Starting phenix.real_space_refine
on Fri Sep 11 13:17:11 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6rjd_4902/09_2026/6rjd_4902.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rjd_4902/09_2026/6rjd_4902.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2026/6rjd_4902.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2026/6rjd_4902.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2026/6rjd_4902.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2026/6rjd_4902.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2026/6rjd_4902.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2026/6rjd_4902.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     123      5.49       5
     S      14      5.16       5
     C    5476      2.51       5
     N    1626      2.21       5
     O    2093      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9332
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 6757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 831, 6757
          Classifications: {'peptide': 831}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 811}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 1656
          Classifications: {'RNAv2': 78}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 9, 'rna3p': 68}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 646
          Classifications: {'DNA': 32}
          Link IDs: {'rna3p': 31}
    Chain: "G"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 273
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
  Time building chain proxies: 2.19, per 1000 atoms: 0.23
  Number of scatterers: 9332
  At special positions: 0
  Unit cell: (100.457, 133.35, 113.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     123     15.00
     O    2093      8.00
     N    1626      7.00
     C    5476      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: 0.64
  Conformation dependent library (CDL) restraints added in 222.5 milliseconds
  

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 6 sheets defined
      43.1% alpha, 11.7% beta
      38 base pairs and 83 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'C' and resid 40 through 73
      removed outlier: 3.725A  pdb=" N   LEU C  44 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER C  73 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 98
      removed outlier: 3.867A  pdb=" N   THR C  97 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 115
      removed outlier: 3.501A  pdb=" N   HIS C 115 " --> pdb=" O   ASN C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 146
      removed outlier: 4.257A  pdb=" N   ILE C 138 " --> pdb=" O   ASP C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 163
    Processing helix  chain 'C' and resid 185 through 204
      removed outlier: 3.732A  pdb=" N   TYR C 189 " --> pdb=" O   PRO C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 220
    Processing helix  chain 'C' and resid 250 through 254
      removed outlier: 3.541A  pdb=" N   GLY C 253 " --> pdb=" O   ASN C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 287
      removed outlier: 3.685A  pdb=" N   LEU C 287 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 311
    Processing helix  chain 'C' and resid 315 through 328
      removed outlier: 3.734A  pdb=" N   LEU C 319 " --> pdb=" O   GLY C 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 358
    Processing helix  chain 'C' and resid 369 through 382
    Processing helix  chain 'C' and resid 384 through 396
      removed outlier: 3.784A  pdb=" N   ILE C 388 " --> pdb=" O   GLU C 384 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE C 396 " --> pdb=" O   LEU C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 416
    Processing helix  chain 'C' and resid 418 through 422
      removed outlier: 3.621A  pdb=" N   GLY C 421 " --> pdb=" O   SER C 418 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   LYS C 422 " --> pdb=" O   ILE C 419 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 418 through 422'
    Processing helix  chain 'C' and resid 428 through 436
    Processing helix  chain 'C' and resid 437 through 439
      No H-bonds generated for 'chain 'C' and resid 437 through 439'
    Processing helix  chain 'C' and resid 445 through 453
    Processing helix  chain 'C' and resid 470 through 475
    Processing helix  chain 'C' and resid 479 through 501
    Processing helix  chain 'C' and resid 691 through 705
    Processing helix  chain 'C' and resid 737 through 748
    Processing helix  chain 'C' and resid 854 through 868
    Processing helix  chain 'C' and resid 869 through 872
      removed outlier: 3.804A  pdb=" N   PHE C 872 " --> pdb=" O   LYS C 869 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 869 through 872'
    Processing helix  chain 'C' and resid 879 through 892
      removed outlier: 3.880A  pdb=" N   GLU C 883 " --> pdb=" O   PRO C 879 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LYS C 884 " --> pdb=" O   GLN C 880 " (cutoff:3.500A)
      Proline residue:  C 888  - end of helix
