Starting phenix.real_space_refine
on Wed Mar  4 10:37:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nh9_12321/03_2026/7nh9_12321.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nh9_12321/03_2026/7nh9_12321.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nh9_12321/03_2026/7nh9_12321.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nh9_12321/03_2026/7nh9_12321.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nh9_12321/03_2026/7nh9_12321.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nh9_12321/03_2026/7nh9_12321.map"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.009
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: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    8320      2.51       5
     N    2375      2.21       5
     O    2395      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13120
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2624
          Classifications: {'peptide': 327}
          Link IDs: {'PTRANS': 12, 'TRANS': 314}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 1.98, per 1000 atoms: 0.15
  Number of scatterers: 13120
  At special positions: 0
  Unit cell: (122.672, 122.016, 126.608, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    2395      8.00
     N    2375      7.00
     C    8320      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: 1.04
  Conformation dependent library (CDL) restraints added in 530.7 milliseconds
  

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3000

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 5 sheets defined
      56.0% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 60
      removed outlier: 3.536A  pdb=" N   GLN A  55 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 73
    Processing helix  chain 'A' and resid 127 through 139
      removed outlier: 3.899A  pdb=" N   ALA A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 182
      removed outlier: 3.701A  pdb=" N   THR A 163 " --> pdb=" O   ASP A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 219
      removed outlier: 3.931A  pdb=" N   TYR A 205 " --> pdb=" O   GLY A 201 " (cutoff:3.500A)
      Proline residue:  A 208  - end of helix
      removed outlier: 3.876A  pdb=" N   ASP A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   TYR A 219 " --> pdb=" O   GLN A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 227
      No H-bonds generated for 'chain 'A' and resid 225 through 227'
    Processing helix  chain 'A' and resid 228 through 289
      Proline residue:  A 284  - end of helix
    Processing helix  chain 'A' and resid 313 through 331
      removed outlier: 3.650A  pdb=" N   GLY A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 60
      removed outlier: 3.536A  pdb=" N   GLN B  55 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 73
    Processing helix  chain 'B' and resid 127 through 139
      removed outlier: 3.899A  pdb=" N   ALA B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 182
      removed outlier: 3.701A  pdb=" N   THR B 163 " --> pdb=" O   ASP B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 219
      removed outlier: 3.932A  pdb=" N   TYR B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
      Proline residue:  B 208  - end of helix
      removed outlier: 3.876A  pdb=" N   ASP B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   TYR B 219 " --> pdb=" O   GLN B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 227
      No H-bonds generated for 'chain 'B' and resid 225 through 227'
    Processing helix  chain 'B' and resid 228 through 289
      Proline residue:  B 284  - end of helix
    Processing helix  chain 'B' and resid 313 through 331
      removed outlier: 3.650A  pdb=" N   GLY B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 60
      removed outlier: 3.536A  pdb=" N   GLN C  55 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 73
    Processing helix  chain 'C' and resid 127 through 139
      removed outlier: 3.899A  pdb=" N   ALA C 131 " --> pdb=" O   LEU C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 182
      removed outlier: 3.701A  pdb=" N   THR C 163 " --> pdb=" O   ASP C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 219
      removed outlier: 3.931A  pdb=" N   TYR C 205 " --> pdb=" O   GLY C 201 " (cutoff:3.500A)
      Proline residue:  C 208  - end of helix
      removed outlier: 3.876A  pdb=" N   ASP C 211 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   TYR C 219 " --> pdb=" O   GLN C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 227
      No H-bonds generated for 'chain 'C' and resid 225 through 227'
    Processing helix  chain 'C' and resid 228 through 289
      Proline residue:  C 284  - end of helix
    Processing helix  chain 'C' and resid 313 through 331
      removed outlier: 3.651A  pdb=" N   GLY C 317 " --> pdb=" O   LEU C 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 60
      removed outlier: 3.535A  pdb=" N   GLN D  55 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 73
    Processing helix  chain 'D' and resid 127 through 139
      removed outlier: 3.899A  pdb=" N   ALA D 131 " --> pdb=" O   LEU D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 145 through 182
      removed outlier: 3.701A  pdb=" N   THR D 163 " --> pdb=" O   ASP D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 191 through 219
      removed outlier: 3.931A  pdb=" N   TYR D 205 " --> pdb=" O   GLY D 201 " (cutoff:3.500A)
      Proline residue:  D 208  - end of helix
      removed outlier: 3.876A  pdb=" N   ASP D 211 " --> pdb=" O   ALA D 207 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   TYR D 219 " --> pdb=" O   GLN D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 225 through 227
      No H-bonds generated for 'chain 'D' and resid 225 through 227'
    Processing helix  chain 'D' and resid 228 through 289
      Proline residue:  D 284  - end of helix
    Processing helix  chain 'D' and resid 313 through 331
      removed outlier: 3.651A  pdb=" N   GLY D 317 " --> pdb=" O   LEU D 313 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
      removed outlier: 3.536A  pdb=" N   GLN E  55 " --> pdb=" O   VAL E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 73
    Processing helix  chain 'E' and resid 127 through 139
      removed outlier: 3.899A  pdb=" N   ALA E 131 " --> pdb=" O   LEU E 127 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 145 through 182
      removed outlier: 3.700A  pdb=" N   THR E 163 " --> pdb=" O   ASP E 159 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 191 through 219
      removed outlier: 3.931A  pdb=" N   TYR E 205 " --> pdb=" O   GLY E 201 " (cutoff:3.500A)
      Proline residue:  E 208  - end of helix
      removed outlier: 3.875A  pdb=" N   ASP E 211 " --> pdb=" O   ALA E 207 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   TYR E 219 " --> pdb=" O   GLN E 215 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 225 through 227
      No H-bonds generated for 'chain 'E' and resid 225 through 227'
    Processing helix  chain 'E' and resid 228 through 289
      Proline residue:  E 284  - end of helix
    Processing helix  chain 'E' and resid 313 through 331
      removed outlier: 3.651A  pdb=" N   GLY E 317 " --> pdb=" O   LEU E 313 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26
      removed outlier: 6.559A  pdb=" N   HIS A  46 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   GLY A  15 " --> pdb=" O   TRP A  44 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   TRP A  44 " --> pdb=" O   GLY A  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 26
      removed outlier: 6.559A  pdb=" N   HIS B  46 " --> pdb=" O   ILE B  13 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   GLY B  15 " --> pdb=" O   TRP B  44 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   TRP B  44 " --> pdb=" O   GLY B  15 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 25 through 26
      removed outlier: 6.560A  pdb=" N   HIS C  46 " --> pdb=" O   ILE C  13 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   GLY C  15 " --> pdb=" O   TRP C  44 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   TRP C  44 " --> pdb=" O   GLY C  15 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 25 through 26
      removed outlier: 6.559A  pdb=" N   HIS D  46 " --> pdb=" O   ILE D  13 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   GLY D  15 " --> pdb=" O   TRP D  44 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   TRP D  44 " --> pdb=" O   GLY D  15 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 25 through 26
      removed outlier: 6.559A  pdb=" N   HIS E  46 " --> pdb=" O   ILE E  13 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   GLY E  15 " --> pdb=" O   TRP E  44 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   TRP E  44 " --> pdb=" O   GLY E  15 " (cutoff:3.500A)

    795 hydrogen bonds defined for protein.
