Starting phenix.real_space_refine
on Tue Jul 29 20:21:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e5f_27911/07_2025/8e5f_27911.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e5f_27911/07_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_27911/07_2025/8e5f_27911.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e5f_27911/07_2025/8e5f_27911.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e5f_27911/07_2025/8e5f_27911.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e5f_27911/07_2025/8e5f_27911.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:
    C, B, E, D
  Time building chain proxies: 6.07, per 1000 atoms: 0.51
  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 C  62 " - pdb=" SG  CYS C  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  62 " - pdb=" SG  CYS E  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  62 " - pdb=" SG  CYS D  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 133 " - pdb=" SG  CYS C 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 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: 3.72
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.55
  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: 3.23

  Time building geometry restraints manager: 4.35 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     29.900
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.940
-------------------------------------------------------------------------------
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 : 22.93
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.005   0.001   TRP E  93 
 HIS   0.004   0.001   HIS E  38 
 PHE   0.015   0.001   PHE C 309 
 TYR   0.010   0.001   TYR C 123 
 ARG   0.006   0.001   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24617 (  260)
  hydrogen bonds       : angle       9.18717 (  675)
  SS BOND              : bond        0.00188 (   10)
  SS BOND              : angle       1.43930 (   20)
  covalent geometry    : bond        0.01670 (12370)
  covalent geometry    : angle       1.16688 (17190)
  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  : 1.282 
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: 0.2305
  time to fit residues: 50.6658
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  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 60 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 131 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  74 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 = 0.3355 r_free = 0.3355 target = 0.110411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.097847 restraints weight = 22078.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.100758 restraints weight = 10804.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.102671 restraints weight = 6534.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.366  12445  Z= 0.174
  Angle     :  0.835  11.083  17210  Z= 0.374
  Chirality :  0.050   0.214   1685
  Planarity :  0.004   0.039   2145
  Dihedral  : 13.071  86.020   1735
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.47 %
    Favored  : 86.53 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 12.43 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.20), residues: 1455
  helix: -0.37 (0.36), residues: 215
  sheet: -2.43 (0.43), residues: 145
  loop : -2.68 (0.17), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  82 
 HIS   0.005   0.001   HIS D 273 
 PHE   0.016   0.002   PHE C 309 
 TYR   0.013   0.002   TYR B 283 
 ARG   0.005   0.001   ARG E 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04785 (  260)
  hydrogen bonds       : angle       6.43418 (  675)
  SS BOND              : bond        0.00328 (   10)
  SS BOND              : angle       1.59151 (   20)
  covalent geometry    : bond        0.00429 (12370)
  covalent geometry    : angle       0.83329 (17190)
  Misc. bond           : bond        0.11058 (   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
  217 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 174
  time to evaluate  : 1.284 
Fit side-chains
REVERT: A   51 SER cc_start: 0.9316 (t) cc_final: 0.9031 (m)
REVERT: A  102 ASN cc_start: 0.8405 (t160) cc_final: 0.7831 (t0)
REVERT: A  130 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7942 (m-80)
REVERT: A  156 ASP cc_start: 0.7723 (p0) cc_final: 0.6921 (p0)
REVERT: A  267 MET cc_start: 0.8834 (tpp) cc_final: 0.8254 (tpt)
REVERT: B   51 SER cc_start: 0.9091 (t) cc_final: 0.8820 (m)
REVERT: B  108 LEU cc_start: 0.8953 (tt) cc_final: 0.8739 (tp)
REVERT: B  130 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7573 (m-80)
REVERT: B  156 ASP cc_start: 0.7634 (p0) cc_final: 0.6782 (p0)
REVERT: B  260 PRO cc_start: 0.8081 (Cg_endo) cc_final: 0.7800 (Cg_endo)
REVERT: C  102 ASN cc_start: 0.8395 (t160) cc_final: 0.7918 (t0)
REVERT: C  130 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7929 (m-80)
REVERT: D   51 SER cc_start: 0.9335 (t) cc_final: 0.9023 (m)
REVERT: D  102 ASN cc_start: 0.8469 (t160) cc_final: 0.7976 (t0)
REVERT: D  130 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7948 (m-10)
REVERT: D  156 ASP cc_start: 0.7975 (p0) cc_final: 0.7323 (p0)
REVERT: D  260 PRO cc_start: 0.7972 (Cg_endo) cc_final: 0.7692 (Cg_endo)
REVERT: E   51 SER cc_start: 0.9254 (t) cc_final: 0.8933 (m)
REVERT: E  102 ASN cc_start: 0.8405 (t160) cc_final: 0.7856 (t0)
REVERT: E  130 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7778 (m-10)
REVERT: E  264 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8731 (t)
