Starting phenix.real_space_refine
on Sat Aug 23 11:08:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e5f_27911/08_2025/8e5f_27911.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e5f_27911/08_2025/8e5f_27911.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e5f_27911/08_2025/8e5f_27911.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e5f_27911/08_2025/8e5f_27911.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e5f_27911/08_2025/8e5f_27911.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e5f_27911/08_2025/8e5f_27911.cif"
  }
  resolution = 3.8
  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
-------------------------------------------------------------------------------
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=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe     20      7.16       5
     S      70      5.16       5
     C    7705      2.51       5
     N    1920      2.21       5
     O    2175      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11890
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2206
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 19, 'TRANS': 273}
    Chain: "A"
      Number of atoms: 172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 172
          Unusual residues: {'HEC': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 1.60, per 1000 atoms: 0.13
  Number of scatterers: 11890
  At special positions: 0
  Unit cell: (71.28, 75.6, 204.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe     20     26.01
     S      70     16.00
     O    2175      8.00
     N    1920      7.00
     C    7705      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  62 " - pdb=" SG  CYS C  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  62 " - pdb=" SG  CYS D  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  62 " - pdb=" SG  CYS E  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 133 " - pdb=" SG  CYS C 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 163 " distance=2.03

  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=65, symmetry=0
  Number of additional bonds: simple=65, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 545.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2640

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 15 sheets defined
      20.5% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 78 through 84
      removed outlier: 4.281A  pdb=" N   TRP A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 97
    Processing helix  chain 'A' and resid 101 through 103
      No H-bonds generated for 'chain 'A' and resid 101 through 103'
    Processing helix  chain 'A' and resid 104 through 112
      removed outlier: 3.604A  pdb=" N   SER A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 190
    Processing helix  chain 'A' and resid 224 through 226
      No H-bonds generated for 'chain 'A' and resid 224 through 226'
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.513A  pdb=" N   SER A 287 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 293
      removed outlier: 3.541A  pdb=" N   TYR A 292 " --> pdb=" O   ARG A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 307
      removed outlier: 3.659A  pdb=" N   PHE A 305 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 84
      removed outlier: 4.281A  pdb=" N   TRP B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 97
    Processing helix  chain 'B' and resid 101 through 103
      No H-bonds generated for 'chain 'B' and resid 101 through 103'
    Processing helix  chain 'B' and resid 104 through 112
      removed outlier: 3.604A  pdb=" N   SER B 110 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 190
    Processing helix  chain 'B' and resid 224 through 226
      No H-bonds generated for 'chain 'B' and resid 224 through 226'
    Processing helix  chain 'B' and resid 283 through 287
      removed outlier: 3.513A  pdb=" N   SER B 287 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 293
      removed outlier: 3.542A  pdb=" N   TYR B 292 " --> pdb=" O   ARG B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 307
      removed outlier: 3.659A  pdb=" N   PHE B 305 " --> pdb=" O   ALA B 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 84
      removed outlier: 4.281A  pdb=" N   TRP C  82 " --> pdb=" O   GLY C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 97
    Processing helix  chain 'C' and resid 101 through 103
      No H-bonds generated for 'chain 'C' and resid 101 through 103'
    Processing helix  chain 'C' and resid 104 through 112
      removed outlier: 3.604A  pdb=" N   SER C 110 " --> pdb=" O   GLY C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 190
    Processing helix  chain 'C' and resid 224 through 226
      No H-bonds generated for 'chain 'C' and resid 224 through 226'
    Processing helix  chain 'C' and resid 283 through 287
      removed outlier: 3.512A  pdb=" N   SER C 287 " --> pdb=" O   ALA C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 293
      removed outlier: 3.540A  pdb=" N   TYR C 292 " --> pdb=" O   ARG C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 307
      removed outlier: 3.660A  pdb=" N   PHE C 305 " --> pdb=" O   ALA C 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 84
      removed outlier: 4.281A  pdb=" N   TRP D  82 " --> pdb=" O   GLY D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 97
    Processing helix  chain 'D' and resid 101 through 103
      No H-bonds generated for 'chain 'D' and resid 101 through 103'
    Processing helix  chain 'D' and resid 104 through 112
      removed outlier: 3.604A  pdb=" N   SER D 110 " --> pdb=" O   GLY D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 190
    Processing helix  chain 'D' and resid 224 through 226
      No H-bonds generated for 'chain 'D' and resid 224 through 226'
    Processing helix  chain 'D' and resid 283 through 287
      removed outlier: 3.513A  pdb=" N   SER D 287 " --> pdb=" O   ALA D 284 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 293
      removed outlier: 3.541A  pdb=" N   TYR D 292 " --> pdb=" O   ARG D 288 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 307
      removed outlier: 3.660A  pdb=" N   PHE D 305 " --> pdb=" O   ALA D 302 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 78 through 84
      removed outlier: 4.281A  pdb=" N   TRP E  82 " --> pdb=" O   GLY E  78 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 89 through 97
    Processing helix  chain 'E' and resid 101 through 103
      No H-bonds generated for 'chain 'E' and resid 101 through 103'
    Processing helix  chain 'E' and resid 104 through 112
      removed outlier: 3.604A  pdb=" N   SER E 110 " --> pdb=" O   GLY E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 190
    Processing helix  chain 'E' and resid 224 through 226
      No H-bonds generated for 'chain 'E' and resid 224 through 226'
    Processing helix  chain 'E' and resid 283 through 287
      removed outlier: 3.513A  pdb=" N   SER E 287 " --> pdb=" O   ALA E 284 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 288 through 293
      removed outlier: 3.540A  pdb=" N   TYR E 292 " --> pdb=" O   ARG E 288 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 302 through 307
      removed outlier: 3.659A  pdb=" N   PHE E 305 " --> pdb=" O   ALA E 302 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 50 through 52
    Processing sheet with id=2, first strand: chain 'A' and resid 172 through 176
      removed outlier: 3.737A  pdb=" N   GLY A 166 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   THR A 193 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'A' and resid 201 through 203
    Processing sheet with id=4, first strand: chain 'B' and resid 50 through 52
    Processing sheet with id=5, first strand: chain 'B' and resid 172 through 176
      removed outlier: 3.736A  pdb=" N   GLY B 166 " --> pdb=" O   TYR B 130 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   THR B 193 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'B' and resid 201 through 203
    Processing sheet with id=7, first strand: chain 'C' and resid 50 through 52
    Processing sheet with id=8, first strand: chain 'C' and resid 172 through 176
      removed outlier: 3.737A  pdb=" N   GLY C 166 " --> pdb=" O   TYR C 130 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   THR C 193 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'C' and resid 201 through 203
    Processing sheet with id=10, first strand: chain 'D' and resid 50 through 52
    Processing sheet with id=11, first strand: chain 'D' and resid 172 through 176
      removed outlier: 3.736A  pdb=" N   GLY D 166 " --> pdb=" O   TYR D 130 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   THR D 193 " --> pdb=" O   PHE D 277 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'D' and resid 201 through 203
    Processing sheet with id=13, first strand: chain 'E' and resid 50 through 52
    Processing sheet with id=14, first strand: chain 'E' and resid 172 through 176
      removed outlier: 3.737A  pdb=" N   GLY E 166 " --> pdb=" O   TYR E 130 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   THR E 193 " --> pdb=" O   PHE E 277 " (cutoff:3.500A)
    Processing sheet with id=15, first strand: chain 'E' and resid 201 through 203

    260 hydrogen bonds defined for protein.