    Processing helix  chain 'C' and resid 910 through 918
    Processing helix  chain 'C' and resid 1000 through 1012
      removed outlier: 3.518A  pdb=" N   TYR C1004 " --> pdb=" O   SER C1000 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 34
      removed outlier: 6.651A  pdb=" N   ILE C  19 " --> pdb=" O   ILE C  28 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   LYS C  30 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL C  17 " --> pdb=" O   LYS C  30 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   SER C  32 " --> pdb=" O   VAL C  15 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   VAL C  15 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ASN C 505 " --> pdb=" O   LEU C   4 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE C 508 " --> pdb=" O   SER C 712 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 169 through 172
      removed outlier: 3.558A  pdb=" N   HIS C 178 " --> pdb=" O   VAL C 171 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 935 through 941
      removed outlier: 5.768A  pdb=" N   LYS C 936 " --> pdb=" O   ILE C 849 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ILE C 849 " --> pdb=" O   LYS C 936 " (cutoff:3.500A)
      removed outlier: 5.643A  pdb=" N   TYR C 938 " --> pdb=" O   GLY C 847 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   GLY C 847 " --> pdb=" O   TYR C 938 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   SER C 940 " --> pdb=" O   VAL C 845 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   ALA C 829 " --> pdb=" O   LEU C 846 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 977 through 984
      removed outlier: 3.553A  pdb=" N   LYS C 977 " --> pdb=" O   ASN C 972 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ARG C 966 " --> pdb=" O   LEU C 983 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE C1021 " --> pdb=" O   VAL C 969 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   PHE C 971 " --> pdb=" O   PHE C1019 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   PHE C1019 " --> pdb=" O   PHE C 971 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 989 through 990
      removed outlier: 3.878A  pdb=" N   GLN C 989 " --> pdb=" O   LYS C 998 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LYS C 998 " --> pdb=" O   GLN C 989 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 1057 through 1059
      removed outlier: 5.516A  pdb=" N   LYS C1059 " --> pdb=" O   PHE C1044 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   PHE C1044 " --> pdb=" O   LYS C1059 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   LEU C1028 " --> pdb=" O   VAL C1099 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL C1099 " --> pdb=" O   LEU C1028 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    819 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      91 hydrogen bonds
      178 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      83 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2012
        1.33 -     1.45: 2680
        1.45 -     1.57: 4789
        1.57 -     1.69: 241
        1.69 -     1.81: 25
  Bond restraints: 9747
  Sorted by residual:
  bond pdb=" C1'  DC E  28 "
       pdb=" N1   DC E  28 "
    ideal  model  delta    sigma   weight residual
    1.468  1.536 -0.068 1.40e-02 5.10e+03 2.34e+01
  bond pdb=" C1'  DC E  35 "
       pdb=" N1   DC E  35 "
    ideal  model  delta    sigma   weight residual
    1.468  1.517 -0.049 1.40e-02 5.10e+03 1.23e+01
  bond pdb=" C3'  DC E  20 "
       pdb=" O3'  DC E  20 "
    ideal  model  delta    sigma   weight residual
    1.435  1.396  0.039 1.30e-02 5.92e+03 8.84e+00
  bond pdb=" C3'  DT E  11 "
       pdb=" O3'  DT E  11 "
    ideal  model  delta    sigma   weight residual
    1.435  1.472 -0.037 1.30e-02 5.92e+03 8.03e+00
  bond pdb=" C1'  DC E  40 "
       pdb=" N1   DC E  40 "
    ideal  model  delta    sigma   weight residual
    1.468  1.506 -0.038 1.40e-02 5.10e+03 7.49e+00
  ... (remaining 9742 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 13003
        2.22 -     4.44: 598
        4.44 -     6.67: 52
        6.67 -     8.89: 12
        8.89 -    11.11: 4
  Bond angle restraints: 13669
  Sorted by residual:
  angle pdb=" O4'  DA G  12 "
        pdb=" C4'  DA G  12 "
        pdb=" C3'  DA G  12 "
      ideal   model   delta    sigma   weight residual
     106.00  102.18    3.82 6.00e-01 2.78e+00 4.06e+01
  angle pdb=" C3'  DG G   4 "
        pdb=" O3'  DG G   4 "
        pdb=" P    DA G   5 "
      ideal   model   delta    sigma   weight residual
     119.70  125.98   -6.28 1.20e+00 6.94e-01 2.74e+01
  angle pdb=" O4'  DG G   4 "
        pdb=" C1'  DG G   4 "
        pdb=" N9   DG G   4 "
      ideal   model   delta    sigma   weight residual
     108.00  111.61   -3.61 7.00e-01 2.04e+00 2.66e+01
  angle pdb=" O4'  DT E  34 "
        pdb=" C4'  DT E  34 "
        pdb=" C3'  DT E  34 "
      ideal   model   delta    sigma   weight residual
     106.00  102.93    3.07 6.00e-01 2.78e+00 2.61e+01
  angle pdb=" O4'  DG G   4 "
