  

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1360

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      37.1% alpha, 20.2% beta
      11 base pairs and 35 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 25
    Processing helix  chain 'A' and resid 34 through 36
      No H-bonds generated for 'chain 'A' and resid 34 through 36'
    Processing helix  chain 'A' and resid 37 through 48
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 3.588A  pdb=" N   GLY A  92 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 107
      removed outlier: 3.545A  pdb=" N   LEU A 101 " --> pdb=" O   TYR A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 216 through 221
    Processing helix  chain 'A' and resid 223 through 239
    Processing helix  chain 'A' and resid 266 through 272
      removed outlier: 3.582A  pdb=" N   LEU A 272 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 303 through 309
      removed outlier: 3.576A  pdb=" N   LYS A 307 " --> pdb=" O   GLN A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 357
    Processing helix  chain 'A' and resid 378 through 381
    Processing helix  chain 'A' and resid 382 through 401
    Processing helix  chain 'A' and resid 406 through 415
    Processing helix  chain 'A' and resid 462 through 475
    Processing helix  chain 'A' and resid 480 through 486
      removed outlier: 3.872A  pdb=" N   TRP A 484 " --> pdb=" O   PHE A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 521
    Processing helix  chain 'A' and resid 528 through 540
    Processing helix  chain 'A' and resid 541 through 544
      removed outlier: 4.140A  pdb=" N   SER A 544 " --> pdb=" O   PRO A 541 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 541 through 544'
    Processing helix  chain 'A' and resid 548 through 562
      removed outlier: 3.564A  pdb=" N   GLY A 562 " --> pdb=" O   ALA A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 580
    Processing helix  chain 'A' and resid 585 through 598
      removed outlier: 3.561A  pdb=" N   ASN A 598 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 680
      removed outlier: 4.303A  pdb=" N   ASP A 670 " --> pdb=" O   ALA A 666 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU A 671 " --> pdb=" O   GLY A 667 " (cutoff:3.500A)
      Proline residue:  A 674  - end of helix
    Processing helix  chain 'A' and resid 694 through 711
      removed outlier: 4.094A  pdb=" N   LYS A 698 " --> pdb=" O   PRO A 694 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN A 710 " --> pdb=" O   SER A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 715
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 5.210A  pdb=" N   LYS A  15 " --> pdb=" O   PRO A 246 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55
      removed outlier: 3.537A  pdb=" N   PHE A  69 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 127
      removed outlier: 4.063A  pdb=" N   LEU A 125 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN A 142 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 127
      removed outlier: 4.063A  pdb=" N   LEU A 125 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   TYR A 196 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 178
      removed outlier: 4.596A  pdb=" N   ILE A 175 " --> pdb=" O   CYS A 188 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 213
    Processing sheet with id=AA7, first strand: chain 'A' and resid 254 through 258
      removed outlier: 4.297A  pdb=" N   SER A 257 " --> pdb=" O   ILE A 622 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ILE A 622 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLU A 629 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   HIS A 633 " --> pdb=" O   GLU A 629 " (cutoff:3.500A)
      removed outlier: 11.623A  pdb=" N   PHE A 634 " --> pdb=" O   PRO A 661 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   THR A 636 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLN A 497 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   LEU A 498 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   VAL A 490 " --> pdb=" O   LEU A 498 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ILE A 500 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ASP A 488 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   PHE A 422 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL A 433 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 453 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL A 435 " --> pdb=" O   LYS A 451 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314
      removed outlier: 6.241A  pdb=" N   SER A 276 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   ILE A 324 " --> pdb=" O   SER A 276 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   ASN A 278 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   VAL A 326 " --> pdb=" O   ASN A 278 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   TYR A 280 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    660 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      27 hydrogen bonds
      54 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2046
        1.34 -     1.46: 1654
        1.46 -     1.58: 3289
        1.58 -     1.70: 98
        1.70 -     1.82: 39
  Bond restraints: 7126
  Sorted by residual:
  bond pdb=" C1'  DA D  12 "
       pdb=" N9   DA D  12 "
    ideal  model  delta    sigma   weight residual
    1.468  1.364  0.104 1.40e-02 5.10e+03 5.54e+01
  bond pdb=" C1'  DA C  31 "
       pdb=" N9   DA C  31 "