    675 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: 1.64

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 5340
        1.39 -     1.56: 6860
        1.56 -     1.73: 10
        1.73 -     1.89: 80
        1.89 -     2.06: 80
  Bond restraints: 12370
  Sorted by residual:
  bond pdb=" C2D HEC D 502 "
       pdb=" C3D HEC D 502 "
    ideal  model  delta    sigma   weight residual
    1.544  1.331  0.213 2.00e-02 2.50e+03 1.13e+02
  bond pdb=" C2D HEC B 502 "
       pdb=" C3D HEC B 502 "
    ideal  model  delta    sigma   weight residual
    1.544  1.332  0.212 2.00e-02 2.50e+03 1.13e+02
  bond pdb=" C2D HEC A 502 "
       pdb=" C3D HEC A 502 "
    ideal  model  delta    sigma   weight residual
    1.544  1.332  0.212 2.00e-02 2.50e+03 1.13e+02
  bond pdb=" C2D HEC E 502 "
       pdb=" C3D HEC E 502 "
    ideal  model  delta    sigma   weight residual
    1.544  1.332  0.212 2.00e-02 2.50e+03 1.13e+02
  bond pdb=" C2D HEC C 502 "
       pdb=" C3D HEC C 502 "
    ideal  model  delta    sigma   weight residual
    1.544  1.332  0.212 2.00e-02 2.50e+03 1.12e+02
  ... (remaining 12365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.31: 16937
        3.31 -     6.63: 173
        6.63 -     9.94: 25
        9.94 -    13.26: 20
       13.26 -    16.57: 35
  Bond angle restraints: 17190
  Sorted by residual:
  angle pdb=" CA  PRO C 260 "
        pdb=" N   PRO C 260 "
        pdb=" CD  PRO C 260 "
      ideal   model   delta    sigma   weight residual
     112.00   95.43   16.57 1.40e+00 5.10e-01 1.40e+02
  angle pdb=" CA  PRO B 260 "
        pdb=" N   PRO B 260 "
        pdb=" CD  PRO B 260 "
      ideal   model   delta    sigma   weight residual
     112.00   95.44   16.56 1.40e+00 5.10e-01 1.40e+02
  angle pdb=" CA  PRO D 260 "
        pdb=" N   PRO D 260 "
        pdb=" CD  PRO D 260 "
      ideal   model   delta    sigma   weight residual
     112.00   95.44   16.56 1.40e+00 5.10e-01 1.40e+02
  angle pdb=" CA  PRO A 260 "
        pdb=" N   PRO A 260 "
        pdb=" CD  PRO A 260 "
      ideal   model   delta    sigma   weight residual
     112.00   95.45   16.55 1.40e+00 5.10e-01 1.40e+02
  angle pdb=" CA  PRO E 260 "
        pdb=" N   PRO E 260 "
        pdb=" CD  PRO E 260 "
      ideal   model   delta    sigma   weight residual
     112.00   95.45   16.55 1.40e+00 5.10e-01 1.40e+02
  ... (remaining 17185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 6020
       17.96 -    35.93: 507
       35.93 -    53.89: 113
       53.89 -    71.85: 45
       71.85 -    89.82: 35
  Dihedral angle restraints: 6720
    sinusoidal: 2530
      harmonic: 4190
  Sorted by residual:
  dihedral pdb=" C2C HEC B 502 "
           pdb=" C3C HEC B 502 "
           pdb=" CAC HEC B 502 "
           pdb=" CBC HEC B 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     240.00  150.18   89.82     2      1.00e+01 1.00e-02 4.80e+01
  dihedral pdb=" C2C HEC E 502 "
           pdb=" C3C HEC E 502 "
           pdb=" CAC HEC E 502 "
           pdb=" CBC HEC E 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     240.00  150.19   89.81     2      1.00e+01 1.00e-02 4.80e+01
  dihedral pdb=" C2C HEC C 502 "
           pdb=" C3C HEC C 502 "
           pdb=" CAC HEC C 502 "
           pdb=" CBC HEC C 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     240.00  150.19   89.81     2      1.00e+01 1.00e-02 4.80e+01
  ... (remaining 6717 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1451
       0.079 -    0.159: 219
       0.159 -    0.238: 0
       0.238 -    0.318: 10
       0.318 -    0.397: 5
  Chirality restraints: 1685
  Sorted by residual:
  chirality pdb=" CA  ARG D 234 "
            pdb=" N   ARG D 234 "
            pdb=" C   ARG D 234 "
            pdb=" CB  ARG D 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CA  ARG E 234 "
            pdb=" N   ARG E 234 "
            pdb=" C   ARG E 234 "
            pdb=" CB  ARG E 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.92e+00
  chirality pdb=" CA  ARG A 234 "
            pdb=" N   ARG A 234 "
            pdb=" C   ARG A 234 "
            pdb=" CB  ARG A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.40 2.00e-01 2.50e+01 3.91e+00
  ... (remaining 1682 not shown)

  Planarity restraints: 2145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 259 "    0.072 5.00e-02 4.00e+02   9.68e-02 1.50e+01
        pdb=" N   PRO D 260 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO D 260 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO D 260 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 259 "    0.072 5.00e-02 4.00e+02   9.68e-02 1.50e+01
        pdb=" N   PRO A 260 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO A 260 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 260 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 259 "    0.072 5.00e-02 4.00e+02   9.67e-02 1.50e+01
        pdb=" N   PRO E 260 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO E 260 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO E 260 "    0.052 5.00e-02 4.00e+02
  ... (remaining 2142 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 134
        2.60 -     3.18: 10270
        3.18 -     3.75: 18205
        3.75 -     4.33: 24745
        4.33 -     4.90: 41796
  Nonbonded interactions: 95150
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS C  89 "
            pdb="FE   HEC C 502 "
     model   vdw
     2.029 3.080
  nonbonded pdb=" NE2 HIS B  89 "
            pdb="FE   HEC B 502 "
     model   vdw
     2.029 3.080
  nonbonded pdb=" NE2 HIS A  89 "
            pdb="FE   HEC A 502 "
     model   vdw
     2.030 3.080
  nonbonded pdb=" NE2 HIS D  89 "
            pdb="FE   HEC D 502 "
     model   vdw
     2.030 3.080
  nonbonded pdb=" NE2 HIS E  89 "
            pdb="FE   HEC E 502 "
     model   vdw
     2.030 3.080
  ... (remaining 95145 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: 0.04
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.330
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
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      :  0.026   0.517  12445  Z= 2.033
  Angle     :  1.167  16.575  17210  Z= 0.561
  Chirality :  0.057   0.397   1685
  Planarity :  0.006   0.097   2145
  Dihedral  : 16.511  89.819   4050
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 21.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.71 %
    Favored  : 87.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.74 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.96 (0.21), residues: 1455
  helix: -0.28 (0.37), residues: 210
  sheet: -1.73 (0.47), residues: 150
  loop : -2.56 (0.17), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 234 
 TYR   0.010   0.001   TYR C 123 
 PHE   0.015   0.001   PHE C 309 
 TRP   0.005   0.001   TRP E  93 
 HIS   0.004   0.001   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.01670 (12370)
  covalent geometry    : angle       1.16688 (17190)
  SS BOND              : bond        0.00188 (   10)
  SS BOND              : angle       1.43930 (   20)
  hydrogen bonds       : bond        0.24617 (  260)
  hydrogen bonds       : angle       9.18717 (  675)
  Misc. bond           : bond        0.27211 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  102 ASN cc_start: 0.8307 (t160) cc_final: 0.7910 (t0)
REVERT: A  267 MET cc_start: 0.8940 (tpp) cc_final: 0.8359 (tpt)
REVERT: B  102 ASN cc_start: 0.8395 (t160) cc_final: 0.8056 (t0)