    2340 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4510
        1.34 -     1.46: 2651
        1.46 -     1.58: 6174
        1.58 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 13385
  Sorted by residual:
  bond pdb=" C   THR A  77 "
       pdb=" N   ARG A  78 "
    ideal  model  delta    sigma   weight residual
    1.331  1.281  0.050 1.59e-02 3.96e+03 9.82e+00
  bond pdb=" C   THR C  77 "
       pdb=" N   ARG C  78 "
    ideal  model  delta    sigma   weight residual
    1.331  1.282  0.049 1.59e-02 3.96e+03 9.65e+00
  bond pdb=" C   THR B  77 "
       pdb=" N   ARG B  78 "
    ideal  model  delta    sigma   weight residual
    1.331  1.282  0.049 1.59e-02 3.96e+03 9.64e+00
  bond pdb=" C   THR E  77 "
       pdb=" N   ARG E  78 "
    ideal  model  delta    sigma   weight residual
    1.331  1.282  0.049 1.59e-02 3.96e+03 9.58e+00
  bond pdb=" C   THR D  77 "
       pdb=" N   ARG D  78 "
    ideal  model  delta    sigma   weight residual
    1.331  1.282  0.049 1.59e-02 3.96e+03 9.55e+00
  ... (remaining 13380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 17185
        1.51 -     3.03: 752
        3.03 -     4.54: 138
        4.54 -     6.06: 60
        6.06 -     7.57: 15
  Bond angle restraints: 18150
  Sorted by residual:
  angle pdb=" C   ARG E 218 "
        pdb=" N   TYR E 219 "
        pdb=" CA  TYR E 219 "
      ideal   model   delta    sigma   weight residual
     121.90  116.20    5.70 1.26e+00 6.30e-01 2.05e+01
  angle pdb=" C   ARG A 218 "
        pdb=" N   TYR A 219 "
        pdb=" CA  TYR A 219 "
      ideal   model   delta    sigma   weight residual
     121.90  116.21    5.69 1.26e+00 6.30e-01 2.04e+01
  angle pdb=" C   ARG D 218 "
        pdb=" N   TYR D 219 "
        pdb=" CA  TYR D 219 "
      ideal   model   delta    sigma   weight residual
     121.90  116.22    5.68 1.26e+00 6.30e-01 2.03e+01
  angle pdb=" C   ARG C 218 "
        pdb=" N   TYR C 219 "
        pdb=" CA  TYR C 219 "
      ideal   model   delta    sigma   weight residual
     121.90  116.22    5.68 1.26e+00 6.30e-01 2.03e+01
  angle pdb=" C   ARG B 218 "
        pdb=" N   TYR B 219 "
        pdb=" CA  TYR B 219 "
      ideal   model   delta    sigma   weight residual
     121.90  116.24    5.66 1.26e+00 6.30e-01 2.02e+01
  ... (remaining 18145 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 7160
       17.92 -    35.84: 640
       35.84 -    53.77: 165
       53.77 -    71.69: 10
       71.69 -    89.61: 15
  Dihedral angle restraints: 7990
    sinusoidal: 3310
      harmonic: 4680
  Sorted by residual:
  dihedral pdb=" CA  LEU C  84 "
           pdb=" C   LEU C  84 "
           pdb=" N   GLY C  85 "
           pdb=" CA  GLY C  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.28   24.72     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  LEU E  84 "
           pdb=" C   LEU E  84 "
           pdb=" N   GLY E  85 "
           pdb=" CA  GLY E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.30   24.70     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  LEU B  84 "
           pdb=" C   LEU B  84 "
           pdb=" N   GLY B  85 "
           pdb=" CA  GLY B  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.31   24.69     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 7987 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1029
       0.027 -    0.054: 577
       0.054 -    0.081: 208
       0.081 -    0.108: 136
       0.108 -    0.135: 40
  Chirality restraints: 1990
  Sorted by residual:
  chirality pdb=" CA  PRO B  39 "
            pdb=" N   PRO B  39 "
            pdb=" C   PRO B  39 "
            pdb=" CB  PRO B  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  PRO A  39 "
            pdb=" N   PRO A  39 "
            pdb=" C   PRO A  39 "
            pdb=" CB  PRO A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  PRO E  39 "
            pdb=" N   PRO E  39 "
            pdb=" C   PRO E  39 "
            pdb=" CB  PRO E  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 1987 not shown)

  Planarity restraints: 2370
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 207 "    0.034 5.00e-02 4.00e+02   5.10e-02 4.16e+00
        pdb=" N   PRO E 208 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO E 208 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E 208 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 207 "    0.034 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO A 208 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 208 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 208 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 207 "   -0.034 5.00e-02 4.00e+02   5.06e-02 4.10e+00
        pdb=" N   PRO C 208 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO C 208 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 208 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 2367 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2722
        2.77 -     3.30: 13245
        3.30 -     3.83: 22022
        3.83 -     4.37: 25326
        4.37 -     4.90: 43650
  Nonbonded interactions: 106965
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 244 "
            pdb=" NH1 ARG E  78 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OD1 ASN C  97 "
            pdb=" ND2 ASN C  99 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN B  97 "
            pdb=" ND2 ASN B  99 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN A  97 "
            pdb=" ND2 ASN A  99 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN E  97 "
            pdb=" ND2 ASN E  99 "
     model   vdw
     2.249 3.120
  ... (remaining 106960 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             3.180
  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:          0.290
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.060
  Find NCS groups from input model:        0.100