  outliers start: 43
  outliers final: 19
  residues processed: 205
  average time/residue: 0.2206
  time to fit residues: 67.1322
Evaluate side-chains
  176 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
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  130 TYR
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  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  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 56 optimal weight:    0.4980
   chunk 90 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0970
   chunk 17 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 102 ASN
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 GLN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 GLN
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 229 GLN
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 229 GLN
** 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 229 GLN
** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 314 GLN ** 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 = 0.3297 r_free = 0.3297 target = 0.106584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.093695 restraints weight = 22619.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.096661 restraints weight = 11157.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.098509 restraints weight = 6741.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.372  12445  Z= 0.197
  Angle     :  0.857  15.686  17210  Z= 0.381
  Chirality :  0.053   0.221   1685
  Planarity :  0.005   0.043   2145
  Dihedral  : 13.104  88.415   1735
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.74 %
    Favored  : 84.26 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.83 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.20), residues: 1455
  helix: -0.30 (0.37), residues: 215
  sheet: -2.57 (0.42), residues: 145
  loop : -2.75 (0.17), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  93 
 HIS   0.006   0.001   HIS D 273 
 PHE   0.014   0.002   PHE B 224 
 TYR   0.014   0.002   TYR A 283 
 ARG   0.004   0.001   ARG E 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04621 (  260)
  hydrogen bonds       : angle       5.89018 (  675)
  SS BOND              : bond        0.00320 (   10)
  SS BOND              : angle       1.75824 (   20)
  covalent geometry    : bond        0.00487 (12370)
  covalent geometry    : angle       0.85562 (17190)
  Misc. bond           : bond        0.12501 (   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
  184 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 147
  time to evaluate  : 1.205 
Fit side-chains
REVERT: A  102 ASN cc_start: 0.8558 (t160) cc_final: 0.8216 (t0)
REVERT: A  130 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8059 (m-80)
REVERT: A  187 GLU cc_start: 0.8913 (tp30) cc_final: 0.8248 (mm-30)
REVERT: B  130 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7753 (m-10)
REVERT: B  229 GLN cc_start: 0.8504 (pt0) cc_final: 0.8255 (pt0)
REVERT: B  260 PRO cc_start: 0.8193 (Cg_endo) cc_final: 0.7961 (Cg_endo)
REVERT: C   51 SER cc_start: 0.9276 (m) cc_final: 0.8963 (t)
REVERT: C  102 ASN cc_start: 0.8590 (t160) cc_final: 0.8075 (t0)
REVERT: C  130 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8067 (m-80)
REVERT: C  187 GLU cc_start: 0.8855 (tp30) cc_final: 0.8359 (mm-30)
REVERT: C  229 GLN cc_start: 0.8412 (pt0) cc_final: 0.8184 (pt0)
REVERT: D  102 ASN cc_start: 0.8616 (t160) cc_final: 0.8131 (t0)
REVERT: D  130 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8044 (m-10)
REVERT: D  156 ASP cc_start: 0.7907 (p0) cc_final: 0.7272 (p0)
REVERT: D  187 GLU cc_start: 0.8788 (tp30) cc_final: 0.8378 (mm-30)
REVERT: D  288 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7816 (mtm-85)
REVERT: E  102 ASN cc_start: 0.8608 (t160) cc_final: 0.8108 (t0)
REVERT: E  130 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7883 (m-10)
REVERT: E  264 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8707 (t)
  outliers start: 37
  outliers final: 23
  residues processed: 180
  average time/residue: 0.1981
  time to fit residues: 54.4618
Evaluate side-chains
  163 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
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  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   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  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  264 THR
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain D residue  304 CYS
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 7 optimal weight:    0.2980
   chunk 143 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 102 ASN
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 102 ASN
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 102 ASN
D 229 GLN
** 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 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 = 0.3324 r_free = 0.3324 target = 0.108358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.095616 restraints weight = 22187.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.098575 restraints weight = 10936.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.100480 restraints weight = 6594.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.314  12445  Z= 0.167
  Angle     :  0.806  13.274  17210  Z= 0.362
  Chirality :  0.051   0.237   1685
  Planarity :  0.004   0.040   2145
  Dihedral  : 12.992  86.948   1735
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.57 %