REVERT: C  102 ASN cc_start: 0.8318 (t160) cc_final: 0.8010 (t0)
REVERT: D  102 ASN cc_start: 0.8348 (t160) cc_final: 0.7961 (t0)
REVERT: D  156 ASP cc_start: 0.7953 (p0) cc_final: 0.7123 (p0)
REVERT: E  260 PRO cc_start: 0.8134 (Cg_endo) cc_final: 0.7874 (Cg_endo)
REVERT: E  264 THR cc_start: 0.9126 (p) cc_final: 0.8906 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1104
  time to fit residues: 24.1511
Evaluate side-chains
  130 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN
C 229 GLN
D 229 GLN
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.105964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.093508 restraints weight = 22004.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.096364 restraints weight = 10710.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.098243 restraints weight = 6501.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.099404 restraints weight = 4500.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.100272 restraints weight = 3482.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.396  12445  Z= 0.192
  Angle     :  0.857  12.502  17210  Z= 0.382
  Chirality :  0.051   0.217   1685
  Planarity :  0.005   0.041   2145
  Dihedral  : 13.149  84.897   1735
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.78 %
    Favored  : 85.22 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 12.17 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.22 (0.20), residues: 1455
  helix: -0.35 (0.36), residues: 215
  sheet: -2.49 (0.43), residues: 145
  loop : -2.70 (0.17), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 288 
 TYR   0.013   0.002   TYR C 123 
 PHE   0.015   0.002   PHE C 309 
 TRP   0.003   0.001   TRP D  82 
 HIS   0.006   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (12370)
  covalent geometry    : angle       0.85527 (17190)
  SS BOND              : bond        0.00333 (   10)
  SS BOND              : angle       1.70036 (   20)
  hydrogen bonds       : bond        0.04983 (  260)
  hydrogen bonds       : angle       6.46366 (  675)
  Misc. bond           : bond        0.12265 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 162
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A  102 ASN cc_start: 0.8472 (t160) cc_final: 0.7983 (t0)
REVERT: A  130 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7996 (m-80)
REVERT: A  156 ASP cc_start: 0.7801 (p0) cc_final: 0.6991 (p0)
REVERT: A  267 MET cc_start: 0.8826 (tpp) cc_final: 0.8286 (tpt)
REVERT: B  102 ASN cc_start: 0.8481 (t160) cc_final: 0.8012 (t0)
REVERT: B  108 LEU cc_start: 0.8948 (tt) cc_final: 0.8738 (tp)
REVERT: B  130 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7614 (m-80)
REVERT: B  156 ASP cc_start: 0.7704 (p0) cc_final: 0.6856 (p0)
REVERT: B  229 GLN cc_start: 0.8526 (pt0) cc_final: 0.8258 (pt0)
REVERT: B  260 PRO cc_start: 0.8164 (Cg_endo) cc_final: 0.7886 (Cg_endo)
REVERT: C  102 ASN cc_start: 0.8464 (t160) cc_final: 0.8021 (t0)
REVERT: C  130 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7925 (m-80)
REVERT: D   51 SER cc_start: 0.9337 (t) cc_final: 0.9024 (m)
REVERT: D  102 ASN cc_start: 0.8525 (t160) cc_final: 0.8141 (t0)
REVERT: D  130 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7984 (m-10)
REVERT: D  156 ASP cc_start: 0.7967 (p0) cc_final: 0.7360 (p0)
REVERT: D  260 PRO cc_start: 0.8057 (Cg_endo) cc_final: 0.7780 (Cg_endo)
REVERT: E  102 ASN cc_start: 0.8468 (t160) cc_final: 0.8055 (t0)
REVERT: E  130 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7877 (m-10)
REVERT: E  264 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8731 (t)
  outliers start: 50
  outliers final: 24
  residues processed: 201
  average time/residue: 0.1066
  time to fit residues: 31.8272
Evaluate side-chains
  171 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  130 TYR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  304 CYS
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  130 TYR
Chi-restraints excluded: chain C residue  221 THR
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  304 CYS
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  264 THR
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   86 ILE
Chi-restraints excluded: chain E residue  130 TYR
Chi-restraints excluded: chain E residue  221 THR
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  304 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0970
   chunk 45 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0000
   chunk 143 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    0.2980
   chunk 114 optimal weight:    0.7980
   overall best weight:    0.4182

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 GLN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.098614 restraints weight = 21618.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.101617 restraints weight = 10607.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.103559 restraints weight = 6351.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.104886 restraints weight = 4361.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.105785 restraints weight = 3283.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.250  12445  Z= 0.140
  Angle     :  0.775  11.215  17210  Z= 0.349
  Chirality :  0.050   0.209   1685
  Planarity :  0.004   0.039   2145
  Dihedral  : 12.906  84.682   1735
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.06 %
    Favored  : 86.94 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.91 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.15 (0.20), residues: 1455
  helix: -0.13 (0.37), residues: 215
  sheet: -2.06 (0.45), residues: 150
  loop : -2.75 (0.17), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 288 
 TYR   0.013   0.001   TYR A 283 
 PHE   0.013   0.001   PHE C 309 
 TRP   0.005   0.001   TRP C  93 
 HIS   0.005   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (12370)
  covalent geometry    : angle       0.77343 (17190)
  SS BOND              : bond        0.00352 (   10)
  SS BOND              : angle       1.54625 (   20)
  hydrogen bonds       : bond        0.04261 (  260)
  hydrogen bonds       : angle       5.83172 (  675)
  Misc. bond           : bond        0.06714 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 172
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A   51 SER cc_start: 0.9160 (t) cc_final: 0.8920 (m)
REVERT: A  130 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7887 (m-80)
REVERT: A  156 ASP cc_start: 0.7542 (p0) cc_final: 0.6707 (p0)
REVERT: A  187 GLU cc_start: 0.8827 (tp30) cc_final: 0.8245 (mm-30)
REVERT: A  264 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8613 (t)
REVERT: A  299 PRO cc_start: 0.9360 (Cg_endo) cc_final: 0.8979 (Cg_exo)
REVERT: B   51 SER cc_start: 0.9076 (t) cc_final: 0.8827 (m)
REVERT: B  130 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7894 (m-10)
REVERT: B  156 ASP cc_start: 0.7498 (p0) cc_final: 0.6756 (p0)
REVERT: B  221 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8617 (p)
REVERT: B  229 GLN cc_start: 0.8486 (pt0) cc_final: 0.8233 (pt0)
REVERT: B  299 PRO cc_start: 0.9345 (Cg_endo) cc_final: 0.9002 (Cg_exo)
REVERT: C  130 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7909 (m-80)
REVERT: C  187 GLU cc_start: 0.8765 (tp30) cc_final: 0.8330 (mm-30)
REVERT: D   51 SER cc_start: 0.9197 (t) cc_final: 0.8980 (m)
REVERT: D  130 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7901 (m-10)