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
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      :  0.007   0.061  13385  Z= 0.293
  Angle     :  0.798   7.570  18150  Z= 0.455
  Chirality :  0.043   0.135   1990
  Planarity :  0.004   0.051   2370
  Dihedral  : 14.804  89.611   4990
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.69 %
    Favored  : 88.31 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  :  8.16 %
    Favored  : 88.53 %
  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: -2.35 (0.19), residues: 1625
  helix: -0.51 (0.16), residues: 920
  sheet: -1.87 (0.32), residues: 230
  loop : -3.31 (0.24), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  80 
 TYR   0.012   0.001   TYR D 151 
 PHE   0.009   0.001   PHE A  92 
 TRP   0.006   0.001   TRP E  57 
 HIS   0.003   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 (13385)
  covalent geometry    : angle       0.79844 (18150)
  hydrogen bonds       : bond        0.13712 (  795)
  hydrogen bonds       : angle       5.57678 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 186
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A  270 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7889 (ttp-110)
REVERT: B  270 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7952 (ttp-110)
REVERT: C  266 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7702 (pp20)
REVERT: C  270 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7943 (ttp-110)
REVERT: C  285 MET cc_start: 0.8524 (tpt) cc_final: 0.8205 (tpp)
REVERT: C  322 GLN cc_start: 0.7832 (mt0) cc_final: 0.7403 (mt0)
REVERT: D  128 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8296 (mmmt)
REVERT: D  233 ASN cc_start: 0.9178 (t0) cc_final: 0.8961 (t0)
REVERT: D  285 MET cc_start: 0.8453 (tpt) cc_final: 0.8243 (tpp)
REVERT: E  270 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7894 (ttp-110)
  outliers start: 45
  outliers final: 20
  residues processed: 217
  average time/residue: 0.1077
  time to fit residues: 34.4028
Evaluate side-chains
  144 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  186 SER
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  186 SER
Chi-restraints excluded: chain D residue  261 SER
Chi-restraints excluded: chain D residue  265 THR
Chi-restraints excluded: chain E residue   34 VAL
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  186 SER
Chi-restraints excluded: chain E residue  261 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    0.0980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 209 GLN
A 242 ASN
A 257 GLN
A 322 GLN
B 190 HIS
B 209 GLN
B 242 ASN
B 257 GLN
B 322 GLN
C 190 HIS
C 209 GLN
C 242 ASN
C 257 GLN
D 190 HIS
D 209 GLN
D 242 ASN
D 257 GLN
D 322 GLN
E 209 GLN
E 242 ASN
E 257 GLN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.109416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.081475 restraints weight = 29117.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.98
r_work: 0.3106 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13385  Z= 0.131
  Angle     :  0.674   9.883  18150  Z= 0.337
  Chirality :  0.041   0.150   1990
  Planarity :  0.004   0.055   2370
  Dihedral  :  6.158  66.193   1882
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.49 %
    Favored  : 88.46 %
  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: -0.52 (0.21), residues: 1625
  helix:  1.17 (0.17), residues: 930
  sheet: -1.68 (0.34), residues: 220
  loop : -2.77 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 184 
 TYR   0.007   0.001   TYR B 151 
 PHE   0.009   0.001   PHE E 281 
 TRP   0.004   0.001   TRP A  57 
 HIS   0.016   0.003   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (13385)
  covalent geometry    : angle       0.67441 (18150)
  hydrogen bonds       : bond        0.03912 (  795)
  hydrogen bonds       : angle       3.64253 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7840 (mm-30)
REVERT: A  234 GLU cc_start: 0.8317 (pp20) cc_final: 0.8100 (pp20)
REVERT: A  270 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.7966 (ttp-110)
REVERT: B   16 TYR cc_start: 0.7926 (t80) cc_final: 0.7534 (t80)
REVERT: B  270 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8063 (ttp-110)
REVERT: C   16 TYR cc_start: 0.7898 (t80) cc_final: 0.7562 (t80)
REVERT: C  128 LYS cc_start: 0.7809 (mmmt) cc_final: 0.7584 (mmmt)
REVERT: C  266 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8144 (tm-30)
REVERT: C  270 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8037 (ttp-110)
REVERT: C  324 TRP cc_start: 0.8637 (t60) cc_final: 0.8332 (t60)
REVERT: D   16 TYR cc_start: 0.7903 (t80) cc_final: 0.7543 (t80)
REVERT: D  128 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7714 (mmmt)
REVERT: D  233 ASN cc_start: 0.9147 (t0) cc_final: 0.8929 (t0)
REVERT: E   16 TYR cc_start: 0.7859 (t80) cc_final: 0.7492 (t80)
REVERT: E  270 ARG cc_start: 0.8591 (tpp-160) cc_final: 0.7942 (ttm170)
  outliers start: 28
  outliers final: 14
  residues processed: 180
  average time/residue: 0.1008
  time to fit residues: 27.6784
Evaluate side-chains
  160 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  261 SER
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  261 SER
Chi-restraints excluded: chain E residue   84 LEU
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  261 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 155 optimal weight:    5.9990
   chunk 139 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 157 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 156 optimal weight:    4.9990
   chunk 110 optimal weight:    0.6980
   chunk 148 optimal weight:    2.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
B 322 GLN
C 322 GLN
D 322 GLN
E 322 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.108580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.080202 restraints weight = 29400.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 3.01