        pdb=" C4'  DG G   4 "
        pdb=" C3'  DG G   4 "
      ideal   model   delta    sigma   weight residual
     106.00  103.00    3.00 6.00e-01 2.78e+00 2.50e+01
  ... (remaining 13664 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.69: 5241
       34.69 -    69.37: 388
       69.37 -   104.06: 18
      104.06 -   138.74: 0
      138.74 -   173.43: 2
  Dihedral angle restraints: 5649
    sinusoidal: 3222
      harmonic: 2427
  Sorted by residual:
  dihedral pdb=" C4'   U D   8 "
           pdb=" C3'   U D   8 "
           pdb=" C2'   U D   8 "
           pdb=" C1'   U D   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -37.61   73.95     1      3.10e+00 1.04e-01 7.23e+02
  dihedral pdb=" C4'   U D  74 "
           pdb=" C3'   U D  74 "
           pdb=" C2'   U D  74 "
           pdb=" C1'   U D  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.57   72.91     1      3.10e+00 1.04e-01 7.05e+02
  dihedral pdb=" C4'   U D  73 "
           pdb=" C3'   U D  73 "
           pdb=" C2'   U D  73 "
           pdb=" C1'   U D  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.48   72.82     1      3.10e+00 1.04e-01 7.04e+02
  ... (remaining 5646 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1267
       0.077 -    0.154: 199
       0.154 -    0.231: 67
       0.231 -    0.308: 45
       0.308 -    0.385: 1
  Chirality restraints: 1579
  Sorted by residual:
  chirality pdb=" C2'   U D   8 "
            pdb=" C3'   U D   8 "
            pdb=" O2'   U D   8 "
            pdb=" C1'   U D   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.40   -0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" C2'   U D  73 "
            pdb=" C3'   U D  73 "
            pdb=" O2'   U D  73 "
            pdb=" C1'   U D  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.50   -0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" C2'   G D  57 "
            pdb=" C3'   G D  57 "
            pdb=" O2'   G D  57 "
            pdb=" C1'   G D  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.51   -0.28 2.00e-01 2.50e+01 2.00e+00
  ... (remaining 1576 not shown)

  Planarity restraints: 1301
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  63 "   -0.030 2.00e-02 2.50e+03   1.81e-02 8.98e+00
        pdb=" N9    A D  63 "    0.049 2.00e-02 2.50e+03
        pdb=" C8    A D  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A D  63 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A D  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A D  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A D  63 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    A D  63 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A D  63 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    A D  63 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A D  63 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 466 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.88e+00
        pdb=" C   LYS C 466 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LYS C 466 "    0.017 2.00e-02 2.50e+03
        pdb=" N   TYR C 467 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 249 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.59e+00
        pdb=" C   ASP C 249 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASP C 249 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN C 250 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1298 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2004
        2.79 -     3.32: 7363
        3.32 -     3.84: 15404
        3.84 -     4.37: 18273
        4.37 -     4.90: 28971
  Nonbonded interactions: 72015
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C  89 "
            pdb=" OP1   A D  63 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ALA C 376 "
            pdb=" OG1 THR C 380 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   SER C 119 "
            pdb=" OG  SER C 119 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OG1 THR C 830 "
            pdb=" O   LYS C 956 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OD2 ASP C 968 "
            pdb=" OH  TYR C1004 "
     model   vdw
     2.346 3.040
  ... (remaining 72010 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:             2.140
  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:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.710
  Find NCS groups from input model:        0.050
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
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   0.068   9747  Z= 0.382
  Angle     :  1.007  11.110  13669  Z= 0.598
  Chirality :  0.078   0.385   1579
  Planarity :  0.006   0.041   1301
  Dihedral  : 19.960 173.426   4089
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 10.28 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.53 (0.23), residues: 817
  helix: -2.01 (0.22), residues: 328
  sheet: -2.03 (0.50), residues: 100
  loop : -2.69 (0.25), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 166 
 TYR   0.038   0.002   TYR C1055 