    ideal  model  delta    sigma   weight residual
    1.468  1.368  0.100 1.40e-02 5.10e+03 5.07e+01
  bond pdb=" C1'  DG C  47 "
       pdb=" N9   DG C  47 "
    ideal  model  delta    sigma   weight residual
    1.468  1.372  0.096 1.40e-02 5.10e+03 4.71e+01
  bond pdb=" C1'  DA C  38 "
       pdb=" N9   DA C  38 "
    ideal  model  delta    sigma   weight residual
    1.468  1.377  0.091 1.40e-02 5.10e+03 4.21e+01
  bond pdb=" C1'  DC C  51 "
       pdb=" N1   DC C  51 "
    ideal  model  delta    sigma   weight residual
    1.468  1.554 -0.086 1.40e-02 5.10e+03 3.78e+01
  ... (remaining 7121 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 9738
        3.47 -     6.95: 81
        6.95 -    10.42: 14
       10.42 -    13.89: 4
       13.89 -    17.36: 2
  Bond angle restraints: 9839
  Sorted by residual:
  angle pdb=" N   ASP A 548 "
        pdb=" CA  ASP A 548 "
        pdb=" C   ASP A 548 "
      ideal   model   delta    sigma   weight residual
     114.31   97.82   16.49 1.29e+00 6.01e-01 1.63e+02
  angle pdb=" N   SER A 547 "
        pdb=" CA  SER A 547 "
        pdb=" C   SER A 547 "
      ideal   model   delta    sigma   weight residual
     110.80  128.16  -17.36 2.13e+00 2.20e-01 6.65e+01
  angle pdb=" N   ALA A  37 "
        pdb=" CA  ALA A  37 "
        pdb=" C   ALA A  37 "
      ideal   model   delta    sigma   weight residual
     111.75  122.04  -10.29 1.28e+00 6.10e-01 6.47e+01
  angle pdb=" N   ASP A  40 "
        pdb=" CA  ASP A  40 "
        pdb=" C   ASP A  40 "
      ideal   model   delta    sigma   weight residual
     111.24  103.12    8.12 1.29e+00 6.01e-01 3.96e+01
  angle pdb=" N   ASP A 548 "
        pdb=" CA  ASP A 548 "
        pdb=" CB  ASP A 548 "
      ideal   model   delta    sigma   weight residual
     110.90  118.31   -7.41 1.33e+00 5.65e-01 3.11e+01
  ... (remaining 9834 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.98: 3696
       29.98 -    59.96: 460
       59.96 -    89.93: 42
       89.93 -   119.91: 2
      119.91 -   149.89: 2
  Dihedral angle restraints: 4202
    sinusoidal: 2101
      harmonic: 2101
  Sorted by residual:
  dihedral pdb=" C   SER A  36 "
           pdb=" N   SER A  36 "
           pdb=" CA  SER A  36 "
           pdb=" CB  SER A  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.52   15.92     0      2.50e+00 1.60e-01 4.05e+01
  dihedral pdb=" N   SER A  36 "
           pdb=" C   SER A  36 "
           pdb=" CA  SER A  36 "
           pdb=" CB  SER A  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.13  -11.33     0      2.50e+00 1.60e-01 2.05e+01
  dihedral pdb=" C4'  DT C  34 "
           pdb=" C3'  DT C  34 "
           pdb=" O3'  DT C  34 "
           pdb=" P    DT C  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.11  149.89     1      3.50e+01 8.16e-04 1.46e+01
  ... (remaining 4199 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.121: 1048
       0.121 -    0.241: 26
       0.241 -    0.362: 2
       0.362 -    0.482: 2
       0.482 -    0.603: 2
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CA  SER A  36 "
            pdb=" N   SER A  36 "
            pdb=" C   SER A  36 "
            pdb=" CB  SER A  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 9.09e+00
  chirality pdb=" C3'  DA C  45 "
            pdb=" C4'  DA C  45 "
            pdb=" O3'  DA C  45 "
            pdb=" C2'  DA C  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.14   -0.59 2.00e-01 2.50e+01 8.80e+00
  chirality pdb=" C3'  DA B   3 "
            pdb=" C4'  DA B   3 "
            pdb=" O3'  DA B   3 "
            pdb=" C2'  DA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.28   -0.45 2.00e-01 2.50e+01 5.05e+00
  ... (remaining 1077 not shown)

  Planarity restraints: 1087
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 250 "    0.015 2.00e-02 2.50e+03   3.13e-02 9.82e+00
        pdb=" C   HIS A 250 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   HIS A 250 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LYS A 251 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  39 "   -0.012 2.00e-02 2.50e+03   2.32e-02 5.39e+00
        pdb=" C   LYS A  39 "    0.040 2.00e-02 2.50e+03
        pdb=" O   LYS A  39 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A  40 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT D   7 "    0.031 2.00e-02 2.50e+03   1.46e-02 5.34e+00
        pdb=" N1   DT D   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DT D   7 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2   DT D   7 "   -0.016 2.00e-02 2.50e+03
        pdb=" N3   DT D   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DT D   7 "    0.005 2.00e-02 2.50e+03
        pdb=" O4   DT D   7 "    0.021 2.00e-02 2.50e+03
        pdb=" C5   DT D   7 "   -0.009 2.00e-02 2.50e+03
        pdb=" C7   DT D   7 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DT D   7 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1084 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 75
        2.52 -     3.12: 5161
        3.12 -     3.71: 11526
        3.71 -     4.31: 15281
        4.31 -     4.90: 24429
  Nonbonded interactions: 56472
  Sorted by model distance:
  nonbonded pdb=" OP1  DA C  49 "
            pdb=" CB  ARG A 585 "
     model   vdw
     1.930 3.440
  nonbonded pdb=" OP2  DG B   2 "
            pdb=" N   THR A 352 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" O   LEU A 260 "
            pdb=" OH  TYR A 690 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" C7   DT B   1 "
            pdb=" CZ  TYR A 339 "