r_work: 0.3115 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13385  Z= 0.141
  Angle     :  0.638   8.894  18150  Z= 0.319
  Chirality :  0.040   0.145   1990
  Planarity :  0.003   0.039   2370
  Dihedral  :  5.519  63.308   1873
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.75 %
    Favored  : 85.44 %
  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: -0.02 (0.21), residues: 1625
  helix:  1.69 (0.17), residues: 935
  sheet: -1.82 (0.33), residues: 220
  loop : -2.69 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 184 
 TYR   0.020   0.001   TYR B 219 
 PHE   0.012   0.001   PHE E 282 
 TRP   0.010   0.001   TRP D 324 
 HIS   0.002   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (13385)
  covalent geometry    : angle       0.63794 (18150)
  hydrogen bonds       : bond        0.03820 (  795)
  hydrogen bonds       : angle       3.45658 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.541 
Fit side-chains
REVERT: A  219 TYR cc_start: 0.7790 (p90) cc_final: 0.7558 (p90)
REVERT: A  270 ARG cc_start: 0.8644 (tpp-160) cc_final: 0.8040 (ttp-170)
REVERT: B   16 TYR cc_start: 0.7971 (t80) cc_final: 0.7634 (t80)
REVERT: B  270 ARG cc_start: 0.8696 (tpp-160) cc_final: 0.8108 (ttp-170)
REVERT: B  324 TRP cc_start: 0.8740 (t60) cc_final: 0.8296 (t60)
REVERT: C   16 TYR cc_start: 0.7942 (t80) cc_final: 0.7658 (t80)
REVERT: C  128 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7685 (mmmt)
REVERT: C  270 ARG cc_start: 0.8677 (tpp-160) cc_final: 0.8049 (ttp-110)
REVERT: C  324 TRP cc_start: 0.8669 (t60) cc_final: 0.8372 (t60)
REVERT: D   16 TYR cc_start: 0.7955 (t80) cc_final: 0.7652 (t80)
REVERT: D  128 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7731 (mmmt)
REVERT: D  219 TYR cc_start: 0.7877 (p90) cc_final: 0.7626 (p90)
REVERT: D  233 ASN cc_start: 0.9172 (t0) cc_final: 0.8960 (t0)
REVERT: D  324 TRP cc_start: 0.8744 (t60) cc_final: 0.8384 (t60)
REVERT: E   16 TYR cc_start: 0.7903 (t80) cc_final: 0.7589 (t80)
REVERT: E  219 TYR cc_start: 0.7856 (p90) cc_final: 0.7605 (p90)
REVERT: E  270 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8050 (ttp-170)
  outliers start: 11
  outliers final: 6
  residues processed: 159
  average time/residue: 0.1133
  time to fit residues: 26.4606
Evaluate side-chains
  140 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 134
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  266 GLU
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 144 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 134 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 157 optimal weight:    0.4980
   chunk 43 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0010
   chunk 135 optimal weight:    2.9990
   overall best weight:    1.4790

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 322 GLN
B 190 HIS
B 322 GLN
C 190 HIS
C 322 GLN
D 322 GLN
E 190 HIS
E 322 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.108249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.079851 restraints weight = 29359.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 3.01
r_work: 0.3107 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13385  Z= 0.150
  Angle     :  0.635   8.881  18150  Z= 0.317
  Chirality :  0.040   0.155   1990
  Planarity :  0.003   0.050   2370
  Dihedral  :  4.794  24.643   1860
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 15.88 %
    Favored  : 83.46 %
  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:  0.26 (0.22), residues: 1625
  helix:  1.99 (0.17), residues: 935
  sheet: -1.92 (0.32), residues: 220
  loop : -2.60 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 184 
 TYR   0.010   0.001   TYR A 205 
 PHE   0.011   0.001   PHE E 282 
 TRP   0.006   0.001   TRP D 324 
 HIS   0.026   0.003   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (13385)
  covalent geometry    : angle       0.63487 (18150)
  hydrogen bonds       : bond        0.03759 (  795)
  hydrogen bonds       : angle       3.36177 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   16 TYR cc_start: 0.8033 (t80) cc_final: 0.7801 (t80)
REVERT: A  184 ARG cc_start: 0.8375 (ptt-90) cc_final: 0.8064 (ptt-90)
REVERT: A  219 TYR cc_start: 0.7808 (p90) cc_final: 0.7542 (p90)
REVERT: A  270 ARG cc_start: 0.8677 (tpp-160) cc_final: 0.8081 (ttp-170)
REVERT: A  324 TRP cc_start: 0.8648 (t60) cc_final: 0.8382 (t60)
REVERT: B   16 TYR cc_start: 0.7987 (t80) cc_final: 0.7666 (t80)
REVERT: B  260 GLU cc_start: 0.8938 (tp30) cc_final: 0.8602 (tp30)
REVERT: B  270 ARG cc_start: 0.8721 (tpp-160) cc_final: 0.8122 (ttp-170)
REVERT: B  324 TRP cc_start: 0.8747 (t60) cc_final: 0.8309 (t60)
REVERT: C   16 TYR cc_start: 0.7940 (t80) cc_final: 0.7669 (t80)
REVERT: C  270 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8119 (ttp-170)
REVERT: C  324 TRP cc_start: 0.8671 (t60) cc_final: 0.8357 (t60)
REVERT: D   16 TYR cc_start: 0.7999 (t80) cc_final: 0.7702 (t80)
REVERT: D  128 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7786 (mmmt)
REVERT: D  219 TYR cc_start: 0.7891 (p90) cc_final: 0.7603 (p90)
REVERT: D  233 ASN cc_start: 0.9195 (t0) cc_final: 0.8983 (t0)
REVERT: D  324 TRP cc_start: 0.8767 (t60) cc_final: 0.8364 (t60)
REVERT: E   16 TYR cc_start: 0.7935 (t80) cc_final: 0.7636 (t80)
REVERT: E  219 TYR cc_start: 0.7862 (p90) cc_final: 0.7570 (p90)
REVERT: E  270 ARG cc_start: 0.8670 (tpp-160) cc_final: 0.8053 (ttm170)
REVERT: E  324 TRP cc_start: 0.8703 (t60) cc_final: 0.8350 (t60)
  outliers start: 9
  outliers final: 7
  residues processed: 150
  average time/residue: 0.1092
  time to fit residues: 24.2566
Evaluate side-chains
  145 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 138
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  184 ARG
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  266 GLU