REVERT: D  156 ASP cc_start: 0.7871 (p0) cc_final: 0.7168 (p0)
REVERT: D  187 GLU cc_start: 0.8733 (tp30) cc_final: 0.8398 (mm-30)
REVERT: D  260 PRO cc_start: 0.7785 (Cg_endo) cc_final: 0.7577 (Cg_endo)
REVERT: D  288 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7646 (mtm-85)
REVERT: E   51 SER cc_start: 0.9181 (t) cc_final: 0.8886 (m)
REVERT: E  130 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7757 (m-10)
REVERT: E  187 GLU cc_start: 0.8855 (tp30) cc_final: 0.8216 (mm-30)
REVERT: E  264 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8621 (t)
REVERT: E  267 MET cc_start: 0.8195 (tpp) cc_final: 0.7868 (tpt)
  outliers start: 25
  outliers final: 13
  residues processed: 187
  average time/residue: 0.0993
  time to fit residues: 28.5982
Evaluate side-chains
  169 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain B residue  130 TYR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  304 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue  130 TYR
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  304 CYS
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
Chi-restraints excluded: chain E residue  130 TYR
Chi-restraints excluded: chain E residue  264 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 100 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 141 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9980
   chunk 94 optimal weight:    0.2980
   chunk 49 optimal weight:    0.2980
   chunk 144 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 102 ASN
B 125 ASN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 102 ASN
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 102 ASN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 102 ASN
E 229 GLN
** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.110260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.097269 restraints weight = 22184.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.100317 restraints weight = 10917.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.102266 restraints weight = 6570.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.103564 restraints weight = 4548.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.104440 restraints weight = 3463.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.294  12445  Z= 0.162
  Angle     :  0.781  12.710  17210  Z= 0.351
  Chirality :  0.051   0.223   1685
  Planarity :  0.004   0.038   2145
  Dihedral  : 13.004  85.619   1735
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.12 %
    Favored  : 84.88 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.51 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.24 (0.20), residues: 1455
  helix: -0.19 (0.37), residues: 215
  sheet: -2.45 (0.42), residues: 145
  loop : -2.76 (0.16), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 288 
 TYR   0.017   0.001   TYR C 123 
 PHE   0.014   0.001   PHE A 224 
 TRP   0.005   0.001   TRP C  82 
 HIS   0.004   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (12370)
  covalent geometry    : angle       0.77993 (17190)
  SS BOND              : bond        0.00319 (   10)
  SS BOND              : angle       1.41546 (   20)
  hydrogen bonds       : bond        0.04226 (  260)
  hydrogen bonds       : angle       5.61398 (  675)
  Misc. bond           : bond        0.09929 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 152
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A   51 SER cc_start: 0.9205 (t) cc_final: 0.8993 (m)
REVERT: A  102 ASN cc_start: 0.8456 (t160) cc_final: 0.7793 (t0)
REVERT: A  130 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8026 (m-80)
REVERT: A  156 ASP cc_start: 0.7701 (p0) cc_final: 0.6904 (p0)
REVERT: A  264 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8617 (t)
REVERT: B   70 VAL cc_start: 0.8277 (p) cc_final: 0.7986 (m)
REVERT: B  130 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7684 (m-10)
REVERT: B  156 ASP cc_start: 0.7512 (p0) cc_final: 0.6838 (p0)
REVERT: B  229 GLN cc_start: 0.8493 (pt0) cc_final: 0.8253 (pt0)
REVERT: B  299 PRO cc_start: 0.9368 (Cg_endo) cc_final: 0.9016 (Cg_exo)
REVERT: C  130 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8144 (m-80)
REVERT: C  187 GLU cc_start: 0.8785 (tp30) cc_final: 0.8136 (mm-30)
REVERT: D  102 ASN cc_start: 0.8374 (t0) cc_final: 0.7805 (t0)
REVERT: D  130 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7999 (m-10)
REVERT: D  156 ASP cc_start: 0.7877 (p0) cc_final: 0.7170 (p0)
REVERT: E  130 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7776 (m-10)
REVERT: E  187 GLU cc_start: 0.8915 (tp30) cc_final: 0.8226 (mm-30)
REVERT: E  264 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8659 (t)
  outliers start: 35
  outliers final: 22
  residues processed: 178
  average time/residue: 0.0883
  time to fit residues: 24.6243
Evaluate side-chains
  170 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  130 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  304 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue  130 TYR
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  304 CYS
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   86 ILE
Chi-restraints excluded: chain E residue  130 TYR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  304 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 94 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9990
   chunk 143 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 0 optimal weight:    0.0000
   chunk 83 optimal weight:    0.9980
   chunk 129 optimal weight:    0.6980
   chunk 136 optimal weight:    0.8980
   chunk 133 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0170
   overall best weight:    0.4222

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 GLN
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  74 GLN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.112618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.099699 restraints weight = 21805.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.102772 restraints weight = 10700.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.104743 restraints weight = 6405.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.106024 restraints weight = 4407.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.106944 restraints weight = 3352.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.187  12445  Z= 0.135
  Angle     :  0.749  11.078  17210  Z= 0.338
  Chirality :  0.050   0.241   1685
  Planarity :  0.004   0.038   2145
  Dihedral  : 12.900  86.271   1735
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.23 %
    Favored  : 87.77 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.28 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.22 (0.20), residues: 1455
  helix: -0.16 (0.37), residues: 215
  sheet: -2.08 (0.44), residues: 150
  loop : -2.81 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 288 
 TYR   0.016   0.001   TYR B 123 
 PHE   0.017   0.001   PHE E 224 
 TRP   0.004   0.001   TRP C  82 
 HIS   0.003   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (12370)
  covalent geometry    : angle       0.74789 (17190)
  SS BOND              : bond        0.00297 (   10)
  SS BOND              : angle       1.32714 (   20)
  hydrogen bonds       : bond        0.03877 (  260)
  hydrogen bonds       : angle       5.45868 (  675)
  Misc. bond           : bond        0.06436 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 164