     model   vdw
     2.192 3.680
  nonbonded pdb=" OP1  DA B   3 "
            pdb="MG    MG B 101 "
     model   vdw
     2.217 2.170
  ... (remaining 56467 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.410
  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:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
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      :  0.005   0.104   7126  Z= 0.383
  Angle     :  0.887  17.364   9839  Z= 0.571
  Chirality :  0.059   0.603   1080
  Planarity :  0.004   0.050   1087
  Dihedral  : 23.443 149.891   2842
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 22.54
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.76 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 24.38 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.31), residues: 710
  helix:  1.10 (0.35), residues: 225
  sheet: -0.09 (0.44), residues: 150
  loop : -1.35 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 502 
 TYR   0.010   0.001   TYR A 481 
 PHE   0.010   0.001   PHE A 673 
 TRP   0.005   0.001   TRP A 484 
 HIS   0.002   0.000   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.38 ( 7126)
  covalent geometry    : angle       0.88716 /  0.57 ( 9839)
  hydrogen bonds       : bond        0.23860 / 25.79 (  253)
  hydrogen bonds       : angle       8.60734 / 10.25 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  709 ARG cc_start: 0.8343 (tpt170) cc_final: 0.8009 (ttm-80)
  outliers start: 15
  outliers final: 3
  residues processed: 59
  average time/residue: 0.0909
  time to fit residues: 7.0768
Evaluate side-chains
  41 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue  429 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.0060
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.9400

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 GLN
A 282 GLN
A 298 HIS
A 376 HIS
A 495 ASN
A 555 GLN
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 711 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.076475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.060191 restraints weight = 22089.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.062155 restraints weight = 11249.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.063476 restraints weight = 7422.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.064342 restraints weight = 5679.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.064843 restraints weight = 4776.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7126  Z= 0.184
  Angle     :  0.753   9.133   9839  Z= 0.410
  Chirality :  0.051   0.237   1080
  Planarity :  0.005   0.052   1087
  Dihedral  : 24.865 156.277   1351
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.49 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 24.53 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.31), residues: 710
  helix:  1.32 (0.33), residues: 237
  sheet: -0.16 (0.42), residues: 155
  loop : -1.26 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 502 
 TYR   0.016   0.001   TYR A 638 
 PHE   0.019   0.002   PHE A 673 
 TRP   0.007   0.001   TRP A 484 
 HIS   0.003   0.001   HIS A 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.18 ( 7126)
  covalent geometry    : angle       0.75337 /  0.41 ( 9839)
  hydrogen bonds       : bond        0.05825 /  6.13 (  253)
  hydrogen bonds       : angle       5.36804 /  6.91 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
  outliers start: 19
  outliers final: 8
  residues processed: 62
  average time/residue: 0.0826
  time to fit residues: 7.1175
Evaluate side-chains
  47 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  633 HIS
Chi-restraints excluded: chain A residue  682 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    0.4980
   chunk 69 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   4 GLN
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 GLN
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 651 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.074676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.058788 restraints weight = 22140.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.060689 restraints weight = 11347.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.061986 restraints weight = 7512.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.062745 restraints weight = 5736.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.063373 restraints weight = 4871.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7126  Z= 0.187
  Angle     :  0.671   8.838   9839  Z= 0.365
  Chirality :  0.047   0.247   1080
  Planarity :  0.005   0.050   1087
  Dihedral  : 24.622 156.982   1350
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.92 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.50 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.31), residues: 710
  helix:  1.77 (0.35), residues: 227
  sheet: -0.33 (0.40), residues: 162
  loop : -1.33 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  57 
 TYR   0.015   0.001   TYR A 638 
 PHE   0.018   0.001   PHE A 673 
 TRP   0.009   0.001   TRP A 484 
 HIS   0.003   0.001   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.19 ( 7126)
  covalent geometry    : angle       0.67124 /  0.37 ( 9839)
  hydrogen bonds       : bond        0.04770 /  5.05 (  253)
  hydrogen bonds       : angle       4.96669 /  6.45 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A  584 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8751 (ttpt)
REVERT: A  625 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9124 (p)
