Starting phenix.real_space_refine
on Wed Sep 17 15:54:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rjd_4902/09_2025/6rjd_4902.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rjd_4902/09_2025/6rjd_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2025/6rjd_4902.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2025/6rjd_4902.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2025/6rjd_4902.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rjd_4902/09_2025/6rjd_4902.map"
  }
  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-2.0-5805/lib/python3.9/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: {'RNA': 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: 2.26, per 1000 atoms: 0.24
  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: 0.88
  Conformation dependent library (CDL) restraints added in 264.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 1.23
  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: 1.80

  Time building geometry restraints manager: 1.16 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=" N   LYS C 706 "
       pdb=" CA  LYS C 706 "
    ideal  model  delta    sigma   weight residual
    1.460  1.485 -0.026 1.54e-02 4.22e+03 2.80e+00
  bond pdb=" C3'  DT E  11 "
       pdb=" O3'  DT E  11 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.76e+00
  bond pdb=" N   GLU C 887 "
       pdb=" CA  GLU C 887 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.022 1.41e-02 5.03e+03 2.42e+00
  bond pdb=" CB  ILE C 827 "
       pdb=" CG2 ILE C 827 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.36e+00
  bond pdb=" C1'  DC E  28 "
       pdb=" N1   DC E  28 "
    ideal  model  delta    sigma   weight residual
    1.490  1.536 -0.046 3.00e-02 1.11e+03 2.32e+00
  ... (remaining 9742 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 13242
        2.22 -     4.44: 377
        4.44 -     6.67: 34
        6.67 -     8.89: 12
        8.89 -    11.11: 4
  Bond angle restraints: 13669
  Sorted by residual:
  angle pdb=" C   LEU C 248 "
        pdb=" N   ASP C 249 "
        pdb=" CA  ASP C 249 "
      ideal   model   delta    sigma   weight residual
     121.54  130.47   -8.93 1.91e+00 2.74e-01 2.19e+01
  angle pdb=" C   HIS C 705 "
        pdb=" N   LYS C 706 "
        pdb=" CA  LYS C 706 "
      ideal   model   delta    sigma   weight residual
     122.46  128.07   -5.61 1.41e+00 5.03e-01 1.58e+01
  angle pdb=" C   LYS C 457 "
        pdb=" N   THR C 458 "
        pdb=" CA  THR C 458 "
      ideal   model   delta    sigma   weight residual
     121.54  129.12   -7.58 1.91e+00 2.74e-01 1.58e+01
  angle pdb=" C3'  DG G   4 "
        pdb=" O3'  DG G   4 "
        pdb=" P    DA G   5 "
      ideal   model   delta    sigma   weight residual
     120.20  125.98   -5.78 1.50e+00 4.44e-01 1.49e+01
  angle pdb=" CA  LYS C 466 "
        pdb=" CB  LYS C 466 "
        pdb=" CG  LYS C 466 "
      ideal   model   delta    sigma   weight residual
     114.10  121.35   -7.25 2.00e+00 2.50e-01 1.31e+01
  ... (remaining 13664 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.69: 5465
       34.69 -    69.37: 405
       69.37 -   104.06: 25
      104.06 -   138.74: 0
      138.74 -   173.43: 2
  Dihedral angle restraints: 5897
    sinusoidal: 3470
      harmonic: 2427
  Sorted by residual:
  dihedral pdb=" CA  ASP C 368 "
           pdb=" C   ASP C 368 "
           pdb=" N   ARG C 369 "
           pdb=" CA  ARG C 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.77   22.23     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  HIS C 115 "
           pdb=" C   HIS C 115 "
           pdb=" N   ARG C 116 "
           pdb=" CA  ARG C 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.11   19.89     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" C4'  DG G   4 "
           pdb=" C3'  DG G   4 "
           pdb=" O3'  DG G   4 "
           pdb=" P    DA G   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   33.43 -173.43     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 5894 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1088
       0.046 -    0.093: 361
       0.093 -    0.139: 106
       0.139 -    0.186: 18
       0.186 -    0.232: 6
  Chirality restraints: 1579
  Sorted by residual:
  chirality pdb=" CB  ILE C 339 "
            pdb=" CA  ILE C 339 "
            pdb=" CG1 ILE C 339 "
            pdb=" CG2 ILE C 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  ILE C 886 "
            pdb=" CA  ILE C 886 "
            pdb=" CG1 ILE C 886 "
            pdb=" CG2 ILE C 886 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" C1'   A D  68 "
            pdb=" O4'   A D  68 "
            pdb=" C2'   A D  68 "