 PHE   0.029   0.002   PHE C 169 
 TRP   0.005   0.002   TRP C 965 
 HIS   0.006   0.001   HIS C 348 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00613 /  0.38 ( 9747)
  covalent geometry    : angle       1.00740 /  0.60 (13669)
  hydrogen bonds       : bond        0.13570 /  8.98 (  369)
  hydrogen bonds       : angle       5.86413 /  4.01 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: C  367 MET cc_start: 0.4696 (mmm) cc_final: 0.4342 (mtp)
REVERT: C  437 PRO cc_start: 0.8637 (Cg_exo) cc_final: 0.8267 (Cg_endo)
REVERT: C  438 GLU cc_start: 0.8051 (mp0) cc_final: 0.7160 (mp0)
REVERT: C  465 THR cc_start: 0.7825 (m) cc_final: 0.7375 (p)
REVERT: C  487 ARG cc_start: 0.7048 (mtp180) cc_final: 0.6255 (mtm180)
REVERT: C  699 GLN cc_start: 0.6582 (mt0) cc_final: 0.6113 (tt0)
REVERT: C  869 LYS cc_start: 0.8139 (mttt) cc_final: 0.7669 (ttpt)
REVERT: C  921 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.8082 (mtp85)
REVERT: C  931 GLU cc_start: 0.7495 (mp0) cc_final: 0.7289 (mp0)
REVERT: C 1047 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7516 (tpt-90)
  outliers start: 2
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1281
  time to fit residues: 19.2577
Evaluate side-chains
  69 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1047 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.4584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 300 GLN
C 494 ASN
C 928 ASN
C1054 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.159884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.127778 restraints weight = 14024.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.92
r_work: 0.3312 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9747  Z= 0.184
  Angle     :  1.015  22.744  13669  Z= 0.442
  Chirality :  0.092   1.206   1579
  Planarity :  0.004   0.034   1301
  Dihedral  : 19.138 162.753   2353
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.21 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.26), residues: 817
  helix: -0.13 (0.26), residues: 336
  sheet: -1.20 (0.55), residues: 84
  loop : -2.51 (0.25), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  57 
 TYR   0.018   0.001   TYR C 467 
 PHE   0.009   0.001   PHE C 872 
 TRP   0.002   0.001   TRP C 965 
 HIS   0.009   0.001   HIS C 178 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.18 ( 9747)
  covalent geometry    : angle       1.01473 /  0.44 (13669)
  hydrogen bonds       : bond        0.05873 /  3.99 (  369)
  hydrogen bonds       : angle       4.54956 /  3.13 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7262 (mp0)
REVERT: C  346 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7309 (tm-30)
REVERT: C  367 MET cc_start: 0.4766 (mmm) cc_final: 0.4391 (mtp)
REVERT: C  438 GLU cc_start: 0.8261 (mp0) cc_final: 0.7586 (mp0)
REVERT: C  465 THR cc_start: 0.7744 (m) cc_final: 0.7383 (p)
REVERT: C  487 ARG cc_start: 0.7606 (mtp180) cc_final: 0.6813 (mtm180)
REVERT: C  699 GLN cc_start: 0.6698 (mt0) cc_final: 0.6168 (tt0)
REVERT: C  869 LYS cc_start: 0.8262 (mttt) cc_final: 0.7809 (ttpt)
REVERT: C  931 GLU cc_start: 0.7758 (mp0) cc_final: 0.7428 (mp0)
  outliers start: 15
  outliers final: 9
  residues processed: 92
  average time/residue: 0.1059
  time to fit residues: 13.3831
Evaluate side-chains
  71 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  499 GLU
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  928 ASN
Chi-restraints excluded: chain C residue 1099 VAL
Chi-restraints excluded: chain C residue 1104 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   chunk 60 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  43 ASN
C1108 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.153218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.117433 restraints weight = 14144.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.90
r_work: 0.3251 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070   9747  Z= 0.337
  Angle     :  0.994  14.976  13669  Z= 0.460
  Chirality :  0.076   0.870   1579
  Planarity :  0.005   0.041   1301
  Dihedral  : 19.093 160.185   2349
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.56 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.27), residues: 817
  helix:  0.16 (0.27), residues: 342
  sheet: -1.34 (0.51), residues: 90
  loop : -2.59 (0.27), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  57 
 TYR   0.032   0.002   TYR C1055 
 PHE   0.023   0.002   PHE C1021 
 TRP   0.006   0.002   TRP C 965 
 HIS   0.006   0.001   HIS C1108 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00741 /  0.34 ( 9747)
  covalent geometry    : angle       0.99403 /  0.46 (13669)
  hydrogen bonds       : bond        0.07842 /  5.37 (  369)
  hydrogen bonds       : angle       4.63538 /  3.18 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7172 (mp0)
REVERT: C  314 MET cc_start: 0.7662 (ptm) cc_final: 0.7433 (ptt)
REVERT: C  339 ILE cc_start: 0.8787 (tt) cc_final: 0.8479 (tp)
REVERT: C  346 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7238 (tm-30)