    Favored  : 85.43 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.20), residues: 1455
  helix: -0.23 (0.38), residues: 215
  sheet: -2.52 (0.42), residues: 145
  loop : -2.81 (0.16), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  82 
 HIS   0.005   0.001   HIS A  89 
 PHE   0.015   0.001   PHE D 224 
 TYR   0.013   0.001   TYR B 123 
 ARG   0.004   0.000   ARG C 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04219 (  260)
  hydrogen bonds       : angle       5.66583 (  675)
  SS BOND              : bond        0.00324 (   10)
  SS BOND              : angle       1.55238 (   20)
  covalent geometry    : bond        0.00415 (12370)
  covalent geometry    : angle       0.80512 (17190)
  Misc. bond           : bond        0.10404 (   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
  185 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 148
  time to evaluate  : 1.203 
Fit side-chains
REVERT: A  102 ASN cc_start: 0.8512 (t0) cc_final: 0.8190 (t0)
REVERT: A  130 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8063 (m-80)
REVERT: A  156 ASP cc_start: 0.7832 (p0) cc_final: 0.6931 (p0)
REVERT: B   70 VAL cc_start: 0.8371 (p) cc_final: 0.8090 (m)
REVERT: B  130 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7692 (m-10)
REVERT: B  229 GLN cc_start: 0.8486 (pt0) cc_final: 0.8252 (pt0)
REVERT: B  299 PRO cc_start: 0.9377 (Cg_endo) cc_final: 0.9019 (Cg_exo)
REVERT: C  102 ASN cc_start: 0.8519 (t0) cc_final: 0.8034 (t0)
REVERT: C  130 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7853 (m-80)
REVERT: D  102 ASN cc_start: 0.8537 (t0) cc_final: 0.7991 (t0)
REVERT: D  130 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7989 (m-10)
REVERT: D  156 ASP cc_start: 0.7751 (p0) cc_final: 0.7152 (p0)
REVERT: E  102 ASN cc_start: 0.8580 (t0) cc_final: 0.8083 (t0)
REVERT: E  130 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7883 (m-10)
REVERT: E  264 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8700 (t)
  outliers start: 37
  outliers final: 21
  residues processed: 177
  average time/residue: 0.1769
  time to fit residues: 49.5449
Evaluate side-chains
  165 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
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  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   54 THR
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  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  257 GLU
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  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 31 optimal weight:    3.9990
   chunk 118 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 73 optimal weight:    9.9990
   chunk 12 optimal weight:    0.2980
   overall best weight:    1.2588

-------------------------------------------------------------------------------
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 125 ASN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 125 ASN ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 314 GLN ** 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 = 0.3272 r_free = 0.3272 target = 0.103480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.090814 restraints weight = 21959.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.093709 restraints weight = 10795.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.095506 restraints weight = 6536.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.329  12445  Z= 0.191
  Angle     :  0.834  14.230  17210  Z= 0.373
  Chirality :  0.052   0.238   1685
  Planarity :  0.004   0.042   2145
  Dihedral  : 13.082  89.934   1735
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.01 %
    Favored  : 83.99 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 16.09 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.20), residues: 1455
  helix: -0.27 (0.38), residues: 215
  sheet: -2.55 (0.42), residues: 145
  loop : -2.83 (0.16), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B  89 
 PHE   0.014   0.002   PHE D 224 
 TYR   0.015   0.002   TYR A 123 
 ARG   0.003   0.000   ARG E 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  260)
  hydrogen bonds       : angle       5.58706 (  675)
  SS BOND              : bond        0.00293 (   10)
  SS BOND              : angle       1.56543 (   20)
  covalent geometry    : bond        0.00479 (12370)
  covalent geometry    : angle       0.83324 (17190)
  Misc. bond           : bond        0.11977 (   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
  193 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 144
  time to evaluate  : 1.295 
Fit side-chains
REVERT: A  102 ASN cc_start: 0.8547 (t0) cc_final: 0.8239 (t0)
REVERT: A  130 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8131 (m-80)
REVERT: A  187 GLU cc_start: 0.8988 (tp30) cc_final: 0.8289 (mm-30)
REVERT: A  229 GLN cc_start: 0.8253 (pt0) cc_final: 0.8013 (pt0)
REVERT: A  280 VAL cc_start: 0.7561 (OUTLIER) cc_final: 0.7300 (m)
REVERT: B   68 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.6507 (tp30)
REVERT: B   70 VAL cc_start: 0.8498 (p) cc_final: 0.8254 (m)
REVERT: B  102 ASN cc_start: 0.8447 (t0) cc_final: 0.8001 (t0)
REVERT: B  130 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7993 (m-10)
REVERT: B  229 GLN cc_start: 0.8477 (pt0) cc_final: 0.8214 (pt0)
REVERT: B  299 PRO cc_start: 0.9387 (Cg_endo) cc_final: 0.9023 (Cg_exo)
REVERT: C  130 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7940 (m-80)
REVERT: C  280 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7381 (m)