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 SER cc_start: 0.9139 (t) cc_final: 0.8923 (m)
REVERT: A   66 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8158 (mm-40)
REVERT: A  130 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.8065 (m-80)
REVERT: A  156 ASP cc_start: 0.7591 (p0) cc_final: 0.6836 (p0)
REVERT: A  187 GLU cc_start: 0.8838 (tp30) cc_final: 0.8277 (mm-30)
REVERT: A  264 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8661 (t)
REVERT: A  267 MET cc_start: 0.8585 (ttm) cc_final: 0.8215 (tpt)
REVERT: A  299 PRO cc_start: 0.9350 (Cg_endo) cc_final: 0.8977 (Cg_exo)
REVERT: B   70 VAL cc_start: 0.8270 (p) cc_final: 0.8010 (m)
REVERT: B  130 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7763 (m-10)
REVERT: B  156 ASP cc_start: 0.7475 (p0) cc_final: 0.6917 (p0)
REVERT: B  229 GLN cc_start: 0.8477 (pt0) cc_final: 0.8236 (pt0)
REVERT: B  299 PRO cc_start: 0.9287 (Cg_endo) cc_final: 0.8926 (Cg_exo)
REVERT: C   70 VAL cc_start: 0.8661 (p) cc_final: 0.8347 (m)
REVERT: C  130 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8149 (m-80)
REVERT: C  280 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7133 (m)
REVERT: D   51 SER cc_start: 0.9126 (m) cc_final: 0.8758 (t)
REVERT: D  130 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8041 (m-10)
REVERT: D  156 ASP cc_start: 0.7706 (p0) cc_final: 0.7005 (p0)
REVERT: D  187 GLU cc_start: 0.8767 (tp30) cc_final: 0.8107 (mm-30)
REVERT: D  288 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7697 (mtm-85)
REVERT: D  299 PRO cc_start: 0.9238 (Cg_endo) cc_final: 0.8868 (Cg_exo)
REVERT: E  130 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.8060 (m-10)
REVERT: E  187 GLU cc_start: 0.8856 (tp30) cc_final: 0.8199 (mm-30)
REVERT: E  264 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8683 (t)
  outliers start: 35
  outliers final: 21
  residues processed: 190
  average time/residue: 0.0901
  time to fit residues: 27.4032
Evaluate side-chains
  181 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  130 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  304 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue  130 TYR
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  304 CYS
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue  130 TYR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  304 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 138 optimal weight:    0.4980
   chunk 128 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 ASN
E 229 GLN
** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.106741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.093896 restraints weight = 21936.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.096907 restraints weight = 10711.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.098803 restraints weight = 6412.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.100111 restraints weight = 4436.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.100917 restraints weight = 3367.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.278  12445  Z= 0.171
  Angle     :  0.790  13.122  17210  Z= 0.352
  Chirality :  0.051   0.245   1685
  Planarity :  0.004   0.037   2145
  Dihedral  : 12.975  88.269   1735
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.67 %
    Favored  : 84.33 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 16.77 %
    Favored  : 79.32 %
  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 aren not related in a simple way.
  whole: -3.29 (0.20), residues: 1455
  helix: -0.19 (0.37), residues: 215
  sheet: -2.44 (0.42), residues: 145
  loop : -2.82 (0.16), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 288 
 TYR   0.031   0.001   TYR B 123 
 PHE   0.017   0.001   PHE E 224 
 TRP   0.010   0.001   TRP A  93 
 HIS   0.004   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (12370)
  covalent geometry    : angle       0.78914 (17190)
  SS BOND              : bond        0.00480 (   10)
  SS BOND              : angle       1.45071 (   20)
  hydrogen bonds       : bond        0.04059 (  260)
  hydrogen bonds       : angle       5.46924 (  675)
  Misc. bond           : bond        0.10497 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 149
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8942 (tp40) cc_final: 0.8659 (mm-40)
REVERT: A  102 ASN cc_start: 0.8401 (t0) cc_final: 0.7759 (t0)
REVERT: A  130 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8041 (m-80)
REVERT: A  187 GLU cc_start: 0.8930 (tp30) cc_final: 0.8205 (mm-30)
REVERT: A  267 MET cc_start: 0.8625 (ttm) cc_final: 0.8255 (tpt)
REVERT: A  280 VAL cc_start: 0.7510 (OUTLIER) cc_final: 0.7221 (m)
REVERT: B   68 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.6589 (tp30)
REVERT: B   70 VAL cc_start: 0.8433 (p) cc_final: 0.8190 (m)
REVERT: B  130 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7720 (m-10)
REVERT: B  229 GLN cc_start: 0.8451 (pt0) cc_final: 0.8232 (pt0)
REVERT: B  299 PRO cc_start: 0.9349 (Cg_endo) cc_final: 0.8980 (Cg_exo)
REVERT: C   70 VAL cc_start: 0.8824 (p) cc_final: 0.8517 (m)
REVERT: C  102 ASN cc_start: 0.8410 (t0) cc_final: 0.7909 (t0)
REVERT: C  130 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8150 (m-80)
REVERT: C  187 GLU cc_start: 0.8760 (tp30) cc_final: 0.8363 (mm-30)
REVERT: C  280 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.7321 (m)
REVERT: D   51 SER cc_start: 0.9107 (m) cc_final: 0.8667 (t)
REVERT: D   66 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8376 (mm-40)
REVERT: D   70 VAL cc_start: 0.8904 (t) cc_final: 0.8543 (m)
REVERT: D  102 ASN cc_start: 0.8337 (t0) cc_final: 0.7815 (t0)
REVERT: D  130 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8010 (m-10)
REVERT: D  280 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7349 (m)
REVERT: E   66 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8224 (mm-40)
REVERT: E  102 ASN cc_start: 0.8445 (t0) cc_final: 0.7763 (t0)
REVERT: E  130 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8217 (m-10)
REVERT: E  280 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.7238 (m)
  outliers start: 46
  outliers final: 28
  residues processed: 182
  average time/residue: 0.0791
  time to fit residues: 23.3206
Evaluate side-chains
  182 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 144
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  130 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  304 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue  130 TYR
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  304 CYS
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   86 ILE
Chi-restraints excluded: chain E residue  115 CYS
Chi-restraints excluded: chain E residue  125 ASN
Chi-restraints excluded: chain E residue  130 TYR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain E residue  304 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 111 optimal weight:    0.6980
   chunk 0 optimal weight:    0.0980
   chunk 143 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 139 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 117 optimal weight:   20.0000
   chunk 80 optimal weight:    2.9990
   chunk 133 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 ASN
** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.095481 restraints weight = 21647.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.098471 restraints weight = 10633.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.100354 restraints weight = 6419.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.101647 restraints weight = 4472.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.102520 restraints weight = 3417.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.227  12445  Z= 0.149
  Angle     :  0.773  11.610  17210  Z= 0.348
  Chirality :  0.051   0.270   1685
  Planarity :  0.004   0.038   2145
  Dihedral  : 12.917  87.458   1735
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.47 %
    Favored  : 86.53 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 18.21 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.31 (0.20), residues: 1455
  helix: -0.19 (0.37), residues: 215
  sheet: -2.42 (0.42), residues: 145
  loop : -2.83 (0.16), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 288 
 TYR   0.016   0.001   TYR E 123 
 PHE   0.014   0.001   PHE E 224 
 TRP   0.008   0.001   TRP A  93 
 HIS   0.003   0.001   HIS E 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (12370)
  covalent geometry    : angle       0.77216 (17190)
  SS BOND              : bond        0.00320 (   10)
  SS BOND              : angle       1.34396 (   20)
  hydrogen bonds       : bond        0.03822 (  260)
  hydrogen bonds       : angle       5.43382 (  675)
  Misc. bond           : bond        0.08512 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 154
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8908 (tp40) cc_final: 0.8640 (mm-40)
REVERT: A   51 SER cc_start: 0.9178 (t) cc_final: 0.8942 (m)
REVERT: A   66 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8002 (mm-40)
REVERT: A  130 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.8159 (m-80)
REVERT: A  267 MET cc_start: 0.8599 (ttm) cc_final: 0.8261 (tpt)
REVERT: A  280 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7203 (m)
REVERT: A  299 PRO cc_start: 0.9361 (Cg_endo) cc_final: 0.9002 (Cg_exo)
REVERT: B   68 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6550 (tp30)
REVERT: B   70 VAL cc_start: 0.8420 (p) cc_final: 0.8203 (m)
REVERT: B  130 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7843 (m-10)
REVERT: B  229 GLN cc_start: 0.8411 (pt0) cc_final: 0.8193 (pt0)
REVERT: B  280 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7306 (m)
REVERT: B  299 PRO cc_start: 0.9324 (Cg_endo) cc_final: 0.8976 (Cg_exo)
REVERT: C   70 VAL cc_start: 0.8780 (p) cc_final: 0.8472 (m)
REVERT: C  130 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8067 (m-80)
REVERT: C  280 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7254 (m)
REVERT: D   51 SER cc_start: 0.9086 (m) cc_final: 0.8702 (t)
REVERT: D   66 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8364 (mm-40)
REVERT: D  130 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8153 (m-10)
REVERT: D  156 ASP cc_start: 0.7766 (p0) cc_final: 0.6929 (p0)
REVERT: D  187 GLU cc_start: 0.8784 (tp30) cc_final: 0.8241 (mm-30)
REVERT: D  229 GLN cc_start: 0.9101 (pp30) cc_final: 0.7981 (pp30)
REVERT: D  280 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7340 (m)
REVERT: D  299 PRO cc_start: 0.9239 (Cg_endo) cc_final: 0.8880 (Cg_exo)
REVERT: E   66 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8189 (mm-40)
REVERT: E  102 ASN cc_start: 0.8431 (t0) cc_final: 0.7767 (t0)
REVERT: E  130 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.8019 (m-10)
REVERT: E  187 GLU cc_start: 0.8853 (tp30) cc_final: 0.8321 (mm-30)
REVERT: E  280 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7175 (m)
  outliers start: 39
  outliers final: 28
  residues processed: 185
  average time/residue: 0.0743
  time to fit residues: 22.1798
Evaluate side-chains
  187 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 148
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  130 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  304 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue  130 TYR
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  304 CYS
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue  115 CYS
Chi-restraints excluded: chain E residue  125 ASN
Chi-restraints excluded: chain E residue  130 TYR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain E residue  304 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 29 optimal weight:    0.0060
   chunk 90 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 36 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.109289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.096386 restraints weight = 21614.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.099399 restraints weight = 10624.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.101358 restraints weight = 6393.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.102640 restraints weight = 4410.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.103524 restraints weight = 3362.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.219  12445  Z= 0.147
  Angle     :  0.769  11.199  17210  Z= 0.347
  Chirality :  0.050   0.231   1685
  Planarity :  0.004   0.036   2145
  Dihedral  : 12.911  87.645   1735
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.16 %
    Favored  : 85.84 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 18.38 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.29 (0.20), residues: 1455
  helix: -0.21 (0.37), residues: 215
  sheet: -2.12 (0.43), residues: 150
  loop : -2.86 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 288 
 TYR   0.016   0.001   TYR E 123 
 PHE   0.013   0.001   PHE E 224 
 TRP   0.008   0.001   TRP E  93 
 HIS   0.003   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (12370)
  covalent geometry    : angle       0.76831 (17190)
  SS BOND              : bond        0.00343 (   10)
  SS BOND              : angle       1.34739 (   20)
  hydrogen bonds       : bond        0.03774 (  260)
  hydrogen bonds       : angle       5.42974 (  675)
  Misc. bond           : bond        0.08188 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 161
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A   51 SER cc_start: 0.9180 (t) cc_final: 0.8932 (m)
REVERT: A   67 GLN cc_start: 0.8088 (tt0) cc_final: 0.7703 (tt0)
REVERT: A  130 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8207 (m-80)
REVERT: A  187 GLU cc_start: 0.8782 (tp30) cc_final: 0.8342 (mm-30)
REVERT: A  267 MET cc_start: 0.8600 (ttm) cc_final: 0.8254 (tpt)
REVERT: A  280 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7202 (m)
REVERT: A  299 PRO cc_start: 0.9343 (Cg_endo) cc_final: 0.8978 (Cg_exo)
REVERT: B   68 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.6485 (tp30)
REVERT: B   70 VAL cc_start: 0.8381 (p) cc_final: 0.8178 (m)
REVERT: B  130 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7922 (m-10)
REVERT: B  187 GLU cc_start: 0.8754 (tp30) cc_final: 0.8340 (mm-30)
REVERT: B  229 GLN cc_start: 0.8385 (pt0) cc_final: 0.8169 (pt0)
REVERT: B  280 VAL cc_start: 0.7601 (OUTLIER) cc_final: 0.7224 (m)
REVERT: B  299 PRO cc_start: 0.9315 (Cg_endo) cc_final: 0.8964 (Cg_exo)
REVERT: C   70 VAL cc_start: 0.8761 (p) cc_final: 0.8448 (m)
REVERT: C  130 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7960 (m-80)
REVERT: C  280 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7129 (m)
REVERT: D   51 SER cc_start: 0.9024 (m) cc_final: 0.8658 (t)
REVERT: D   66 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8375 (mm-40)
