Starting phenix.real_space_refine
on Wed Mar 12 19:44:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cr1_30444/03_2025/7cr1_30444_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cr1_30444/03_2025/7cr1_30444.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cr1_30444/03_2025/7cr1_30444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cr1_30444/03_2025/7cr1_30444.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cr1_30444/03_2025/7cr1_30444_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cr1_30444/03_2025/7cr1_30444_trim.cif"
  }
  resolution = 3.4
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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: 6
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     Cl      4      4.86       5
     C    5464      2.51       5
     N    1384      2.21       5
     O    1328      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8220
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2038
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 2038
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 4, 'TRANS': 245}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'GB9': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 3.99, per 1000 atoms: 0.49
  Number of scatterers: 8220
  At special positions: 0
  Unit cell: (124.722, 124.722, 75.036, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      4     17.00
     S      36     16.00
     F       4      9.00
     O    1328      8.00
     N    1384      7.00
     C    5464      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.04
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1848

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      85.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 86
    Processing helix  chain 'A' and resid 91 through 115
      removed outlier: 4.155A  pdb=" N   TYR A  95 " --> pdb=" O   TRP A  91 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ILE A 115 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 147
    Processing helix  chain 'A' and resid 148 through 151
      removed outlier: 3.979A  pdb=" N   CYS A 151 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 148 through 151'
    Processing helix  chain 'A' and resid 157 through 165
    Processing helix  chain 'A' and resid 166 through 183
    Processing helix  chain 'A' and resid 196 through 211
      removed outlier: 3.667A  pdb=" N   MET A 208 " --> pdb=" O   GLN A 204 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   MET A 211 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 228
    Processing helix  chain 'A' and resid 228 through 255
    Processing helix  chain 'A' and resid 263 through 276
      removed outlier: 3.645A  pdb=" N   THR A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 306
      removed outlier: 3.805A  pdb=" N   THR A 296 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   SER A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 329
      removed outlier: 3.827A  pdb=" N   GLY A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 86
    Processing helix  chain 'B' and resid 91 through 115
      removed outlier: 4.154A  pdb=" N   TYR B  95 " --> pdb=" O   TRP B  91 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ILE B 115 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 147
    Processing helix  chain 'B' and resid 148 through 151
      removed outlier: 3.979A  pdb=" N   CYS B 151 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 148 through 151'
    Processing helix  chain 'B' and resid 157 through 165
    Processing helix  chain 'B' and resid 166 through 183
    Processing helix  chain 'B' and resid 196 through 211
      removed outlier: 3.667A  pdb=" N   MET B 208 " --> pdb=" O   GLN B 204 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE B 209 " --> pdb=" O   ILE B 205 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   MET B 211 " --> pdb=" O   ARG B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 228
    Processing helix  chain 'B' and resid 228 through 255
    Processing helix  chain 'B' and resid 263 through 276
      removed outlier: 3.645A  pdb=" N   THR B 276 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 306
      removed outlier: 3.806A  pdb=" N   THR B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LEU B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   SER B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 329
      removed outlier: 3.826A  pdb=" N   GLY B 310 " --> pdb=" O   ALA B 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 86
    Processing helix  chain 'C' and resid 91 through 115
      removed outlier: 4.154A  pdb=" N   TYR C  95 " --> pdb=" O   TRP C  91 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ILE C 115 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 147
    Processing helix  chain 'C' and resid 148 through 151
      removed outlier: 3.978A  pdb=" N   CYS C 151 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 148 through 151'
    Processing helix  chain 'C' and resid 157 through 165
    Processing helix  chain 'C' and resid 166 through 183
    Processing helix  chain 'C' and resid 196 through 211
      removed outlier: 3.666A  pdb=" N   MET C 208 " --> pdb=" O   GLN C 204 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE C 209 " --> pdb=" O   ILE C 205 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   MET C 211 " --> pdb=" O   ARG C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 228
    Processing helix  chain 'C' and resid 228 through 255
    Processing helix  chain 'C' and resid 263 through 276
      removed outlier: 3.645A  pdb=" N   THR C 276 " --> pdb=" O   LEU C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 306
      removed outlier: 3.806A  pdb=" N   THR C 296 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LEU C 299 " --> pdb=" O   ALA C 295 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   SER C 303 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 329
      removed outlier: 3.826A  pdb=" N   GLY C 310 " --> pdb=" O   ALA C 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 86
    Processing helix  chain 'D' and resid 91 through 115
      removed outlier: 4.154A  pdb=" N   TYR D  95 " --> pdb=" O   TRP D  91 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ILE D 115 " --> pdb=" O   VAL D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 147
    Processing helix  chain 'D' and resid 148 through 151
      removed outlier: 3.978A  pdb=" N   CYS D 151 " --> pdb=" O   ALA D 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 148 through 151'
    Processing helix  chain 'D' and resid 157 through 165
    Processing helix  chain 'D' and resid 166 through 183
    Processing helix  chain 'D' and resid 196 through 211
      removed outlier: 3.667A  pdb=" N   MET D 208 " --> pdb=" O   GLN D 204 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE D 209 " --> pdb=" O   ILE D 205 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   MET D 211 " --> pdb=" O   ARG D 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 215 through 228
    Processing helix  chain 'D' and resid 228 through 255
    Processing helix  chain 'D' and resid 263 through 276
      removed outlier: 3.645A  pdb=" N   THR D 276 " --> pdb=" O   LEU D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 306
      removed outlier: 3.806A  pdb=" N   THR D 296 " --> pdb=" O   LEU D 292 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU D 299 " --> pdb=" O   ALA D 295 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   SER D 303 " --> pdb=" O   LEU D 299 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 329
      removed outlier: 3.826A  pdb=" N   GLY D 310 " --> pdb=" O   ALA D 306 " (cutoff:3.500A)