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 126 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 140 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 141 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 159 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 134 optimal weight:    3.9990
   chunk 153 optimal weight:    4.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
B 322 GLN
C 322 GLN
D 322 GLN
E 190 HIS
E 322 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.107947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.079564 restraints weight = 29322.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 3.00
r_work: 0.3100 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13385  Z= 0.151
  Angle     :  0.623   8.470  18150  Z= 0.312
  Chirality :  0.040   0.133   1990
  Planarity :  0.003   0.040   2370
  Dihedral  :  4.746  24.326   1860
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.81 %
    Favored  : 82.79 %
  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:  0.45 (0.22), residues: 1625
  helix:  2.14 (0.17), residues: 935
  sheet: -1.89 (0.31), residues: 220
  loop : -2.50 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 184 
 TYR   0.009   0.001   TYR A 205 
 PHE   0.018   0.001   PHE E 321 
 TRP   0.005   0.001   TRP D 324 
 HIS   0.016   0.001   HIS E 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13385)
  covalent geometry    : angle       0.62266 (18150)
  hydrogen bonds       : bond        0.03747 (  795)
  hydrogen bonds       : angle       3.31885 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.550 
Fit side-chains
REVERT: A  219 TYR cc_start: 0.7808 (p90) cc_final: 0.7521 (p90)
REVERT: A  270 ARG cc_start: 0.8687 (tpp-160) cc_final: 0.8117 (ttp-170)
REVERT: A  324 TRP cc_start: 0.8677 (t60) cc_final: 0.8404 (t60)
REVERT: B   16 TYR cc_start: 0.8001 (t80) cc_final: 0.7687 (t80)
REVERT: B  260 GLU cc_start: 0.8940 (tp30) cc_final: 0.8591 (tp30)
REVERT: B  270 ARG cc_start: 0.8731 (tpp-160) cc_final: 0.8127 (ttp-170)
REVERT: B  324 TRP cc_start: 0.8744 (t60) cc_final: 0.8307 (t60)
REVERT: C   16 TYR cc_start: 0.7961 (t80) cc_final: 0.7689 (t80)
REVERT: C  219 TYR cc_start: 0.7771 (p90) cc_final: 0.7469 (p90)
REVERT: C  270 ARG cc_start: 0.8722 (tpp-160) cc_final: 0.8127 (ttp-170)
REVERT: C  324 TRP cc_start: 0.8690 (t60) cc_final: 0.8361 (t60)
REVERT: D   16 TYR cc_start: 0.7989 (t80) cc_final: 0.7708 (t80)
REVERT: D  128 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7802 (mmmt)
REVERT: D  219 TYR cc_start: 0.7923 (p90) cc_final: 0.7578 (p90)
REVERT: D  233 ASN cc_start: 0.9219 (t0) cc_final: 0.9008 (t0)
REVERT: D  324 TRP cc_start: 0.8783 (t60) cc_final: 0.8367 (t60)
REVERT: E   16 TYR cc_start: 0.7978 (t80) cc_final: 0.7692 (t80)
REVERT: E  219 TYR cc_start: 0.7876 (p90) cc_final: 0.7557 (p90)
REVERT: E  270 ARG cc_start: 0.8664 (tpp-160) cc_final: 0.8085 (ttp-170)
REVERT: E  324 TRP cc_start: 0.8713 (t60) cc_final: 0.8357 (t60)
  outliers start: 19
  outliers final: 9
  residues processed: 154
  average time/residue: 0.1074
  time to fit residues: 24.4030
Evaluate side-chains
  142 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  266 GLU
Chi-restraints excluded: chain E residue   84 LEU
Chi-restraints excluded: chain E residue  184 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 121 optimal weight:    7.9990
   chunk 122 optimal weight:    4.9990
   chunk 141 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 322 GLN
B 269 ASN
B 322 GLN
C 322 GLN
D 322 GLN
E 269 ASN
E 322 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.108035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.079650 restraints weight = 29237.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 3.00
r_work: 0.3101 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13385  Z= 0.149
  Angle     :  0.643  13.861  18150  Z= 0.315
  Chirality :  0.040   0.167   1990
  Planarity :  0.003   0.036   2370
  Dihedral  :  4.720  24.069   1860
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.84 %
    Favored  : 82.06 %
  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:  0.60 (0.22), residues: 1625
  helix:  2.24 (0.17), residues: 935
  sheet: -1.89 (0.31), residues: 220
  loop : -2.37 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 184 
 TYR   0.008   0.001   TYR A 205 
 PHE   0.010   0.001   PHE E 321 
 TRP   0.009   0.001   TRP A 323 
 HIS   0.026   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (13385)
  covalent geometry    : angle       0.64316 (18150)
  hydrogen bonds       : bond        0.03716 (  795)
  hydrogen bonds       : angle       3.30510 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A  184 ARG cc_start: 0.8316 (ptt-90) cc_final: 0.8020 (ptt-90)
REVERT: A  219 TYR cc_start: 0.7814 (p90) cc_final: 0.7516 (p90)
REVERT: A  260 GLU cc_start: 0.8818 (tp30) cc_final: 0.8493 (tp30)
REVERT: A  270 ARG cc_start: 0.8676 (tpp-160) cc_final: 0.8098 (ttp-170)
REVERT: A  324 TRP cc_start: 0.8703 (t60) cc_final: 0.8452 (t60)
REVERT: B   16 TYR cc_start: 0.8004 (t80) cc_final: 0.7698 (t80)
REVERT: B  219 TYR cc_start: 0.7835 (p90) cc_final: 0.7493 (p90)
REVERT: B  260 GLU cc_start: 0.8947 (tp30) cc_final: 0.8597 (tp30)
REVERT: B  270 ARG cc_start: 0.8737 (tpp-160) cc_final: 0.8124 (ttp-170)
REVERT: B  324 TRP cc_start: 0.8748 (t60) cc_final: 0.8318 (t60)
REVERT: C   16 TYR cc_start: 0.7984 (t80) cc_final: 0.7713 (t80)
REVERT: C  219 TYR cc_start: 0.7785 (p90) cc_final: 0.7479 (p90)
REVERT: C  260 GLU cc_start: 0.8841 (tp30) cc_final: 0.8387 (tp30)
REVERT: C  270 ARG cc_start: 0.8724 (tpp-160) cc_final: 0.8185 (ttp-170)
REVERT: C  324 TRP cc_start: 0.8688 (t60) cc_final: 0.8377 (t60)
REVERT: D   16 TYR cc_start: 0.8019 (t80) cc_final: 0.7720 (t80)
REVERT: D  128 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7775 (mmmt)
REVERT: D  219 TYR cc_start: 0.7911 (p90) cc_final: 0.7564 (p90)