REVERT: D  130 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8206 (m-10)
REVERT: D  156 ASP cc_start: 0.7762 (p0) cc_final: 0.6882 (p0)
REVERT: D  187 GLU cc_start: 0.8746 (tp30) cc_final: 0.8108 (mm-30)
REVERT: D  229 GLN cc_start: 0.9100 (pp30) cc_final: 0.7995 (pp30)
REVERT: D  280 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7312 (m)
REVERT: D  299 PRO cc_start: 0.9217 (Cg_endo) cc_final: 0.8855 (Cg_exo)
REVERT: E   66 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8183 (mm-40)
REVERT: E  102 ASN cc_start: 0.8417 (t0) cc_final: 0.7765 (t0)
REVERT: E  130 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8156 (m-10)
REVERT: E  187 GLU cc_start: 0.8862 (tp30) cc_final: 0.8229 (mm-30)
REVERT: E  280 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7127 (m)
  outliers start: 42
  outliers final: 28
  residues processed: 193
  average time/residue: 0.0787
  time to fit residues: 24.4580
Evaluate side-chains
  192 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 153
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  130 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  304 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue  130 TYR
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  304 CYS
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  125 ASN
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue  115 CYS
Chi-restraints excluded: chain E residue  125 ASN
Chi-restraints excluded: chain E residue  130 TYR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain E residue  304 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 110 optimal weight:    0.0970
   chunk 74 optimal weight:    3.9990
   chunk 127 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 0 optimal weight:    0.2980
   chunk 45 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 142 optimal weight:    0.4980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.110216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.097215 restraints weight = 21543.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.100291 restraints weight = 10540.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.102245 restraints weight = 6309.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.103575 restraints weight = 4350.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.104445 restraints weight = 3300.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.213  12445  Z= 0.141
  Angle     :  0.759  10.424  17210  Z= 0.343
  Chirality :  0.050   0.254   1685
  Planarity :  0.004   0.037   2145
  Dihedral  : 12.884  87.227   1735
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.54 %
    Favored  : 86.46 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.72 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.30 (0.20), residues: 1455
  helix: -0.22 (0.37), residues: 215
  sheet: -2.12 (0.43), residues: 150
  loop : -2.87 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 288 
 TYR   0.015   0.001   TYR D 123 
 PHE   0.019   0.001   PHE E 224 
 TRP   0.008   0.001   TRP E  93 
 HIS   0.005   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12370)
  covalent geometry    : angle       0.75783 (17190)
  SS BOND              : bond        0.00296 (   10)
  SS BOND              : angle       1.25972 (   20)
  hydrogen bonds       : bond        0.03705 (  260)
  hydrogen bonds       : angle       5.41999 (  675)
  Misc. bond           : bond        0.07725 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 168
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 SER cc_start: 0.9111 (t) cc_final: 0.8878 (m)
REVERT: A   66 GLN cc_start: 0.8514 (mm-40) cc_final: 0.7948 (mm-40)
REVERT: A  130 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8198 (m-80)
REVERT: A  187 GLU cc_start: 0.8823 (tp30) cc_final: 0.8287 (mm-30)
REVERT: A  267 MET cc_start: 0.8544 (ttm) cc_final: 0.8205 (tpt)
REVERT: A  280 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7141 (m)
REVERT: A  299 PRO cc_start: 0.9313 (Cg_endo) cc_final: 0.8951 (Cg_exo)
REVERT: B   68 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.6516 (tp30)
REVERT: B   70 VAL cc_start: 0.8314 (p) cc_final: 0.8109 (m)
REVERT: B  130 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.8139 (m-10)
REVERT: B  187 GLU cc_start: 0.8781 (tp30) cc_final: 0.8426 (mm-30)
REVERT: B  280 VAL cc_start: 0.7576 (OUTLIER) cc_final: 0.7190 (m)
REVERT: B  299 PRO cc_start: 0.9295 (Cg_endo) cc_final: 0.8943 (Cg_exo)
REVERT: C   46 ASN cc_start: 0.8266 (m-40) cc_final: 0.8022 (t0)
REVERT: C   70 VAL cc_start: 0.8713 (p) cc_final: 0.8408 (m)
REVERT: C  130 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7863 (m-80)
REVERT: C  280 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7036 (m)
REVERT: D   51 SER cc_start: 0.8984 (m) cc_final: 0.8641 (t)
REVERT: D  130 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.8254 (m-80)
REVERT: D  156 ASP cc_start: 0.7734 (p0) cc_final: 0.6847 (p0)
REVERT: D  187 GLU cc_start: 0.8752 (tp30) cc_final: 0.8118 (mm-30)
REVERT: D  229 GLN cc_start: 0.9113 (pp30) cc_final: 0.8050 (pp30)
REVERT: D  280 VAL cc_start: 0.7616 (OUTLIER) cc_final: 0.7254 (m)
REVERT: D  299 PRO cc_start: 0.9190 (Cg_endo) cc_final: 0.8837 (Cg_exo)
REVERT: E   66 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8183 (mm-40)
REVERT: E  102 ASN cc_start: 0.8378 (t0) cc_final: 0.7740 (t0)
REVERT: E  187 GLU cc_start: 0.8857 (tp30) cc_final: 0.8222 (mm-30)
  outliers start: 40
  outliers final: 27
  residues processed: 197
  average time/residue: 0.0771
  time to fit residues: 24.4628
Evaluate side-chains
  198 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  130 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  304 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue  130 TYR
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  304 CYS
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  125 ASN
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue  115 CYS
Chi-restraints excluded: chain E residue  125 ASN
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain E residue  304 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 132 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 109 optimal weight:    0.3980
   chunk 84 optimal weight:    0.5980
   chunk 115 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 110 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0770
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 ASN
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.111584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.098606 restraints weight = 21532.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.101682 restraints weight = 10557.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.103647 restraints weight = 6350.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.104972 restraints weight = 4378.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.105883 restraints weight = 3314.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.236  12445  Z= 0.138
  Angle     :  0.762   9.566  17210  Z= 0.343
  Chirality :  0.050   0.251   1685
  Planarity :  0.004   0.035   2145
  Dihedral  : 12.868  86.819   1735
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.54 %
    Favored  : 86.46 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 18.89 %
    Favored  : 77.79 %
  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 aren not related in a simple way.