REVERT: D   66 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8500 (mm-40)
REVERT: D  102 ASN cc_start: 0.8552 (t0) cc_final: 0.7993 (t0)
REVERT: D  130 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7885 (m-10)
REVERT: D  187 GLU cc_start: 0.8775 (tp30) cc_final: 0.8433 (mm-30)
REVERT: D  280 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7602 (m)
REVERT: E   66 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8212 (mm-40)
REVERT: E  130 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7883 (m-10)
REVERT: E  264 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8732 (t)
REVERT: E  280 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7426 (m)
  outliers start: 49
  outliers final: 28
  residues processed: 185
  average time/residue: 0.1881
  time to fit residues: 55.0958
Evaluate side-chains
  177 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 138
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
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  221 THR
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  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   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  257 GLU
Chi-restraints excluded: chain D residue  264 THR
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  130 TYR
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  280 VAL
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 91 optimal weight:    0.2980
   chunk 123 optimal weight:    0.4980
   chunk 63 optimal weight:    0.0670
   chunk 73 optimal weight:    0.6980
   chunk 143 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0020
   chunk 2 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.3126

-------------------------------------------------------------------------------
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 229 GLN
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  89 HIS

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 = 0.109457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.096578 restraints weight = 21760.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.099587 restraints weight = 10630.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.101564 restraints weight = 6405.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.176  12445  Z= 0.139
  Angle     :  0.773  11.258  17210  Z= 0.349
  Chirality :  0.050   0.249   1685
  Planarity :  0.004   0.037   2145
  Dihedral  : 12.776  85.222   1735
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.95 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.70 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.20), residues: 1455
  helix: -0.34 (0.38), residues: 205
  sheet: -2.16 (0.43), residues: 150
  loop : -2.92 (0.16), residues: 1100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  82 
 HIS   0.005   0.001   HIS A  89 
 PHE   0.012   0.001   PHE B 309 
 TYR   0.020   0.001   TYR B 123 
 ARG   0.003   0.000   ARG E 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03794 (  260)
  hydrogen bonds       : angle       5.49168 (  675)
  SS BOND              : bond        0.00332 (   10)
  SS BOND              : angle       1.42548 (   20)
  covalent geometry    : bond        0.00342 (12370)
  covalent geometry    : angle       0.77175 (17190)
  Misc. bond           : bond        0.06578 (   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
  206 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 1.189 
Fit side-chains
REVERT: A   51 SER cc_start: 0.9115 (t) cc_final: 0.8875 (m)
REVERT: A  102 ASN cc_start: 0.8405 (t0) cc_final: 0.7776 (t0)
REVERT: A  130 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.8145 (m-80)
REVERT: A  280 VAL cc_start: 0.7415 (OUTLIER) cc_final: 0.7146 (m)
REVERT: A  299 PRO cc_start: 0.9324 (Cg_endo) cc_final: 0.8947 (Cg_exo)
REVERT: B   68 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.6465 (tp30)
REVERT: B   70 VAL cc_start: 0.8298 (p) cc_final: 0.8085 (m)
REVERT: B  130 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7807 (m-10)
REVERT: B  280 VAL cc_start: 0.7623 (OUTLIER) cc_final: 0.7228 (m)
REVERT: B  299 PRO cc_start: 0.9289 (Cg_endo) cc_final: 0.8950 (Cg_exo)
REVERT: C  130 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7842 (m-80)
REVERT: C  280 VAL cc_start: 0.7488 (OUTLIER) cc_final: 0.7109 (m)
REVERT: D   51 SER cc_start: 0.9127 (t) cc_final: 0.8906 (m)
REVERT: D   63 ASP cc_start: 0.8385 (t0) cc_final: 0.8185 (m-30)
REVERT: D   66 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8403 (mm-40)
REVERT: D  102 ASN cc_start: 0.8369 (t0) cc_final: 0.7864 (t0)
REVERT: D  130 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7890 (m-10)
REVERT: D  156 ASP cc_start: 0.7760 (p0) cc_final: 0.6885 (p0)
REVERT: D  187 GLU cc_start: 0.8788 (tp30) cc_final: 0.8307 (mm-30)
REVERT: D  280 VAL cc_start: 0.7633 (OUTLIER) cc_final: 0.7283 (m)
REVERT: D  299 PRO cc_start: 0.9212 (Cg_endo) cc_final: 0.8868 (Cg_exo)
REVERT: E   66 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8195 (mm-40)
REVERT: E  102 ASN cc_start: 0.8456 (t0) cc_final: 0.7817 (t0)
REVERT: E  130 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7880 (m-10)
REVERT: E  187 GLU cc_start: 0.8906 (tp30) cc_final: 0.8337 (mm-30)
REVERT: E  264 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8757 (t)
REVERT: E  280 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7070 (m)
  outliers start: 40
  outliers final: 24
  residues processed: 194
  average time/residue: 0.1750