            pdb=" N9    A D  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.24    0.22 2.00e-01 2.50e+01 1.23e+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:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.910
  Find NCS groups from input model:        0.040
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
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   0.051   9747  Z= 0.263
  Angle     :  0.900  11.110  13669  Z= 0.489
  Chirality :  0.052   0.232   1579
  Planarity :  0.006   0.041   1301
  Dihedral  : 20.281 173.426   4337
  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 aren 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
  covalent geometry    : bond        0.00567 ( 9747)
  covalent geometry    : angle       0.90034 (13669)
  hydrogen bonds       : bond        0.13570 (  369)
  hydrogen bonds       : angle       5.86413 (  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  : 0.291 
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: 0.7496 (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: 0.1298
  time to fit residues: 19.3930
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  : 0.297 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
C 145 GLN
C 300 GLN
C 494 ASN
C 928 ASN
C1054 HIS
C1108 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.159696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.124142 restraints weight = 14159.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.93
r_work: 0.3342 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9747  Z= 0.145
  Angle     :  0.572   6.917  13669  Z= 0.307
  Chirality :  0.036   0.130   1579
  Planarity :  0.003   0.032   1301
  Dihedral  : 20.424 174.784   2601
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.21 %
    Favored  : 83.63 %
  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 aren not related in a simple way.
  whole: -1.91 (0.26), residues: 817
  helix:  0.08 (0.27), residues: 337
  sheet: -1.64 (0.49), residues: 100
  loop : -2.45 (0.26), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  58 
 TYR   0.019   0.001   TYR C1055 
 PHE   0.010   0.001   PHE C1021 
 TRP   0.002   0.001   TRP C 965 
 HIS   0.005   0.001   HIS C 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9747)
  covalent geometry    : angle       0.57152 (13669)
  hydrogen bonds       : bond        0.05147 (  369)
  hydrogen bonds       : angle       4.25650 (  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
  95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7207 (mp0)
REVERT: C  339 ILE cc_start: 0.8752 (tt) cc_final: 0.8461 (tp)
REVERT: C  346 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7333 (tm-30)
REVERT: C  367 MET cc_start: 0.4821 (mmm) cc_final: 0.4597 (mtp)
REVERT: C  438 GLU cc_start: 0.8247 (mp0) cc_final: 0.7493 (mp0)
REVERT: C  465 THR cc_start: 0.7587 (m) cc_final: 0.7161 (p)
REVERT: C  487 ARG cc_start: 0.7463 (mtp180) cc_final: 0.6512 (mtm180)
REVERT: C  695 LEU cc_start: 0.8212 (tt) cc_final: 0.7995 (tt)
REVERT: C  699 GLN cc_start: 0.6684 (mt0) cc_final: 0.6121 (tt0)
REVERT: C  869 LYS cc_start: 0.8235 (mttt) cc_final: 0.7762 (ttpt)
REVERT: C  921 ARG cc_start: 0.8520 (mtt-85) cc_final: 0.8296 (mtp85)
REVERT: C  931 GLU cc_start: 0.7807 (mp0) cc_final: 0.7535 (mp0)
  outliers start: 16
  outliers final: 10
  residues processed: 93
  average time/residue: 0.1084
  time to fit residues: 13.6180
Evaluate side-chains
  75 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
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  691 SER
Chi-restraints excluded: chain C residue  877 HIS
Chi-restraints excluded: chain C residue  928 ASN
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=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:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 78 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 45 optimal weight:   20.0000
   overall best weight:    4.1386

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

Flipped N/Q/H residues before XYZ refinement:
C  43 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.154044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.121477 restraints weight = 14198.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.04
r_work: 0.3224 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   9747  Z= 0.302
  Angle     :  0.705   8.966  13669  Z= 0.371
  Chirality :  0.043   0.140   1579
  Planarity :  0.004   0.044   1301
  Dihedral  : 20.449 171.854   2597
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 15.70 %
    Favored  : 80.65 %
  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 aren not related in a simple way.