  outliers start: 21
  outliers final: 6
  residues processed: 65
  average time/residue: 0.0834
  time to fit residues: 7.4971
Evaluate side-chains
  47 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  633 HIS
Chi-restraints excluded: chain A residue  682 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0270
   chunk 2 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    2.0044

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
A 557 GLN
** A 592 ASN ** 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 = 0.3285 r_free = 0.3285 target = 0.073272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.057115 restraints weight = 22453.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.059044 restraints weight = 11229.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.060365 restraints weight = 7326.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.061105 restraints weight = 5560.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.061699 restraints weight = 4712.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7126  Z= 0.200
  Angle     :  0.660   7.004   9839  Z= 0.356
  Chirality :  0.046   0.225   1080
  Planarity :  0.005   0.049   1087
  Dihedral  : 24.551 160.490   1349
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.21 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 24.22 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.32), residues: 710
  helix:  1.96 (0.35), residues: 226
  sheet: -0.40 (0.41), residues: 165
  loop : -1.32 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 184 
 TYR   0.017   0.001   TYR A 638 
 PHE   0.017   0.001   PHE A 673 
 TRP   0.006   0.001   TRP A 528 
 HIS   0.004   0.001   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00427 /  0.20 ( 7126)
  covalent geometry    : angle       0.66038 /  0.36 ( 9839)
  hydrogen bonds       : bond        0.04387 /  4.52 (  253)
  hydrogen bonds       : angle       4.84546 /  6.32 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 37
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 LEU cc_start: 0.8761 (tp) cc_final: 0.8425 (tt)
REVERT: A  376 HIS cc_start: 0.8594 (m90) cc_final: 0.8341 (m-70)
REVERT: A  584 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8780 (ttpt)
  outliers start: 16
  outliers final: 10
  residues processed: 49
  average time/residue: 0.0870
  time to fit residues: 5.8578
Evaluate side-chains
  46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  557 GLN
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 41 optimal weight:    6.9990
   chunk 42 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 2 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 3 optimal weight:    8.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 592 ASN ** 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 = 0.3300 r_free = 0.3300 target = 0.073912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.057901 restraints weight = 22295.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.059878 restraints weight = 10931.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.061207 restraints weight = 7014.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.062005 restraints weight = 5286.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.062588 restraints weight = 4443.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7126  Z= 0.150
  Angle     :  0.633   7.759   9839  Z= 0.340
  Chirality :  0.044   0.208   1080
  Planarity :  0.004   0.048   1087
  Dihedral  : 24.489 162.700   1349
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.49 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 24.84 %
    Favored  : 72.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.32), residues: 710
  helix:  1.89 (0.34), residues: 227
  sheet: -0.29 (0.41), residues: 165
  loop : -1.30 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 540 
 TYR   0.017   0.001   TYR A 638 
 PHE   0.014   0.001   PHE A 673 
 TRP   0.004   0.001   TRP A 528 
 HIS   0.002   0.001   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.15 ( 7126)
  covalent geometry    : angle       0.63295 /  0.34 ( 9839)
  hydrogen bonds       : bond        0.04098 /  4.20 (  253)
  hydrogen bonds       : angle       4.77318 /  6.39 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  584 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8773 (ttpt)
  outliers start: 14
  outliers final: 9
  residues processed: 51
  average time/residue: 0.0827
  time to fit residues: 5.9821
Evaluate side-chains
  46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.074417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.058341 restraints weight = 22299.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.060297 restraints weight = 10902.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.061648 restraints weight = 7011.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.062502 restraints weight = 5280.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.062974 restraints weight = 4409.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7126  Z= 0.136
  Angle     :  0.627   9.276   9839  Z= 0.330
  Chirality :  0.043   0.205   1080
  Planarity :  0.004   0.056   1087
  Dihedral  : 24.407 165.371   1349
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.92 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 24.38 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.32), residues: 710
  helix:  1.93 (0.34), residues: 226
  sheet: -0.20 (0.41), residues: 165