  time to fit residues: 53.8609
Evaluate side-chains
  191 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 155
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  221 THR
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   54 THR
Chi-restraints excluded: chain C residue   68 GLU
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   68 GLU
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  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  130 TYR
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  280 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 20 optimal weight:    0.1980
   chunk 63 optimal weight:    0.0980
   chunk 27 optimal weight:    2.9990
   chunk 123 optimal weight:    0.0040
   chunk 58 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 134 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0770
   overall best weight:    0.6752

-------------------------------------------------------------------------------
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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 HIS ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  89 HIS
E 125 ASN
E 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.108352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.095456 restraints weight = 21885.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.098450 restraints weight = 10700.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.100422 restraints weight = 6476.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.215  12445  Z= 0.148
  Angle     :  0.774  11.039  17210  Z= 0.346
  Chirality :  0.050   0.236   1685
  Planarity :  0.004   0.038   2145
  Dihedral  : 12.813  87.072   1735
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.43 %
    Favored  : 85.57 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.04 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.20), residues: 1455
  helix: -0.26 (0.37), residues: 215
  sheet: -2.08 (0.43), residues: 150
  loop : -2.92 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  93 
 HIS   0.005   0.001   HIS B  89 
 PHE   0.014   0.001   PHE E 224 
 TYR   0.013   0.001   TYR C 123 
 ARG   0.002   0.000   ARG E 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  260)
  hydrogen bonds       : angle       5.41272 (  675)
  SS BOND              : bond        0.00339 (   10)
  SS BOND              : angle       1.36301 (   20)
  covalent geometry    : bond        0.00378 (12370)
  covalent geometry    : angle       0.77273 (17190)
  Misc. bond           : bond        0.08177 (   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
  207 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 160
  time to evaluate  : 1.199 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8895 (tp40) cc_final: 0.8659 (mm-40)
REVERT: A   51 SER cc_start: 0.9120 (t) cc_final: 0.8894 (m)
REVERT: A   66 GLN cc_start: 0.8515 (mm-40) cc_final: 0.7934 (mm-40)
REVERT: A  102 ASN cc_start: 0.8373 (t0) cc_final: 0.7747 (t0)
REVERT: A  130 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8169 (m-80)
REVERT: A  280 VAL cc_start: 0.7491 (OUTLIER) cc_final: 0.7182 (m)
REVERT: A  299 PRO cc_start: 0.9330 (Cg_endo) cc_final: 0.8954 (Cg_exo)
REVERT: B   66 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8137 (mm-40)
REVERT: B   68 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.6475 (tp30)
REVERT: B  130 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7807 (m-10)
REVERT: B  140 ARG cc_start: 0.8184 (tpm170) cc_final: 0.7898 (tpm170)
REVERT: B  280 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7225 (m)
REVERT: B  299 PRO cc_start: 0.9306 (Cg_endo) cc_final: 0.8961 (Cg_exo)
REVERT: C  130 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8189 (m-80)
REVERT: C  280 VAL cc_start: 0.7487 (OUTLIER) cc_final: 0.7115 (m)
REVERT: D   51 SER cc_start: 0.9117 (t) cc_final: 0.8913 (m)
REVERT: D   66 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8483 (mm-40)
REVERT: D  102 ASN cc_start: 0.8329 (t0) cc_final: 0.7773 (t0)
REVERT: D  130 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8081 (m-10)
REVERT: D  156 ASP cc_start: 0.7797 (p0) cc_final: 0.6963 (p0)
REVERT: D  187 GLU cc_start: 0.8752 (tp30) cc_final: 0.8198 (mm-30)
REVERT: D  280 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7367 (m)
REVERT: D  299 PRO cc_start: 0.9229 (Cg_endo) cc_final: 0.8868 (Cg_exo)
REVERT: E   66 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8189 (mm-40)
REVERT: E   70 VAL cc_start: 0.8788 (t) cc_final: 0.8542 (m)
REVERT: E  102 ASN cc_start: 0.8449 (t0) cc_final: 0.7792 (t0)
REVERT: E  130 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.8142 (m-10)
REVERT: E  187 GLU cc_start: 0.8903 (tp30) cc_final: 0.8331 (mm-30)
REVERT: E  264 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8737 (t)
REVERT: E  280 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7131 (m)
  outliers start: 47
  outliers final: 29
  residues processed: 198
  average time/residue: 0.1770
  time to fit residues: 55.8845
Evaluate side-chains
  192 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  221 THR
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   68 GLU
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   68 GLU
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  264 THR
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  264 THR
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 2 optimal weight:    7.9990
   chunk 131 optimal weight:    0.0270