  whole: -1.60 (0.27), residues: 817
  helix:  0.43 (0.27), residues: 341
  sheet: -1.13 (0.53), residues: 87
  loop : -2.50 (0.27), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  62 
 TYR   0.028   0.002   TYR C1055 
 PHE   0.019   0.002   PHE C1021 
 TRP   0.005   0.002   TRP C 965 
 HIS   0.004   0.001   HIS C  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00678 ( 9747)
  covalent geometry    : angle       0.70456 (13669)
  hydrogen bonds       : bond        0.07032 (  369)
  hydrogen bonds       : angle       4.40519 (  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
  96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7295 (mp0)
REVERT: C  337 TYR cc_start: 0.7738 (p90) cc_final: 0.7325 (p90)
REVERT: C  339 ILE cc_start: 0.8765 (tt) cc_final: 0.8432 (tp)
REVERT: C  346 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7422 (tm-30)
REVERT: C  438 GLU cc_start: 0.8338 (mp0) cc_final: 0.7449 (mp0)
REVERT: C  441 GLU cc_start: 0.8457 (mp0) cc_final: 0.7852 (pt0)
REVERT: C  465 THR cc_start: 0.7173 (m) cc_final: 0.6692 (p)
REVERT: C  487 ARG cc_start: 0.7697 (mtp180) cc_final: 0.6904 (mtm110)
REVERT: C  695 LEU cc_start: 0.8298 (tt) cc_final: 0.8066 (tt)
REVERT: C  699 GLN cc_start: 0.6760 (mt0) cc_final: 0.6240 (tt0)
REVERT: C  931 GLU cc_start: 0.8203 (mp0) cc_final: 0.7713 (mp0)
  outliers start: 27
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1041
  time to fit residues: 13.5754
Evaluate side-chains
  80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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  208 THR
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  486 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  928 ASN
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:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 75 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
C 145 GLN
C 928 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.158252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.122534 restraints weight = 14381.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.94
r_work: 0.3318 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1725

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= 0.136
  Angle     :  0.563  12.034  13669  Z= 0.297
  Chirality :  0.036   0.134   1579
  Planarity :  0.003   0.034   1301
  Dihedral  : 20.420 173.941   2597
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.46 %
    Favored  : 79.57 %
  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 aren not related in a simple way.
  whole: -1.02 (0.28), residues: 817
  helix:  1.13 (0.28), residues: 337
  sheet: -1.49 (0.47), residues: 101
  loop : -2.20 (0.28), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 413 
 TYR   0.013   0.001   TYR C 215 
 PHE   0.010   0.001   PHE C1066 
 TRP   0.002   0.001   TRP C 965 
 HIS   0.003   0.000   HIS C 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9747)
  covalent geometry    : angle       0.56278 (13669)
  hydrogen bonds       : bond        0.04905 (  369)
  hydrogen bonds       : angle       4.01999 (  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
  91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7202 (mp0)
REVERT: C  337 TYR cc_start: 0.7698 (p90) cc_final: 0.7348 (p90)
REVERT: C  339 ILE cc_start: 0.8734 (tt) cc_final: 0.8399 (tp)
REVERT: C  346 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7305 (tm-30)
REVERT: C  367 MET cc_start: 0.5116 (mmm) cc_final: 0.3933 (mtp)
REVERT: C  438 GLU cc_start: 0.8266 (mp0) cc_final: 0.7523 (mp0)
REVERT: C  487 ARG cc_start: 0.7482 (mtp180) cc_final: 0.6524 (mtm110)
REVERT: C  699 GLN cc_start: 0.6657 (mt0) cc_final: 0.6135 (tt0)
REVERT: C  851 ASP cc_start: 0.8102 (t0) cc_final: 0.7869 (t0)
  outliers start: 22
  outliers final: 17
  residues processed: 90
  average time/residue: 0.0974
  time to fit residues: 12.2122
Evaluate side-chains
  78 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
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  208 THR
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  442 THR
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  928 ASN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 45 optimal weight:    8.9990
   chunk 73 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 86 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
C 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.155574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.123072 restraints weight = 14310.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 2.00
r_work: 0.3252 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9747  Z= 0.212
  Angle     :  0.615  11.392  13669  Z= 0.322
  Chirality :  0.039   0.135   1579
  Planarity :  0.004   0.042   1301
  Dihedral  : 20.415 173.803   2597
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 17.19 %
    Favored  : 78.62 %
  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 aren not related in a simple way.