REVERT: C  438 GLU cc_start: 0.8327 (mp0) cc_final: 0.7650 (mp0)
REVERT: C  465 THR cc_start: 0.7507 (m) cc_final: 0.7053 (p)
REVERT: C  487 ARG cc_start: 0.7586 (mtp180) cc_final: 0.6769 (mtm110)
REVERT: C  699 GLN cc_start: 0.6772 (mt0) cc_final: 0.6276 (tt0)
REVERT: C  869 LYS cc_start: 0.8279 (mttt) cc_final: 0.7792 (ttpt)
  outliers start: 29
  outliers final: 19
  residues processed: 94
  average time/residue: 0.1026
  time to fit residues: 13.5821
Evaluate side-chains
  79 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   70 PHE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain C residue  486 VAL
Chi-restraints excluded: chain C residue  499 GLU
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  881 THR
Chi-restraints excluded: chain C residue  886 ILE
Chi-restraints excluded: chain C residue 1022 THR
Chi-restraints excluded: chain C residue 1047 ARG
Chi-restraints excluded: chain C residue 1058 LEU
Chi-restraints excluded: chain C residue 1099 VAL
Chi-restraints excluded: chain C residue 1104 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 83 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 12 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.157686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.125840 restraints weight = 14311.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.00
r_work: 0.3281 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9747  Z= 0.169
  Angle     :  0.821  16.247  13669  Z= 0.378
  Chirality :  0.065   0.667   1579
  Planarity :  0.003   0.035   1301
  Dihedral  : 18.994 155.093   2349
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.46 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.28), residues: 817
  helix:  0.80 (0.28), residues: 337
  sheet: -1.18 (0.51), residues: 92
  loop : -2.41 (0.27), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  50 
 TYR   0.016   0.001   TYR C 215 
 PHE   0.009   0.001   PHE C1021 
 TRP   0.002   0.001   TRP C 965 
 HIS   0.004   0.001   HIS C 178 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.17 ( 9747)
  covalent geometry    : angle       0.82097 /  0.38 (13669)
  hydrogen bonds       : bond        0.05507 /  3.72 (  369)
  hydrogen bonds       : angle       4.25822 /  2.91 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7234 (mp0)
REVERT: C  337 TYR cc_start: 0.7619 (p90) cc_final: 0.7272 (p90)
REVERT: C  339 ILE cc_start: 0.8780 (tt) cc_final: 0.8434 (tp)
REVERT: C  346 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7184 (tm-30)
REVERT: C  438 GLU cc_start: 0.8304 (mp0) cc_final: 0.7566 (mp0)
REVERT: C  465 THR cc_start: 0.7370 (m) cc_final: 0.6887 (p)
REVERT: C  487 ARG cc_start: 0.7585 (mtp180) cc_final: 0.6767 (mtm180)
REVERT: C  699 GLN cc_start: 0.6656 (mt0) cc_final: 0.6188 (tt0)
REVERT: C  869 LYS cc_start: 0.8253 (mttt) cc_final: 0.7988 (mtmt)
  outliers start: 26
  outliers final: 20
  residues processed: 92
  average time/residue: 0.0984
  time to fit residues: 12.7116
Evaluate side-chains
  84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue   70 PHE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  477 ILE
Chi-restraints excluded: chain C residue  507 VAL
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  886 ILE
Chi-restraints excluded: chain C residue  887 GLU
Chi-restraints excluded: chain C residue 1047 ARG
Chi-restraints excluded: chain C residue 1058 LEU
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain C residue 1099 VAL
Chi-restraints excluded: chain C residue 1101 THR
Chi-restraints excluded: chain C residue 1104 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 50 optimal weight:    0.2980
   chunk 45 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 90 optimal weight:   20.0000
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.160320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.129301 restraints weight = 13995.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.05
r_work: 0.3289 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9747  Z= 0.154
  Angle     :  0.756  14.669  13669  Z= 0.351
  Chirality :  0.058   0.544   1579
  Planarity :  0.003   0.036   1301
  Dihedral  : 18.820 156.304   2349
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.67 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.28), residues: 817
  helix:  1.20 (0.28), residues: 337
  sheet: -1.05 (0.53), residues: 87
  loop : -2.27 (0.27), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 385 
 TYR   0.014   0.001   TYR C1055 
 PHE   0.009   0.001   PHE C1066 
 TRP   0.002   0.001   TRP C 965 
 HIS   0.004   0.001   HIS C 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.15 ( 9747)
  covalent geometry    : angle       0.75633 /  0.35 (13669)
  hydrogen bonds       : bond        0.04920 /  3.29 (  369)
  hydrogen bonds       : angle       4.02409 /  2.74 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7237 (mp0)
REVERT: C  314 MET cc_start: 0.7637 (ptm) cc_final: 0.7360 (ptt)
REVERT: C  337 TYR cc_start: 0.7679 (p90) cc_final: 0.7341 (p90)