REVERT: D  233 ASN cc_start: 0.9215 (t0) cc_final: 0.9011 (t0)
REVERT: D  260 GLU cc_start: 0.8877 (tp30) cc_final: 0.8563 (tp30)
REVERT: D  266 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8158 (tm-30)
REVERT: D  324 TRP cc_start: 0.8789 (t60) cc_final: 0.8371 (t60)
REVERT: E   16 TYR cc_start: 0.7996 (t80) cc_final: 0.7717 (t80)
REVERT: E  219 TYR cc_start: 0.7862 (p90) cc_final: 0.7490 (p90)
REVERT: E  270 ARG cc_start: 0.8677 (tpp-160) cc_final: 0.8048 (ttp-170)
REVERT: E  324 TRP cc_start: 0.8724 (t60) cc_final: 0.8371 (t60)
  outliers start: 15
  outliers final: 8
  residues processed: 157
  average time/residue: 0.1024
  time to fit residues: 23.9558
Evaluate side-chains
  145 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  190 HIS
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  248 LEU
Chi-restraints excluded: chain D residue  266 GLU
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 155 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9980
   chunk 134 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 158 optimal weight:    0.0870
   chunk 99 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 149 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0670
   chunk 116 optimal weight:    1.9990
   overall best weight:    0.5696

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 269 ASN
A 322 GLN
B 322 GLN
C 269 ASN
C 322 GLN
D 322 GLN
E 190 HIS
E 322 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.110044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.081958 restraints weight = 29099.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.02
r_work: 0.3146 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13385  Z= 0.114
  Angle     :  0.617  12.402  18150  Z= 0.304
  Chirality :  0.039   0.157   1990
  Planarity :  0.003   0.035   2370
  Dihedral  :  4.536  23.670   1860
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 17.57 %
    Favored  : 81.32 %
  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:  0.78 (0.22), residues: 1625
  helix:  2.43 (0.17), residues: 930
  sheet: -1.92 (0.31), residues: 220
  loop : -2.27 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 184 
 TYR   0.008   0.001   TYR A  16 
 PHE   0.011   0.001   PHE E 281 
 TRP   0.007   0.001   TRP A 323 
 HIS   0.029   0.002   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (13385)
  covalent geometry    : angle       0.61653 (18150)
  hydrogen bonds       : bond        0.03344 (  795)
  hydrogen bonds       : angle       3.22420 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  219 TYR cc_start: 0.7784 (p90) cc_final: 0.7455 (p90)
REVERT: A  260 GLU cc_start: 0.8792 (tp30) cc_final: 0.8473 (tp30)
REVERT: A  270 ARG cc_start: 0.8666 (tpp-160) cc_final: 0.8076 (ttp-170)
REVERT: A  324 TRP cc_start: 0.8701 (t60) cc_final: 0.8471 (t60)
REVERT: B   16 TYR cc_start: 0.7969 (t80) cc_final: 0.7685 (t80)
REVERT: B  219 TYR cc_start: 0.7819 (p90) cc_final: 0.7445 (p90)
REVERT: B  260 GLU cc_start: 0.8920 (tp30) cc_final: 0.8565 (tp30)
REVERT: B  270 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8128 (ttp-170)
REVERT: B  324 TRP cc_start: 0.8731 (t60) cc_final: 0.8341 (t60)
REVERT: C   16 TYR cc_start: 0.7941 (t80) cc_final: 0.7694 (t80)
REVERT: C  219 TYR cc_start: 0.7716 (p90) cc_final: 0.7387 (p90)
REVERT: C  260 GLU cc_start: 0.8790 (tp30) cc_final: 0.8315 (tp30)
REVERT: C  266 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7953 (tm-30)
REVERT: C  270 ARG cc_start: 0.8702 (tpp-160) cc_final: 0.8122 (ttp-170)
REVERT: C  324 TRP cc_start: 0.8697 (t60) cc_final: 0.8406 (t60)
REVERT: D   16 TYR cc_start: 0.7967 (t80) cc_final: 0.7704 (t80)
REVERT: D  128 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7666 (mmmt)
REVERT: D  219 TYR cc_start: 0.7902 (p90) cc_final: 0.7524 (p90)
REVERT: D  233 ASN cc_start: 0.9186 (t0) cc_final: 0.8978 (t0)
REVERT: D  260 GLU cc_start: 0.8833 (tp30) cc_final: 0.8518 (tp30)
REVERT: D  266 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8005 (tm-30)
REVERT: D  324 TRP cc_start: 0.8767 (t60) cc_final: 0.8382 (t60)
REVERT: E   16 TYR cc_start: 0.7948 (t80) cc_final: 0.7690 (t80)
REVERT: E  219 TYR cc_start: 0.7817 (p90) cc_final: 0.7451 (p90)
REVERT: E  260 GLU cc_start: 0.8843 (tp30) cc_final: 0.8314 (tp30)
REVERT: E  270 ARG cc_start: 0.8646 (tpp-160) cc_final: 0.8073 (ttp-170)
REVERT: E  324 TRP cc_start: 0.8713 (t60) cc_final: 0.8395 (t60)
  outliers start: 15
  outliers final: 11
  residues processed: 168
  average time/residue: 0.1032
  time to fit residues: 26.0289
Evaluate side-chains
  155 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  248 LEU
Chi-restraints excluded: chain D residue  266 GLU
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 30 optimal weight:   40.0000
   chunk 60 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0020
   chunk 122 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
B 242 ASN
B 322 GLN
C 322 GLN
E 322 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.110425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.082299 restraints weight = 29108.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.02
r_work: 0.3154 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13385  Z= 0.115
  Angle     :  0.609  11.469  18150  Z= 0.302
  Chirality :  0.039   0.154   1990
  Planarity :  0.003   0.032   2370
  Dihedral  :  4.506  23.038   1860
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 17.72 %
    Favored  : 81.40 %
  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:  0.89 (0.22), residues: 1625
  helix:  2.52 (0.17), residues: 930
  sheet: -1.89 (0.31), residues: 220
  loop : -2.22 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 184 
 TYR   0.020   0.001   TYR A  16 
 PHE   0.009   0.001   PHE E 281 
 TRP   0.008   0.001   TRP A 323 
 HIS   0.002   0.000   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13385)