  whole: -0.92 (0.28), residues: 817
  helix:  1.21 (0.28), residues: 337
  sheet: -0.98 (0.53), residues: 87
  loop : -2.27 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  62 
 TYR   0.018   0.002   TYR C1055 
 PHE   0.014   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
  covalent geometry    : bond        0.00472 ( 9747)
  covalent geometry    : angle       0.61543 (13669)
  hydrogen bonds       : bond        0.05729 (  369)
  hydrogen bonds       : angle       4.08182 (  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
  90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 59
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7276 (mp0)
REVERT: C  337 TYR cc_start: 0.7803 (p90) cc_final: 0.7436 (p90)
REVERT: C  438 GLU cc_start: 0.8327 (mp0) cc_final: 0.7337 (mp0)
REVERT: C  487 ARG cc_start: 0.7599 (mtp180) cc_final: 0.6666 (mtm110)
REVERT: C  699 GLN cc_start: 0.6680 (mt0) cc_final: 0.6205 (tt0)
  outliers start: 31
  outliers final: 23
  residues processed: 87
  average time/residue: 0.1092
  time to fit residues: 13.1228
Evaluate side-chains
  80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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   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  331 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain C residue  448 THR
Chi-restraints excluded: chain C residue  477 ILE
Chi-restraints excluded: chain C residue  486 VAL
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  928 ASN
Chi-restraints excluded: chain C residue 1022 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 68 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 43 optimal weight:    0.4980
   chunk 38 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C 928 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.160884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.129086 restraints weight = 14285.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.05
r_work: 0.3326 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9747  Z= 0.112
  Angle     :  0.522  10.178  13669  Z= 0.274
  Chirality :  0.035   0.130   1579
  Planarity :  0.003   0.033   1301
  Dihedral  : 20.296 176.364   2597
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.32 %
    Favored  : 79.16 %
  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 aren not related in a simple way.
  whole: -0.47 (0.29), residues: 817
  helix:  1.69 (0.28), residues: 337
  sheet: -1.22 (0.49), residues: 100
  loop : -2.00 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 413 
 TYR   0.010   0.001   TYR C1055 
 PHE   0.010   0.001   PHE C1066 
 TRP   0.004   0.001   TRP C 965 
 HIS   0.002   0.000   HIS C 945 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9747)
  covalent geometry    : angle       0.52176 (13669)
  hydrogen bonds       : bond        0.03998 (  369)
  hydrogen bonds       : angle       3.78089 (  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
  99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7221 (mp0)
REVERT: C  178 HIS cc_start: 0.6650 (p-80) cc_final: 0.6411 (p90)
REVERT: C  186 THR cc_start: 0.9089 (t) cc_final: 0.8779 (m)
REVERT: C  337 TYR cc_start: 0.7776 (p90) cc_final: 0.7408 (p90)
REVERT: C  339 ILE cc_start: 0.8768 (tt) cc_final: 0.8400 (tp)
REVERT: C  367 MET cc_start: 0.4671 (mmm) cc_final: 0.3496 (mtp)
REVERT: C  438 GLU cc_start: 0.8168 (mp0) cc_final: 0.7135 (mp0)
REVERT: C  487 ARG cc_start: 0.7507 (mtp180) cc_final: 0.6615 (mtm110)
REVERT: C  699 GLN cc_start: 0.6654 (mt0) cc_final: 0.6161 (tt0)
REVERT: C 1047 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.5546 (tpt-90)
  outliers start: 26
  outliers final: 18
  residues processed: 97
  average time/residue: 0.0942
  time to fit residues: 12.9892
Evaluate side-chains
  77 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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  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  507 VAL
Chi-restraints excluded: chain C residue  691 SER
Chi-restraints excluded: chain C residue  886 ILE
Chi-restraints excluded: chain C residue  887 GLU
Chi-restraints excluded: chain C residue  928 ASN
Chi-restraints excluded: chain C residue 1022 THR
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 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:    0.8980
   chunk 23 optimal weight:    0.0040
   chunk 76 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 85 optimal weight:    7.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    2.1798

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

Flipped N/Q/H residues before XYZ refinement:
C 928 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.157422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.125101 restraints weight = 14231.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.06
r_work: 0.3272 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9747  Z= 0.177
  Angle     :  0.572   9.652  13669  Z= 0.299
  Chirality :  0.037   0.135   1579
  Planarity :  0.003   0.035   1301
  Dihedral  : 20.191 176.608   2597
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.54 %
    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 aren not related in a simple way.