  loop : -1.23 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 589 
 TYR   0.016   0.001   TYR A 638 
 PHE   0.015   0.001   PHE A 673 
 TRP   0.004   0.001   TRP A 528 
 HIS   0.002   0.000   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.14 ( 7126)
  covalent geometry    : angle       0.62718 /  0.33 ( 9839)
  hydrogen bonds       : bond        0.03941 /  3.94 (  253)
  hydrogen bonds       : angle       4.63153 /  6.15 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  584 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8754 (ttpt)
REVERT: A  611 LEU cc_start: 0.9153 (mm) cc_final: 0.8652 (tt)
  outliers start: 16
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0899
  time to fit residues: 5.9067
Evaluate side-chains
  40 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 ASN
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.072715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.056703 restraints weight = 22123.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.058600 restraints weight = 11027.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.059858 restraints weight = 7149.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.060752 restraints weight = 5462.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.061155 restraints weight = 4550.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7126  Z= 0.196
  Angle     :  0.643   8.249   9839  Z= 0.339
  Chirality :  0.043   0.221   1080
  Planarity :  0.005   0.056   1087
  Dihedral  : 24.397 169.383   1349
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.20 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 25.00 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.32), residues: 710
  helix:  2.00 (0.35), residues: 226
  sheet: -0.27 (0.41), residues: 164
  loop : -1.26 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 184 
 TYR   0.015   0.001   TYR A 638 
 PHE   0.016   0.001   PHE A 673 
 TRP   0.008   0.001   TRP A 528 
 HIS   0.003   0.001   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00426 /  0.20 ( 7126)
  covalent geometry    : angle       0.64319 /  0.34 ( 9839)
  hydrogen bonds       : bond        0.03984 /  4.12 (  253)
  hydrogen bonds       : angle       4.72813 /  6.37 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 MET cc_start: 0.8534 (mmt) cc_final: 0.8321 (mmt)
REVERT: A  584 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8782 (ttpt)
REVERT: A  611 LEU cc_start: 0.9177 (mm) cc_final: 0.8625 (tt)
REVERT: A  702 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8298 (mm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 43
  average time/residue: 0.0899
  time to fit residues: 5.3570
Evaluate side-chains
  43 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.073153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.056855 restraints weight = 22425.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.058802 restraints weight = 11192.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.060104 restraints weight = 7266.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.060824 restraints weight = 5525.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.061447 restraints weight = 4720.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7126  Z= 0.160
  Angle     :  0.633   9.492   9839  Z= 0.332
  Chirality :  0.042   0.219   1080
  Planarity :  0.004   0.056   1087
  Dihedral  : 24.409 169.257   1349
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.49 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 25.47 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.32), residues: 710
  helix:  2.00 (0.35), residues: 227
  sheet: -0.21 (0.41), residues: 165
  loop : -1.21 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 652 
 TYR   0.017   0.001   TYR A 638 
 PHE   0.015   0.001   PHE A 673 
 TRP   0.004   0.001   TRP A 528 
 HIS   0.002   0.000   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 ( 7126)
  covalent geometry    : angle       0.63314 /  0.33 ( 9839)
  hydrogen bonds       : bond        0.03737 /  3.80 (  253)
  hydrogen bonds       : angle       4.56961 /  6.16 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 MET cc_start: 0.8492 (mmt) cc_final: 0.8271 (mmt)
REVERT: A  584 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8811 (ttpt)
REVERT: A  611 LEU cc_start: 0.9185 (mm) cc_final: 0.8658 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 43
  average time/residue: 0.0900
  time to fit residues: 5.3680
Evaluate side-chains
  40 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0050
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.7796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 108 GLN
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 HIS
** A 592 ASN ** 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 = 0.3308 r_free = 0.3308 target = 0.074309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.058184 restraints weight = 22230.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.060150 restraints weight = 11051.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.061497 restraints weight = 7146.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.062265 restraints weight = 5399.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.062857 restraints weight = 4558.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7126  Z= 0.126
  Angle     :  0.615  10.020   9839  Z= 0.322
  Chirality :  0.042   0.212   1080
  Planarity :  0.004   0.056   1087
  Dihedral  : 24.404 166.384   1349