   chunk 40 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 140 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0670
   chunk 107 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7778

-------------------------------------------------------------------------------
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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 HIS ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  89 HIS
E 125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.110460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.097378 restraints weight = 22288.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.100414 restraints weight = 10994.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.102381 restraints weight = 6623.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.240  12445  Z= 0.155
  Angle     :  0.787  11.153  17210  Z= 0.351
  Chirality :  0.050   0.273   1685
  Planarity :  0.004   0.037   2145
  Dihedral  : 12.825  87.583   1735
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.95 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 17.87 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.20), residues: 1455
  helix: -0.29 (0.37), residues: 215
  sheet: -2.08 (0.43), residues: 150
  loop : -2.94 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  93 
 HIS   0.005   0.001   HIS B  89 
 PHE   0.019   0.001   PHE E 224 
 TYR   0.019   0.001   TYR E 123 
 ARG   0.002   0.000   ARG E 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03791 (  260)
  hydrogen bonds       : angle       5.41007 (  675)
  SS BOND              : bond        0.00315 (   10)
  SS BOND              : angle       1.32197 (   20)
  covalent geometry    : bond        0.00397 (12370)
  covalent geometry    : angle       0.78591 (17190)
  Misc. bond           : bond        0.08757 (   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
  205 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 158
  time to evaluate  : 1.284 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8912 (tp40) cc_final: 0.8685 (mm-40)
REVERT: A   51 SER cc_start: 0.9124 (t) cc_final: 0.8884 (m)
REVERT: A   66 GLN cc_start: 0.8538 (mm-40) cc_final: 0.7963 (mm-40)
REVERT: A  102 ASN cc_start: 0.8339 (t0) cc_final: 0.7730 (t0)
REVERT: A  130 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8129 (m-80)
REVERT: A  280 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7171 (m)
REVERT: A  299 PRO cc_start: 0.9342 (Cg_endo) cc_final: 0.8969 (Cg_exo)
REVERT: B   66 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8165 (mm-40)
REVERT: B   68 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6479 (tp30)
REVERT: B  130 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7781 (m-10)
REVERT: B  140 ARG cc_start: 0.8254 (tpm170) cc_final: 0.7948 (tpm170)
REVERT: B  187 GLU cc_start: 0.8754 (tp30) cc_final: 0.8354 (mm-30)
REVERT: B  280 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7261 (m)
REVERT: B  299 PRO cc_start: 0.9312 (Cg_endo) cc_final: 0.8974 (Cg_exo)
REVERT: C  130 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8250 (m-80)
REVERT: C  280 VAL cc_start: 0.7583 (OUTLIER) cc_final: 0.7218 (m)
REVERT: D   51 SER cc_start: 0.9109 (t) cc_final: 0.8907 (m)
REVERT: D  102 ASN cc_start: 0.8315 (t0) cc_final: 0.7830 (t0)
REVERT: D  130 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8227 (m-10)
REVERT: D  156 ASP cc_start: 0.7792 (p0) cc_final: 0.6951 (p0)
REVERT: D  187 GLU cc_start: 0.8780 (tp30) cc_final: 0.8214 (mm-30)
REVERT: D  280 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7405 (m)
REVERT: D  299 PRO cc_start: 0.9231 (Cg_endo) cc_final: 0.8872 (Cg_exo)
REVERT: E   66 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8195 (mm-40)
REVERT: E   70 VAL cc_start: 0.8845 (t) cc_final: 0.8616 (m)
REVERT: E  102 ASN cc_start: 0.8457 (t0) cc_final: 0.7804 (t0)
REVERT: E  187 GLU cc_start: 0.8911 (tp30) cc_final: 0.8338 (mm-30)
REVERT: E  280 VAL cc_start: 0.7551 (OUTLIER) cc_final: 0.7176 (m)
  outliers start: 47
  outliers final: 32
  residues processed: 195
  average time/residue: 0.1785
  time to fit residues: 55.2564
Evaluate side-chains
  192 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 150
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  221 THR
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   68 GLU
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  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  160 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  264 THR
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   68 GLU
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  192 VAL
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 124 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 105 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0870
   chunk 99 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 135 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.7158

-------------------------------------------------------------------------------
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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 HIS
** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.108051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.095178 restraints weight = 21835.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.098196 restraints weight = 10629.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.100142 restraints weight = 6390.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.283  12445  Z= 0.155
  Angle     :  0.798  17.013  17210  Z= 0.355