  covalent geometry    : angle       0.60920 (18150)
  hydrogen bonds       : bond        0.03273 (  795)
  hydrogen bonds       : angle       3.18427 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A  184 ARG cc_start: 0.8212 (ptt-90) cc_final: 0.7896 (ptt-90)
REVERT: A  219 TYR cc_start: 0.7749 (p90) cc_final: 0.7402 (p90)
REVERT: A  260 GLU cc_start: 0.8821 (tp30) cc_final: 0.8481 (tp30)
REVERT: A  270 ARG cc_start: 0.8709 (tpp-160) cc_final: 0.8122 (ttp-170)
REVERT: A  324 TRP cc_start: 0.8708 (t60) cc_final: 0.8496 (t60)
REVERT: B   16 TYR cc_start: 0.7962 (t80) cc_final: 0.7698 (t80)
REVERT: B  219 TYR cc_start: 0.7788 (p90) cc_final: 0.7444 (p90)
REVERT: B  260 GLU cc_start: 0.8953 (tp30) cc_final: 0.8578 (tp30)
REVERT: B  266 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: B  270 ARG cc_start: 0.8766 (tpp-160) cc_final: 0.8109 (ttm170)
REVERT: B  324 TRP cc_start: 0.8746 (t60) cc_final: 0.8416 (t60)
REVERT: C   16 TYR cc_start: 0.7969 (t80) cc_final: 0.7734 (t80)
REVERT: C  219 TYR cc_start: 0.7729 (p90) cc_final: 0.7419 (p90)
REVERT: C  260 GLU cc_start: 0.8843 (tp30) cc_final: 0.8349 (tp30)
REVERT: C  266 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7952 (tm-30)
REVERT: C  270 ARG cc_start: 0.8759 (tpp-160) cc_final: 0.8181 (ttp-170)
REVERT: C  323 TRP cc_start: 0.6972 (m100) cc_final: 0.6712 (m100)
REVERT: C  324 TRP cc_start: 0.8708 (t60) cc_final: 0.8437 (t60)
REVERT: D   16 TYR cc_start: 0.7991 (t80) cc_final: 0.7748 (t80)
REVERT: D  128 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7608 (mmmt)
REVERT: D  219 TYR cc_start: 0.7870 (p90) cc_final: 0.7520 (p90)
REVERT: D  233 ASN cc_start: 0.9194 (t0) cc_final: 0.8990 (t0)
REVERT: D  260 GLU cc_start: 0.8859 (tp30) cc_final: 0.8656 (tp30)
REVERT: D  266 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8001 (tm-30)
REVERT: D  324 TRP cc_start: 0.8796 (t60) cc_final: 0.8435 (t60)
REVERT: E   16 TYR cc_start: 0.7971 (t80) cc_final: 0.7734 (t80)
REVERT: E  219 TYR cc_start: 0.7759 (p90) cc_final: 0.7392 (p90)
REVERT: E  260 GLU cc_start: 0.8879 (tp30) cc_final: 0.8356 (tp30)
REVERT: E  270 ARG cc_start: 0.8720 (tpp-160) cc_final: 0.8098 (ttm170)
REVERT: E  324 TRP cc_start: 0.8744 (t60) cc_final: 0.8461 (t60)
  outliers start: 12
  outliers final: 7
  residues processed: 169
  average time/residue: 0.1103
  time to fit residues: 27.0352
Evaluate side-chains
  154 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  266 GLU
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9980
   chunk 96 optimal weight:    7.9990
   chunk 22 optimal weight:    0.1980
   chunk 124 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 143 optimal weight:    4.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 242 ASN
A 322 GLN
B 190 HIS
C 242 ASN
C 322 GLN
E 322 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.108668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.080232 restraints weight = 29410.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 3.02
r_work: 0.3111 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13385  Z= 0.150
  Angle     :  0.648  10.926  18150  Z= 0.323
  Chirality :  0.040   0.156   1990
  Planarity :  0.003   0.030   2370
  Dihedral  :  4.598  23.170   1860
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 18.31 %
    Favored  : 80.88 %
  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:  0.86 (0.22), residues: 1625
  helix:  2.46 (0.17), residues: 930
  sheet: -1.24 (0.34), residues: 185
  loop : -2.47 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 210 
 TYR   0.011   0.001   TYR A  16 
 PHE   0.017   0.001   PHE B 321 
 TRP   0.007   0.001   TRP A 323 
 HIS   0.022   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13385)
  covalent geometry    : angle       0.64781 (18150)
  hydrogen bonds       : bond        0.03590 (  795)
  hydrogen bonds       : angle       3.20518 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A  184 ARG cc_start: 0.8243 (ptt-90) cc_final: 0.7940 (ptt-90)
REVERT: A  219 TYR cc_start: 0.7765 (p90) cc_final: 0.7422 (p90)
REVERT: A  260 GLU cc_start: 0.8826 (tp30) cc_final: 0.8483 (tp30)
REVERT: A  270 ARG cc_start: 0.8717 (tpp-160) cc_final: 0.8130 (ttp-170)
REVERT: A  324 TRP cc_start: 0.8712 (t60) cc_final: 0.8474 (t60)
REVERT: B   16 TYR cc_start: 0.7980 (t80) cc_final: 0.7694 (t80)
REVERT: B  219 TYR cc_start: 0.7804 (p90) cc_final: 0.7447 (p90)
REVERT: B  260 GLU cc_start: 0.8966 (tp30) cc_final: 0.8620 (tp30)
REVERT: B  266 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: B  270 ARG cc_start: 0.8759 (tpp-160) cc_final: 0.8113 (ttm170)
REVERT: B  324 TRP cc_start: 0.8781 (t60) cc_final: 0.8427 (t60)
REVERT: C   16 TYR cc_start: 0.7985 (t80) cc_final: 0.7720 (t80)
REVERT: C  219 TYR cc_start: 0.7723 (p90) cc_final: 0.7379 (p90)
REVERT: C  260 GLU cc_start: 0.8847 (tp30) cc_final: 0.8356 (tp30)
REVERT: C  266 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7949 (tm-30)
REVERT: C  270 ARG cc_start: 0.8758 (tpp-160) cc_final: 0.8185 (ttp-170)
REVERT: C  323 TRP cc_start: 0.6963 (m100) cc_final: 0.6682 (m100)
REVERT: C  324 TRP cc_start: 0.8714 (t60) cc_final: 0.8435 (t60)
REVERT: D   16 TYR cc_start: 0.8004 (t80) cc_final: 0.7717 (t80)
REVERT: D   87 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6860 (pm20)
REVERT: D  128 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7734 (mmmt)
REVERT: D  219 TYR cc_start: 0.7881 (p90) cc_final: 0.7517 (p90)
REVERT: D  233 ASN cc_start: 0.9209 (t0) cc_final: 0.9003 (t0)
REVERT: D  260 GLU cc_start: 0.8875 (tp30) cc_final: 0.8557 (tp30)
REVERT: D  266 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8001 (tm-30)
REVERT: D  324 TRP cc_start: 0.8805 (t60) cc_final: 0.8465 (t60)
REVERT: E   16 TYR cc_start: 0.7983 (t80) cc_final: 0.7705 (t80)
REVERT: E  219 TYR cc_start: 0.7817 (p90) cc_final: 0.7433 (p90)