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.92 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 25.47 %
    Favored  : 72.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.32), residues: 710
  helix:  2.07 (0.34), residues: 226
  sheet: -0.08 (0.41), residues: 163
  loop : -1.22 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 652 
 TYR   0.015   0.001   TYR A 638 
 PHE   0.012   0.001   PHE A 673 
 TRP   0.003   0.001   TRP A 368 
 HIS   0.001   0.000   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.13 ( 7126)
  covalent geometry    : angle       0.61471 /  0.32 ( 9839)
  hydrogen bonds       : bond        0.03653 /  3.62 (  253)
  hydrogen bonds       : angle       4.49717 /  6.02 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 MET cc_start: 0.8535 (mmt) cc_final: 0.8321 (mmt)
REVERT: A  584 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8736 (ttpt)
REVERT: A  611 LEU cc_start: 0.9182 (mm) cc_final: 0.8607 (tt)
  outliers start: 10
  outliers final: 7
  residues processed: 44
  average time/residue: 0.0887
  time to fit residues: 5.4570
Evaluate side-chains
  43 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  584 LYS
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0670
   chunk 69 optimal weight:    0.0040
   chunk 22 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.6134

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 592 ASN ** 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 = 0.3319 r_free = 0.3319 target = 0.074876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.058918 restraints weight = 22072.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.060864 restraints weight = 10922.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.062238 restraints weight = 7035.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.063132 restraints weight = 5280.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.063512 restraints weight = 4384.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7126  Z= 0.119
  Angle     :  0.618  10.230   9839  Z= 0.319
  Chirality :  0.042   0.219   1080
  Planarity :  0.004   0.056   1087
  Dihedral  : 24.420 165.139   1349
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.35 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 25.47 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.32), residues: 710
  helix:  2.12 (0.35), residues: 226
  sheet: -0.04 (0.42), residues: 163
  loop : -1.23 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 652 
 TYR   0.015   0.001   TYR A 638 
 PHE   0.014   0.001   PHE A 673 
 TRP   0.002   0.000   TRP A 368 
 HIS   0.001   0.000   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.12 ( 7126)
  covalent geometry    : angle       0.61828 /  0.32 ( 9839)
  hydrogen bonds       : bond        0.03547 /  3.51 (  253)
  hydrogen bonds       : angle       4.40831 /  5.88 (  714)

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

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

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1420 Ramachandran restraints generated.
    710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 MET cc_start: 0.8506 (mmt) cc_final: 0.8289 (mmt)
REVERT: A   18 MET cc_start: 0.9168 (tpp) cc_final: 0.8913 (tpp)
REVERT: A  237 LEU cc_start: 0.9176 (tp) cc_final: 0.8894 (tt)
REVERT: A  611 LEU cc_start: 0.9195 (mm) cc_final: 0.8601 (tt)
  outliers start: 8
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0689
  time to fit residues: 4.6100
Evaluate side-chains
  45 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue  201 ASN
Chi-restraints excluded: chain A residue  223 SER
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  429 PHE
Chi-restraints excluded: chain A residue  563 MET
Chi-restraints excluded: chain A residue  633 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0870
   overall best weight:    0.7362

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 592 ASN ** 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 = 0.3324 r_free = 0.3324 target = 0.075187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.059283 restraints weight = 21952.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.061289 restraints weight = 10751.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.062639 restraints weight = 6875.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.063413 restraints weight = 5152.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.064032 restraints weight = 4332.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7126  Z= 0.122
  Angle     :  0.599  10.338   9839  Z= 0.312
  Chirality :  0.042   0.220   1080
  Planarity :  0.004   0.056   1087
  Dihedral  : 24.387 162.566   1349
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.49 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 25.47 %
    Favored  : 72.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.32), residues: 710
  helix:  2.23 (0.34), residues: 225
  sheet:  0.04 (0.42), residues: 163
  loop : -1.23 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 652 
 TYR   0.016   0.001   TYR A 638 
 PHE   0.013   0.001   PHE A 673 
 TRP   0.013   0.001   TRP A 621 
 HIS   0.002   0.000   HIS A 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.12 ( 7126)
  covalent geometry    : angle       0.59893 /  0.31 ( 9839)
  hydrogen bonds       : bond        0.03509 /  3.45 (  253)
  hydrogen bonds       : angle       4.38603 /  5.82 (  714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1118.40 seconds
wall clock time: 20 minutes 7.09 seconds (1207.09 seconds total)