  whole: -3.28 (0.20), residues: 1455
  helix: -0.19 (0.37), residues: 215
  sheet: -2.05 (0.43), residues: 150
  loop : -2.87 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 288 
 TYR   0.022   0.001   TYR E 148 
 PHE   0.024   0.001   PHE E 224 
 TRP   0.007   0.001   TRP E  93 
 HIS   0.007   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12370)
  covalent geometry    : angle       0.76088 (17190)
  SS BOND              : bond        0.00282 (   10)
  SS BOND              : angle       1.21783 (   20)
  hydrogen bonds       : bond        0.03629 (  260)
  hydrogen bonds       : angle       5.45784 (  675)
  Misc. bond           : bond        0.07053 (   65)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 179
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8020 (mm-40)
REVERT: A  130 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8137 (m-80)
REVERT: A  187 GLU cc_start: 0.8791 (tp30) cc_final: 0.8246 (mm-30)
REVERT: A  267 MET cc_start: 0.8512 (ttm) cc_final: 0.8181 (tpt)
REVERT: A  280 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7012 (m)
REVERT: A  299 PRO cc_start: 0.9278 (Cg_endo) cc_final: 0.8919 (Cg_exo)
REVERT: B   68 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.6609 (tp30)
REVERT: B   70 VAL cc_start: 0.8316 (p) cc_final: 0.8101 (m)
REVERT: B  130 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8072 (m-10)
REVERT: B  140 ARG cc_start: 0.8062 (tpp-160) cc_final: 0.7848 (tpm170)
REVERT: B  187 GLU cc_start: 0.8740 (tp30) cc_final: 0.8468 (mm-30)
REVERT: B  263 GLU cc_start: 0.7999 (mp0) cc_final: 0.6509 (tt0)
REVERT: B  280 VAL cc_start: 0.7436 (OUTLIER) cc_final: 0.7027 (m)
REVERT: B  299 PRO cc_start: 0.9267 (Cg_endo) cc_final: 0.8925 (Cg_exo)
REVERT: C   46 ASN cc_start: 0.8169 (m-40) cc_final: 0.7950 (t0)
REVERT: C   70 VAL cc_start: 0.8684 (p) cc_final: 0.8369 (m)
REVERT: C  130 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7935 (m-80)
REVERT: C  219 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7781 (tt)
REVERT: D   51 SER cc_start: 0.8986 (m) cc_final: 0.8651 (t)
REVERT: D  130 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8228 (m-10)
REVERT: D  187 GLU cc_start: 0.8767 (tp30) cc_final: 0.8148 (mm-30)
REVERT: D  229 GLN cc_start: 0.9105 (pp30) cc_final: 0.8078 (pp30)
REVERT: D  280 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7187 (m)
REVERT: D  299 PRO cc_start: 0.9154 (Cg_endo) cc_final: 0.8806 (Cg_exo)
REVERT: E   66 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8183 (mm-40)
REVERT: E  102 ASN cc_start: 0.8304 (t0) cc_final: 0.7739 (t0)
REVERT: E  131 THR cc_start: 0.8039 (m) cc_final: 0.7796 (m)
REVERT: E  187 GLU cc_start: 0.8866 (tp30) cc_final: 0.8334 (mm-30)
REVERT: E  280 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.6973 (m)
  outliers start: 39
  outliers final: 25
  residues processed: 207
  average time/residue: 0.0772
  time to fit residues: 25.6350
Evaluate side-chains
  205 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 170
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  125 ASN
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain B residue   68 GLU
Chi-restraints excluded: chain B residue  130 TYR
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  304 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue  130 TYR
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain C residue  304 CYS
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  125 ASN
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  280 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   86 ILE
Chi-restraints excluded: chain E residue  115 CYS
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain E residue  280 VAL
Chi-restraints excluded: chain E residue  304 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 86 optimal weight:    0.0020
   chunk 85 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0570
   chunk 94 optimal weight:    0.2980
   chunk 66 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0670
   chunk 132 optimal weight:    0.0270
   chunk 135 optimal weight:    8.9990
   chunk 80 optimal weight:    6.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.0902

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.122869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.109460 restraints weight = 20979.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.112721 restraints weight = 10511.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114845 restraints weight = 6380.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.116257 restraints weight = 4375.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.117200 restraints weight = 3274.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.165  12445  Z= 0.138
  Angle     :  0.765  17.275  17210  Z= 0.348
  Chirality :  0.049   0.260   1685
  Planarity :  0.004   0.035   2145
  Dihedral  : 12.805  87.189   1735
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.91 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.23 (0.20), residues: 1455
  helix: -0.10 (0.37), residues: 215
  sheet: -1.92 (0.44), residues: 150
  loop : -2.86 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 288 
 TYR   0.032   0.001   TYR B 148 
 PHE   0.017   0.001   PHE E 224 
 TRP   0.008   0.001   TRP A  93 
 HIS   0.008   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (12370)
  covalent geometry    : angle       0.76333 (17190)
  SS BOND              : bond        0.00534 (   10)
  SS BOND              : angle       1.64083 (   20)
  hydrogen bonds       : bond        0.03613 (  260)
  hydrogen bonds       : angle       5.61034 (  675)
  Misc. bond           : bond        0.05045 (   65)

===============================================================================
Job complete
usr+sys time: 1699.42 seconds
wall clock time: 30 minutes 21.08 seconds (1821.08 seconds total)