REVERT: C  339 ILE cc_start: 0.8782 (tt) cc_final: 0.8441 (tp)
REVERT: C  346 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7143 (tm-30)
REVERT: C  438 GLU cc_start: 0.8285 (mp0) cc_final: 0.7495 (mp0)
REVERT: C  465 THR cc_start: 0.7340 (m) cc_final: 0.6849 (p)
REVERT: C  487 ARG cc_start: 0.7576 (mtp180) cc_final: 0.6610 (mtm180)
REVERT: C  699 GLN cc_start: 0.6670 (mt0) cc_final: 0.6246 (tt0)
REVERT: C  869 LYS cc_start: 0.8230 (mttt) cc_final: 0.7962 (mtmt)
  outliers start: 25
  outliers final: 20
  residues processed: 96
  average time/residue: 0.0999
  time to fit residues: 13.4586
Evaluate side-chains
  83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   70 PHE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  477 ILE
Chi-restraints excluded: chain C residue  507 VAL
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  886 ILE
Chi-restraints excluded: chain C residue  887 GLU
Chi-restraints excluded: chain C residue 1047 ARG
Chi-restraints excluded: chain C residue 1058 LEU
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain C residue 1099 VAL
Chi-restraints excluded: chain C residue 1101 THR
Chi-restraints excluded: chain C residue 1104 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 2 optimal weight:    0.3980
   chunk 24 optimal weight:    0.4980
   chunk 9 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 70 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.160594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.129268 restraints weight = 14269.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 2.06
r_work: 0.3312 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9747  Z= 0.133
  Angle     :  0.722  13.713  13669  Z= 0.336
  Chirality :  0.055   0.483   1579
  Planarity :  0.003   0.034   1301
  Dihedral  : 18.633 157.272   2349
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 18.94 %
    Favored  : 77.40 %
  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: -0.64 (0.29), residues: 817
  helix:  1.46 (0.28), residues: 337
  sheet: -0.85 (0.54), residues: 86
  loop : -2.11 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 413 
 TYR   0.011   0.001   TYR C 215 
 PHE   0.009   0.001   PHE C1066 
 TRP   0.002   0.001   TRP C 424 
 HIS   0.003   0.001   HIS C1108 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.13 ( 9747)
  covalent geometry    : angle       0.72178 /  0.34 (13669)
  hydrogen bonds       : bond        0.04446 /  2.96 (  369)
  hydrogen bonds       : angle       3.86309 /  2.64 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7236 (mp0)
REVERT: C  314 MET cc_start: 0.7606 (ptm) cc_final: 0.7337 (ptt)
REVERT: C  337 TYR cc_start: 0.7682 (p90) cc_final: 0.7370 (p90)
REVERT: C  339 ILE cc_start: 0.8780 (tt) cc_final: 0.8434 (tp)
REVERT: C  438 GLU cc_start: 0.8242 (mp0) cc_final: 0.7429 (mp0)
REVERT: C  465 THR cc_start: 0.7239 (m) cc_final: 0.6780 (p)
REVERT: C  487 ARG cc_start: 0.7589 (mtp180) cc_final: 0.6668 (mtm110)
REVERT: C  699 GLN cc_start: 0.6684 (mt0) cc_final: 0.6204 (tt0)
REVERT: C  869 LYS cc_start: 0.8239 (mttt) cc_final: 0.7989 (mtmt)
  outliers start: 27
  outliers final: 20
  residues processed: 95
  average time/residue: 0.0921
  time to fit residues: 12.3276
Evaluate side-chains
  83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue   70 PHE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  477 ILE
Chi-restraints excluded: chain C residue  507 VAL
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  886 ILE
Chi-restraints excluded: chain C residue  887 GLU
Chi-restraints excluded: chain C residue 1047 ARG
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain C residue 1075 VAL
Chi-restraints excluded: chain C residue 1099 VAL
Chi-restraints excluded: chain C residue 1101 THR
Chi-restraints excluded: chain C residue 1104 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0970
   chunk 1 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0870
   chunk 61 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    1.0360

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.161211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.129672 restraints weight = 14228.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.03
r_work: 0.3322 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9747  Z= 0.131
  Angle     :  0.709  12.805  13669  Z= 0.332
  Chirality :  0.053   0.430   1579
  Planarity :  0.003   0.034   1301
  Dihedral  : 18.513 158.119   2349
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.81 %
    Favored  : 77.67 %
  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: -0.43 (0.29), residues: 817
  helix:  1.64 (0.28), residues: 338
  sheet: -0.67 (0.56), residues: 84
  loop : -2.03 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 385 
 TYR   0.012   0.001   TYR C 978 
 PHE   0.009   0.001   PHE C1066 
 TRP   0.002   0.001   TRP C 965 
 HIS   0.003   0.000   HIS C 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.13 ( 9747)
  covalent geometry    : angle       0.70867 /  0.33 (13669)