  Chirality :  0.050   0.244   1685
  Planarity :  0.004   0.038   2145
  Dihedral  : 12.834  88.307   1735
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.36 %
    Favored  : 85.64 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 18.98 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.20), residues: 1455
  helix: -0.30 (0.37), residues: 215
  sheet: -2.00 (0.43), residues: 150
  loop : -2.92 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  93 
 HIS   0.005   0.001   HIS B  89 
 PHE   0.024   0.001   PHE E 224 
 TYR   0.021   0.001   TYR E 123 
 ARG   0.002   0.000   ARG E 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  260)
  hydrogen bonds       : angle       5.49590 (  675)
  SS BOND              : bond        0.00835 (   10)
  SS BOND              : angle       2.27451 (   20)
  covalent geometry    : bond        0.00399 (12370)
  covalent geometry    : angle       0.79501 (17190)
  Misc. bond           : bond        0.08782 (   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
  197 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 153
  time to evaluate  : 1.642 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8890 (tp40) cc_final: 0.8661 (mm-40)
REVERT: A   51 SER cc_start: 0.9120 (t) cc_final: 0.8888 (m)
REVERT: A   66 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7832 (mm-40)
REVERT: A  102 ASN cc_start: 0.8325 (t0) cc_final: 0.7727 (t0)
REVERT: A  130 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8125 (m-80)
REVERT: A  280 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.7199 (m)
REVERT: A  299 PRO cc_start: 0.9338 (Cg_endo) cc_final: 0.8961 (Cg_exo)
REVERT: B   68 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.6463 (tp30)
REVERT: B  130 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7840 (m-10)
REVERT: B  140 ARG cc_start: 0.8255 (tpm170) cc_final: 0.7978 (tpm170)
REVERT: B  183 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7729 (mmp)
REVERT: B  187 GLU cc_start: 0.8813 (tp30) cc_final: 0.8448 (mm-30)
REVERT: B  280 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7265 (m)
REVERT: B  299 PRO cc_start: 0.9309 (Cg_endo) cc_final: 0.8961 (Cg_exo)
REVERT: C  130 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.8166 (m-10)
REVERT: C  280 VAL cc_start: 0.7545 (OUTLIER) cc_final: 0.7174 (m)
REVERT: D  102 ASN cc_start: 0.8301 (t0) cc_final: 0.7739 (t0)
REVERT: D  130 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8433 (m-80)
REVERT: D  140 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7876 (tpm170)
REVERT: D  156 ASP cc_start: 0.7767 (p0) cc_final: 0.6940 (p0)
REVERT: D  187 GLU cc_start: 0.8737 (tp30) cc_final: 0.8139 (mm-30)
REVERT: D  280 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7404 (m)
REVERT: D  299 PRO cc_start: 0.9223 (Cg_endo) cc_final: 0.8871 (Cg_exo)
REVERT: E   66 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8215 (mm-40)
REVERT: E  102 ASN cc_start: 0.8454 (t0) cc_final: 0.7789 (t0)
REVERT: E  128 ASP cc_start: 0.7773 (p0) cc_final: 0.7096 (p0)
REVERT: E  187 GLU cc_start: 0.8931 (tp30) cc_final: 0.8344 (mm-30)
REVERT: E  280 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7153 (m)
  outliers start: 44
  outliers final: 29
  residues processed: 186
  average time/residue: 0.2417
  time to fit residues: 70.4557
Evaluate side-chains
  188 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 148
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  221 THR
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  183 MET
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   68 GLU
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   68 GLU
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  264 THR
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   68 GLU
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  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 12 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 123 optimal weight:    0.4980
   chunk 32 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0980
   chunk 94 optimal weight:    0.0970
   chunk 25 optimal weight:    4.9990
   chunk 121 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 135 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   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  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 HIS
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  74 GLN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  89 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.113001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.100035 restraints weight = 21909.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.103094 restraints weight = 10828.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.105083 restraints weight = 6520.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.239  12445  Z= 0.142
  Angle     :  0.780  15.249  17210  Z= 0.350
  Chirality :  0.049   0.249   1685
  Planarity :  0.004   0.036   2145
  Dihedral  : 12.770  87.705   1735
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.68 %
    Favored  : 86.32 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.32 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.20), residues: 1455
  helix: -0.22 (0.37), residues: 215
  sheet: -1.88 (0.43), residues: 150
  loop : -2.92 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  93 