REVERT: E  270 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8084 (ttp-170)
REVERT: E  324 TRP cc_start: 0.8747 (t60) cc_final: 0.8448 (t60)
  outliers start: 11
  outliers final: 8
  residues processed: 159
  average time/residue: 0.1033
  time to fit residues: 24.4873
Evaluate side-chains
  157 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 147
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  190 HIS
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   87 GLU
Chi-restraints excluded: chain D residue  266 GLU
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 29 optimal weight:   10.0000
   chunk 108 optimal weight:    2.9990
   chunk 150 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0570
   chunk 17 optimal weight:    6.9990
   chunk 146 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    1.1500

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
B 190 HIS
C 322 GLN
E 242 ASN
E 322 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.109135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.080798 restraints weight = 29288.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 3.01
r_work: 0.3124 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13385  Z= 0.136
  Angle     :  0.636  10.697  18150  Z= 0.319
  Chirality :  0.040   0.149   1990
  Planarity :  0.003   0.032   2370
  Dihedral  :  4.584  23.389   1860
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 18.24 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.22), residues: 1625
  helix:  2.49 (0.17), residues: 930
  sheet: -1.20 (0.34), residues: 185
  loop : -2.44 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 210 
 TYR   0.009   0.001   TYR A  16 
 PHE   0.020   0.001   PHE D 321 
 TRP   0.007   0.001   TRP A 323 
 HIS   0.027   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (13385)
  covalent geometry    : angle       0.63582 (18150)
  hydrogen bonds       : bond        0.03498 (  795)
  hydrogen bonds       : angle       3.18641 ( 2340)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  184 ARG cc_start: 0.8219 (ptt-90) cc_final: 0.7909 (ptt-90)
REVERT: A  219 TYR cc_start: 0.7756 (p90) cc_final: 0.7418 (p90)
REVERT: A  260 GLU cc_start: 0.8812 (tp30) cc_final: 0.8468 (tp30)
REVERT: A  270 ARG cc_start: 0.8714 (tpp-160) cc_final: 0.8121 (ttp-170)
REVERT: A  324 TRP cc_start: 0.8723 (t60) cc_final: 0.8491 (t60)
REVERT: B   16 TYR cc_start: 0.7971 (t80) cc_final: 0.7711 (t80)
REVERT: B  219 TYR cc_start: 0.7811 (p90) cc_final: 0.7457 (p90)
REVERT: B  260 GLU cc_start: 0.8961 (tp30) cc_final: 0.8617 (tp30)
REVERT: B  266 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: B  270 ARG cc_start: 0.8745 (tpp-160) cc_final: 0.8107 (ttm170)
REVERT: B  324 TRP cc_start: 0.8787 (t60) cc_final: 0.8434 (t60)
REVERT: C   16 TYR cc_start: 0.7982 (t80) cc_final: 0.7750 (t80)
REVERT: C  219 TYR cc_start: 0.7736 (p90) cc_final: 0.7400 (p90)
REVERT: C  260 GLU cc_start: 0.8839 (tp30) cc_final: 0.8350 (tp30)
REVERT: C  266 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7929 (tm-30)
REVERT: C  270 ARG cc_start: 0.8747 (tpp-160) cc_final: 0.8171 (ttp-170)
REVERT: C  323 TRP cc_start: 0.6959 (m100) cc_final: 0.6693 (m100)
REVERT: C  324 TRP cc_start: 0.8724 (t60) cc_final: 0.8438 (t60)
REVERT: D   16 TYR cc_start: 0.8000 (t80) cc_final: 0.7764 (t80)
REVERT: D   87 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6836 (pm20)
REVERT: D  128 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7706 (mmmt)
REVERT: D  219 TYR cc_start: 0.7845 (p90) cc_final: 0.7448 (p90)
REVERT: D  233 ASN cc_start: 0.9199 (t0) cc_final: 0.8994 (t0)
REVERT: D  260 GLU cc_start: 0.8869 (tp30) cc_final: 0.8550 (tp30)
REVERT: D  266 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7961 (tm-30)
REVERT: D  324 TRP cc_start: 0.8848 (t60) cc_final: 0.8497 (t60)
REVERT: E   16 TYR cc_start: 0.7977 (t80) cc_final: 0.7729 (t80)
REVERT: E  219 TYR cc_start: 0.7803 (p90) cc_final: 0.7415 (p90)
REVERT: E  270 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8088 (ttm170)
REVERT: E  324 TRP cc_start: 0.8753 (t60) cc_final: 0.8455 (t60)
  outliers start: 13
  outliers final: 10
  residues processed: 154
  average time/residue: 0.1129
  time to fit residues: 25.4849
Evaluate side-chains
  156 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  190 HIS
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   87 GLU
Chi-restraints excluded: chain D residue  266 GLU
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 140 optimal weight:    0.5980
   chunk 155 optimal weight:    5.9990
   chunk 156 optimal weight:    0.0980
   chunk 127 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
B 190 HIS
C 322 GLN
D 269 ASN
E 322 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.110236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.081971 restraints weight = 29398.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 3.03
r_work: 0.3172 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13385  Z= 0.120
  Angle     :  0.623  10.340  18150  Z= 0.313
  Chirality :  0.039   0.145   1990
  Planarity :  0.003   0.033   2370
  Dihedral  :  4.491  23.027   1860
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 18.09 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.22), residues: 1625
  helix:  2.56 (0.17), residues: 930
  sheet: -1.57 (0.31), residues: 210
  loop : -2.29 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 210 
 TYR   0.007   0.001   TYR A  16 
 PHE   0.019   0.001   PHE C 321 
 TRP   0.012   0.001   TRP E 323 
 HIS   0.027   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (13385)
  covalent geometry    : angle       0.62349 (18150)
  hydrogen bonds       : bond        0.03315 (  795)
  hydrogen bonds       : angle       3.15202 ( 2340)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3166.37 seconds
wall clock time: 54 minutes 44.50 seconds (3284.50 seconds total)