  hydrogen bonds       : bond        0.04311 /  2.88 (  369)
  hydrogen bonds       : angle       3.81982 /  2.60 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7274 (mp0)
REVERT: C  314 MET cc_start: 0.7612 (ptm) cc_final: 0.7353 (ptt)
REVERT: C  337 TYR cc_start: 0.7725 (p90) cc_final: 0.7423 (p90)
REVERT: C  339 ILE cc_start: 0.8776 (tt) cc_final: 0.8427 (tp)
REVERT: C  414 LYS cc_start: 0.7851 (mttm) cc_final: 0.7346 (tttm)
REVERT: C  438 GLU cc_start: 0.8230 (mp0) cc_final: 0.7381 (mp0)
REVERT: C  465 THR cc_start: 0.7309 (m) cc_final: 0.6853 (p)
REVERT: C  487 ARG cc_start: 0.7573 (mtp180) cc_final: 0.6659 (mtm110)
REVERT: C  699 GLN cc_start: 0.6658 (mt0) cc_final: 0.6169 (tt0)
REVERT: C  869 LYS cc_start: 0.8226 (mttt) cc_final: 0.7982 (mtmt)
  outliers start: 26
  outliers final: 22
  residues processed: 91
  average time/residue: 0.1032
  time to fit residues: 13.2427
Evaluate side-chains
  86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue   70 PHE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  477 ILE
Chi-restraints excluded: chain C residue  507 VAL
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  886 ILE
Chi-restraints excluded: chain C residue  887 GLU
Chi-restraints excluded: chain C residue 1047 ARG
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain C residue 1075 VAL
Chi-restraints excluded: chain C residue 1099 VAL
Chi-restraints excluded: chain C residue 1101 THR
Chi-restraints excluded: chain C residue 1104 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 90 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.161485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.126171 restraints weight = 14173.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.92
r_work: 0.3368 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9747  Z= 0.132
  Angle     :  0.697  12.005  13669  Z= 0.327
  Chirality :  0.052   0.384   1579
  Planarity :  0.003   0.034   1301
  Dihedral  : 18.413 158.821   2349
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.49 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.29), residues: 817
  helix:  1.75 (0.28), residues: 338
  sheet: -0.68 (0.57), residues: 84
  loop : -1.98 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  33 
 TYR   0.011   0.001   TYR C1055 
 PHE   0.012   0.001   PHE C 503 
 TRP   0.002   0.001   TRP C 965 
 HIS   0.003   0.000   HIS C 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.13 ( 9747)
  covalent geometry    : angle       0.69694 /  0.33 (13669)
  hydrogen bonds       : bond        0.04199 /  2.80 (  369)
  hydrogen bonds       : angle       3.77487 /  2.57 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7205 (mp0)
REVERT: C  314 MET cc_start: 0.7580 (ptm) cc_final: 0.7325 (ptt)
REVERT: C  337 TYR cc_start: 0.7688 (p90) cc_final: 0.7365 (p90)
REVERT: C  339 ILE cc_start: 0.8755 (tt) cc_final: 0.8399 (tp)
REVERT: C  438 GLU cc_start: 0.8189 (mp0) cc_final: 0.7313 (mp0)
REVERT: C  465 THR cc_start: 0.7271 (m) cc_final: 0.6811 (p)
REVERT: C  487 ARG cc_start: 0.7425 (mtp180) cc_final: 0.6499 (mtm110)
REVERT: C  699 GLN cc_start: 0.6652 (mt0) cc_final: 0.6163 (tt0)
  outliers start: 22
  outliers final: 20
  residues processed: 85
  average time/residue: 0.1053
  time to fit residues: 12.4811
Evaluate side-chains
  83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue   70 PHE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  477 ILE
Chi-restraints excluded: chain C residue  507 VAL
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  886 ILE
Chi-restraints excluded: chain C residue  887 GLU
Chi-restraints excluded: chain C residue 1047 ARG
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain C residue 1099 VAL
Chi-restraints excluded: chain C residue 1104 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 34 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    2.3988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.158469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.122815 restraints weight = 14145.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.92
r_work: 0.3314 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9747  Z= 0.194
  Angle     :  0.760  10.916  13669  Z= 0.356
  Chirality :  0.056   0.361   1579
  Planarity :  0.003   0.035   1301
  Dihedral  : 18.356 158.325   2349
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.62 %
    Favored  : 77.27 %
  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: -0.48 (0.29), residues: 817
  helix:  1.60 (0.28), residues: 342
  sheet: -0.76 (0.57), residues: 85
  loop : -2.08 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  62 
 TYR   0.019   0.001   TYR C 978 
 PHE   0.013   0.002   PHE C 184 
 TRP   0.003   0.001   TRP C 965 
 HIS   0.003   0.001   HIS C  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00421 /  0.19 ( 9747)
  covalent geometry    : angle       0.76039 /  0.36 (13669)
  hydrogen bonds       : bond        0.05168 /  3.49 (  369)
  hydrogen bonds       : angle       3.89523 /  2.64 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7205 (mp0)