 HIS   0.006   0.001   HIS A  89 
 PHE   0.019   0.001   PHE E 224 
 TYR   0.011   0.001   TYR E 130 
 ARG   0.002   0.000   ARG E 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (  260)
  hydrogen bonds       : angle       5.53501 (  675)
  SS BOND              : bond        0.00588 (   10)
  SS BOND              : angle       1.97407 (   20)
  covalent geometry    : bond        0.00368 (12370)
  covalent geometry    : angle       0.77789 (17190)
  Misc. bond           : bond        0.07254 (   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
  204 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 164
  time to evaluate  : 1.329 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.8573 (mm-40) cc_final: 0.7810 (mm-40)
REVERT: A  130 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8154 (m-80)
REVERT: A  229 GLN cc_start: 0.8860 (pp30) cc_final: 0.8257 (pp30)
REVERT: A  280 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7080 (m)
REVERT: A  299 PRO cc_start: 0.9285 (Cg_endo) cc_final: 0.8907 (Cg_exo)
REVERT: B   68 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.6556 (tp30)
REVERT: B  130 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8021 (m-10)
REVERT: B  140 ARG cc_start: 0.8243 (tpm170) cc_final: 0.7996 (tpm170)
REVERT: B  187 GLU cc_start: 0.8827 (tp30) cc_final: 0.8483 (mm-30)
REVERT: B  263 GLU cc_start: 0.7885 (mp0) cc_final: 0.6381 (tt0)
REVERT: B  280 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7213 (m)
REVERT: B  299 PRO cc_start: 0.9236 (Cg_endo) cc_final: 0.8893 (Cg_exo)
REVERT: C  130 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.8125 (m-80)
REVERT: C  280 VAL cc_start: 0.7430 (OUTLIER) cc_final: 0.7031 (m)
REVERT: D   51 SER cc_start: 0.9056 (m) cc_final: 0.8760 (t)
REVERT: D  130 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8329 (m-80)
REVERT: D  140 ARG cc_start: 0.8124 (tpp-160) cc_final: 0.7856 (tpm170)
REVERT: D  156 ASP cc_start: 0.7669 (p0) cc_final: 0.6859 (p0)
REVERT: D  187 GLU cc_start: 0.8715 (tp30) cc_final: 0.8154 (mm-30)
REVERT: D  280 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7312 (m)
REVERT: D  299 PRO cc_start: 0.9171 (Cg_endo) cc_final: 0.8834 (Cg_exo)
REVERT: E   66 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8112 (mm-40)
REVERT: E  102 ASN cc_start: 0.8377 (t0) cc_final: 0.7755 (t0)
REVERT: E  128 ASP cc_start: 0.8017 (p0) cc_final: 0.7790 (p0)
REVERT: E  187 GLU cc_start: 0.8922 (tp30) cc_final: 0.8307 (mm-30)
REVERT: E  280 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7004 (m)
  outliers start: 40
  outliers final: 26
  residues processed: 194
  average time/residue: 0.2479
  time to fit residues: 75.9330
Evaluate side-chains
  193 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 157
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  221 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   68 GLU
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   68 GLU
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  264 THR
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   68 GLU
Chi-restraints excluded: chain E residue  192 VAL
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 139 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 143 optimal weight:    0.0270
   chunk 86 optimal weight:    1.9990
   chunk 73 optimal weight:    0.3980
   chunk 81 optimal weight:    0.7980
   chunk 130 optimal weight:    1.9990
   chunk 110 optimal weight:    0.4980
   chunk 76 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0980
   overall best weight:    0.3438

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

Flipped N/Q/H residues before XYZ refinement:
A  89 HIS
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 HIS
** 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 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 314 GLN ** 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 = 0.3401 r_free = 0.3401 target = 0.112462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.099498 restraints weight = 21486.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.102584 restraints weight = 10640.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.104562 restraints weight = 6415.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.244  12445  Z= 0.138
  Angle     :  0.781  17.724  17210  Z= 0.348
  Chirality :  0.049   0.264   1685
  Planarity :  0.004   0.036   2145
  Dihedral  : 12.760  87.719   1735
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.92 %
    Favored  : 87.08 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.74 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.29 (0.20), residues: 1455
  helix: -0.24 (0.37), residues: 215
  sheet: -1.74 (0.44), residues: 150
  loop : -2.92 (0.16), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  93 
 HIS   0.007   0.001   HIS C  89 
 PHE   0.018   0.001   PHE E 224 
 TYR   0.011   0.001   TYR E 123 
 ARG   0.002   0.000   ARG E 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 (  260)
  hydrogen bonds       : angle       5.60000 (  675)
  SS BOND              : bond        0.00758 (   10)
  SS BOND              : angle       2.40262 (   20)
  covalent geometry    : bond        0.00359 (12370)
  covalent geometry    : angle       0.77764 (17190)
  Misc. bond           : bond        0.06597 (   65)

===============================================================================
Job complete
usr+sys time: 3683.91 seconds
wall clock time: 67 minutes 15.44 seconds (4035.44 seconds total)