  whole: -0.48 (0.29), residues: 817
  helix:  1.65 (0.28), residues: 337
  sheet: -0.73 (0.55), residues: 85
  loop : -2.10 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 413 
 TYR   0.014   0.001   TYR C1055 
 PHE   0.011   0.001   PHE C1021 
 TRP   0.003   0.001   TRP C 965 
 HIS   0.004   0.001   HIS C 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9747)
  covalent geometry    : angle       0.57196 (13669)
  hydrogen bonds       : bond        0.04942 (  369)
  hydrogen bonds       : angle       3.89776 (  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
  90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 61
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7308 (mp0)
REVERT: C  178 HIS cc_start: 0.6655 (p-80) cc_final: 0.6385 (p90)
REVERT: C  337 TYR cc_start: 0.7836 (p90) cc_final: 0.7451 (p90)
REVERT: C  367 MET cc_start: 0.5018 (mmm) cc_final: 0.3806 (mtp)
REVERT: C  438 GLU cc_start: 0.8221 (mp0) cc_final: 0.7194 (mp0)
REVERT: C  487 ARG cc_start: 0.7606 (mtp180) cc_final: 0.6705 (mtm110)
REVERT: C  699 GLN cc_start: 0.6686 (mt0) cc_final: 0.6149 (tt0)
  outliers start: 29
  outliers final: 26
  residues processed: 89
  average time/residue: 0.1064
  time to fit residues: 13.2342
Evaluate side-chains
  86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 59
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
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  148 THR
Chi-restraints excluded: chain C residue  157 GLU
Chi-restraints excluded: chain C residue  170 THR
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  442 THR
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  928 ASN
Chi-restraints excluded: chain C residue  983 LEU
Chi-restraints excluded: chain C residue 1022 THR
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 1104 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0980
   chunk 14 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
C 928 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.158806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.123156 restraints weight = 14156.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.93
r_work: 0.3324 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2138

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= 0.143
  Angle     :  0.553   9.210  13669  Z= 0.290
  Chirality :  0.036   0.133   1579
  Planarity :  0.003   0.034   1301
  Dihedral  : 20.139 176.591   2597
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 18.54 %
    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 aren not related in a simple way.
  whole: -0.36 (0.29), residues: 817
  helix:  1.75 (0.28), residues: 337
  sheet: -0.63 (0.57), residues: 85
  loop : -2.04 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C1047 
 TYR   0.012   0.001   TYR C 215 
 PHE   0.009   0.001   PHE C 503 
 TRP   0.003   0.001   TRP C 965 
 HIS   0.002   0.001   HIS C 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9747)
  covalent geometry    : angle       0.55315 (13669)
  hydrogen bonds       : bond        0.04608 (  369)
  hydrogen bonds       : angle       3.84486 (  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
  91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 60
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7201 (mp0)
REVERT: C  178 HIS cc_start: 0.6641 (p-80) cc_final: 0.6368 (p90)
REVERT: C  337 TYR cc_start: 0.7862 (p90) cc_final: 0.7477 (p90)
REVERT: C  367 MET cc_start: 0.4954 (mmm) cc_final: 0.3792 (mtp)
REVERT: C  438 GLU cc_start: 0.8186 (mp0) cc_final: 0.7186 (mp0)
REVERT: C  487 ARG cc_start: 0.7465 (mtp180) cc_final: 0.6554 (mtm110)
REVERT: C  699 GLN cc_start: 0.6658 (mt0) cc_final: 0.6149 (tt0)
  outliers start: 31
  outliers final: 26
  residues processed: 89
  average time/residue: 0.1083
  time to fit residues: 13.4155
Evaluate side-chains
  85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 58
  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  170 THR
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  331 VAL
Chi-restraints excluded: chain C residue  442 THR
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  928 ASN
Chi-restraints excluded: chain C residue  983 LEU
Chi-restraints excluded: chain C residue 1022 THR
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 1104 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0050
   chunk 65 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    2.2002

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

Flipped N/Q/H residues before XYZ refinement:
C 928 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.157452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.125191 restraints weight = 14154.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.03
r_work: 0.3267 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9747  Z= 0.179
  Angle     :  0.583   8.900  13669  Z= 0.305
  Chirality :  0.037   0.135   1579
  Planarity :  0.003   0.035   1301
  Dihedral  : 20.084 175.992   2597
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 18.81 %
    Favored  : 76.86 %
  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 aren not related in a simple way.