REVERT: C  314 MET cc_start: 0.7609 (ptm) cc_final: 0.7342 (ptt)
REVERT: C  337 TYR cc_start: 0.7712 (p90) cc_final: 0.7397 (p90)
REVERT: C  414 LYS cc_start: 0.7839 (mttm) cc_final: 0.7355 (tttm)
REVERT: C  438 GLU cc_start: 0.8259 (mp0) cc_final: 0.7233 (mp0)
REVERT: C  465 THR cc_start: 0.7366 (m) cc_final: 0.6882 (p)
REVERT: C  487 ARG cc_start: 0.7524 (mtp180) cc_final: 0.6597 (mtm110)
REVERT: C  699 GLN cc_start: 0.6663 (mt0) cc_final: 0.6159 (tt0)
  outliers start: 23
  outliers final: 21
  residues processed: 83
  average time/residue: 0.1022
  time to fit residues: 12.1967
Evaluate side-chains
  81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue   70 PHE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  477 ILE
Chi-restraints excluded: chain C residue  507 VAL
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  886 ILE
Chi-restraints excluded: chain C residue 1047 ARG
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain C residue 1075 VAL
Chi-restraints excluded: chain C residue 1099 VAL
Chi-restraints excluded: chain C residue 1101 THR
Chi-restraints excluded: chain C residue 1104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 1 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0060
   chunk 45 optimal weight:    8.9990
   chunk 88 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    1.4002

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.159937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.128370 restraints weight = 14220.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.01
r_work: 0.3310 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9747  Z= 0.147
  Angle     :  0.717  11.171  13669  Z= 0.336
  Chirality :  0.053   0.339   1579
  Planarity :  0.003   0.034   1301
  Dihedral  : 18.371 159.521   2349
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.89 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.29), residues: 817
  helix:  1.77 (0.28), residues: 338
  sheet: -0.72 (0.57), residues: 85
  loop : -2.04 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  33 
 TYR   0.015   0.001   TYR C 978 
 PHE   0.014   0.001   PHE C 503 
 TRP   0.002   0.001   TRP C 965 
 HIS   0.002   0.000   HIS C 425 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.15 ( 9747)
  covalent geometry    : angle       0.71702 /  0.34 (13669)
  hydrogen bonds       : bond        0.04597 /  3.08 (  369)
  hydrogen bonds       : angle       3.83745 /  2.59 (  997)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7266 (mp0)
REVERT: C  314 MET cc_start: 0.7606 (ptm) cc_final: 0.7350 (ptt)
REVERT: C  337 TYR cc_start: 0.7728 (p90) cc_final: 0.7408 (p90)
REVERT: C  414 LYS cc_start: 0.7824 (mttm) cc_final: 0.7347 (tttm)
REVERT: C  438 GLU cc_start: 0.8252 (mp0) cc_final: 0.7398 (mp0)
REVERT: C  487 ARG cc_start: 0.7593 (mtp180) cc_final: 0.6661 (mtm110)
REVERT: C  699 GLN cc_start: 0.6649 (mt0) cc_final: 0.6169 (tt0)
  outliers start: 23
  outliers final: 22
  residues processed: 83
  average time/residue: 0.0967
  time to fit residues: 11.4258
Evaluate side-chains
  84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue   70 PHE
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  477 ILE
Chi-restraints excluded: chain C residue  507 VAL
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  881 THR
Chi-restraints excluded: chain C residue  886 ILE
Chi-restraints excluded: chain C residue  887 GLU
Chi-restraints excluded: chain C residue 1047 ARG
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain C residue 1099 VAL
Chi-restraints excluded: chain C residue 1101 THR
Chi-restraints excluded: chain C residue 1104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 55 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    1.2982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.162083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.127311 restraints weight = 13910.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 1.83
r_work: 0.3359 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9747  Z= 0.140
  Angle     :  0.701  10.595  13669  Z= 0.329
  Chirality :  0.052   0.317   1579
  Planarity :  0.003   0.034   1301
  Dihedral  : 18.320 159.624   2349
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.76 %
    Favored  : 77.13 %
  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: -0.24 (0.29), residues: 817
  helix:  1.87 (0.28), residues: 338
  sheet: -0.59 (0.58), residues: 85
  loop : -2.00 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 385 
 TYR   0.014   0.001   TYR C 978 
 PHE   0.018   0.001   PHE C 503 
 TRP   0.002   0.001   TRP C 965 
 HIS   0.002   0.000   HIS C  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.14 ( 9747)
  covalent geometry    : angle       0.70123 /  0.33 (13669)
  hydrogen bonds       : bond        0.04392 /  2.94 (  369)
  hydrogen bonds       : angle       3.79479 /  2.56 (  997)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2052.30 seconds
wall clock time: 35 minutes 53.10 seconds (2153.10 seconds total)