  whole: -0.38 (0.29), residues: 817
  helix:  1.74 (0.28), residues: 337
  sheet: -0.64 (0.57), residues: 85
  loop : -2.06 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1047 
 TYR   0.014   0.001   TYR C1055 
 PHE   0.011   0.001   PHE C 503 
 TRP   0.003   0.001   TRP C 965 
 HIS   0.003   0.001   HIS C  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9747)
  covalent geometry    : angle       0.58273 (13669)
  hydrogen bonds       : bond        0.05058 (  369)
  hydrogen bonds       : angle       3.89603 (  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
  90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 58
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7294 (mp0)
REVERT: C  337 TYR cc_start: 0.7848 (p90) cc_final: 0.7452 (p90)
REVERT: C  367 MET cc_start: 0.5009 (mmm) cc_final: 0.3846 (mtp)
REVERT: C  414 LYS cc_start: 0.7900 (mttm) cc_final: 0.7427 (tttm)
REVERT: C  438 GLU cc_start: 0.8264 (mp0) cc_final: 0.7350 (mp0)
REVERT: C  487 ARG cc_start: 0.7675 (mtp180) cc_final: 0.6782 (mtm110)
REVERT: C  699 GLN cc_start: 0.6664 (mt0) cc_final: 0.6155 (tt0)
  outliers start: 32
  outliers final: 30
  residues processed: 89
  average time/residue: 0.1044
  time to fit residues: 12.9750
Evaluate side-chains
  87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 56
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
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  170 THR
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain C residue  448 THR
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  928 ASN
Chi-restraints excluded: chain C residue  983 LEU
Chi-restraints excluded: chain C residue 1022 THR
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 1104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 45 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
C 928 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.155530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.123414 restraints weight = 14235.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.03
r_work: 0.3246 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9747  Z= 0.231
  Angle     :  0.630   8.776  13669  Z= 0.329
  Chirality :  0.039   0.137   1579
  Planarity :  0.004   0.039   1301
  Dihedral  : 20.090 173.972   2597
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 18.81 %
    Favored  : 76.86 %
  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 aren not related in a simple way.
  whole: -0.57 (0.29), residues: 817
  helix:  1.51 (0.28), residues: 341
  sheet: -0.74 (0.56), residues: 85
  loop : -2.13 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1047 
 TYR   0.018   0.002   TYR C1055 
 PHE   0.014   0.002   PHE C1021 
 TRP   0.004   0.001   TRP C 965 
 HIS   0.003   0.001   HIS C 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 9747)
  covalent geometry    : angle       0.63013 (13669)
  hydrogen bonds       : bond        0.05827 (  369)
  hydrogen bonds       : angle       4.04047 (  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
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 56
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: C  157 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6625 (mp0)
REVERT: C  367 MET cc_start: 0.5075 (mmm) cc_final: 0.3877 (mtp)
REVERT: C  438 GLU cc_start: 0.8330 (mp0) cc_final: 0.7393 (mp0)
REVERT: C  487 ARG cc_start: 0.7631 (mtp180) cc_final: 0.6718 (mtm110)
REVERT: C  699 GLN cc_start: 0.6717 (mt0) cc_final: 0.6198 (tt0)
  outliers start: 32
  outliers final: 28
  residues processed: 86
  average time/residue: 0.1064
  time to fit residues: 12.7892
Evaluate side-chains
  85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 56
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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  170 THR
Chi-restraints excluded: chain C residue  249 ASP
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain C residue  448 THR
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  983 LEU
Chi-restraints excluded: chain C residue 1022 THR
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 1104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    2.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.156498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.124192 restraints weight = 14138.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.98
r_work: 0.3254 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9747  Z= 0.172
  Angle     :  0.593   8.762  13669  Z= 0.311
  Chirality :  0.038   0.135   1579
  Planarity :  0.003   0.035   1301
  Dihedral  : 20.087 174.431   2597
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 19.35 %
    Favored  : 76.73 %
  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 aren not related in a simple way.
  whole: -0.53 (0.29), residues: 817
  helix:  1.55 (0.28), residues: 341
  sheet: -0.74 (0.57), residues: 85
  loop : -2.10 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1047 
 TYR   0.015   0.001   TYR C 215 
 PHE   0.016   0.001   PHE C 503 
 TRP   0.004   0.001   TRP C 965 
 HIS   0.003   0.001   HIS C  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 9747)
  covalent geometry    : angle       0.59324 (13669)
  hydrogen bonds       : bond        0.05381 (  369)
  hydrogen bonds       : angle       3.98561 (  997)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2005.36 seconds
wall clock time: 35 minutes 11.20 seconds (2111.20 seconds total)