    625 hydrogen bonds defined for protein.
    1875 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: 2.29

  Time building geometry restraints manager: 2.40 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1184
        1.31 -     1.43: 2633
        1.43 -     1.56: 4579
        1.56 -     1.68: 0
        1.68 -     1.81: 52
  Bond restraints: 8448
  Sorted by residual:
  bond pdb=" C12 GB9 D 801 "
       pdb=" N2  GB9 D 801 "
    ideal  model  delta    sigma   weight residual
    1.306  1.481 -0.175 2.00e-02 2.50e+03 7.67e+01
  bond pdb=" C12 GB9 C 801 "
       pdb=" N2  GB9 C 801 "
    ideal  model  delta    sigma   weight residual
    1.306  1.481 -0.175 2.00e-02 2.50e+03 7.62e+01
  bond pdb=" C12 GB9 B 801 "
       pdb=" N2  GB9 B 801 "
    ideal  model  delta    sigma   weight residual
    1.306  1.481 -0.175 2.00e-02 2.50e+03 7.62e+01
  bond pdb=" C12 GB9 A 801 "
       pdb=" N2  GB9 A 801 "
    ideal  model  delta    sigma   weight residual
    1.306  1.481 -0.175 2.00e-02 2.50e+03 7.62e+01
  bond pdb=" C5  GB9 C 801 "
       pdb=" C8  GB9 C 801 "
    ideal  model  delta    sigma   weight residual
    1.386  1.524 -0.138 2.00e-02 2.50e+03 4.77e+01
  ... (remaining 8443 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 10693
        1.35 -     2.70: 593
        2.70 -     4.04: 112
        4.04 -     5.39: 29
        5.39 -     6.74: 9
  Bond angle restraints: 11436
  Sorted by residual:
  angle pdb=" N   ASN D 258 "
        pdb=" CA  ASN D 258 "
        pdb=" C   ASN D 258 "
      ideal   model   delta    sigma   weight residual
     109.07  114.91   -5.84 1.61e+00 3.86e-01 1.32e+01
  angle pdb=" N   GLU A 257 "
        pdb=" CA  GLU A 257 "
        pdb=" C   GLU A 257 "
      ideal   model   delta    sigma   weight residual
     111.36  115.28   -3.92 1.09e+00 8.42e-01 1.29e+01
  angle pdb=" N   ASN B 258 "
        pdb=" CA  ASN B 258 "
        pdb=" C   ASN B 258 "
      ideal   model   delta    sigma   weight residual
     109.07  114.86   -5.79 1.61e+00 3.86e-01 1.29e+01
  angle pdb=" N   ASN C 258 "
        pdb=" CA  ASN C 258 "
        pdb=" C   ASN C 258 "
      ideal   model   delta    sigma   weight residual
     109.07  114.86   -5.79 1.61e+00 3.86e-01 1.29e+01
  angle pdb=" N   GLU C 257 "
        pdb=" CA  GLU C 257 "
        pdb=" C   GLU C 257 "
      ideal   model   delta    sigma   weight residual
     111.36  115.28   -3.92 1.09e+00 8.42e-01 1.29e+01
  ... (remaining 11431 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 4188
       17.35 -    34.69: 456
       34.69 -    52.04: 92
       52.04 -    69.38: 20
       69.38 -    86.73: 16
  Dihedral angle restraints: 4772
    sinusoidal: 1876
      harmonic: 2896
  Sorted by residual:
  dihedral pdb=" CA  ARG D 153 "
           pdb=" C   ARG D 153 "
           pdb=" N   TYR D 154 "
           pdb=" CA  TYR D 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.79  -17.21     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  ARG A 153 "
           pdb=" C   ARG A 153 "
           pdb=" N   TYR A 154 "
           pdb=" CA  TYR A 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.80  -17.20     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  ARG B 153 "
           pdb=" C   ARG B 153 "
           pdb=" N   TYR B 154 "
           pdb=" CA  TYR B 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.83  -17.17     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 4769 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 658
       0.030 -    0.060: 397
       0.060 -    0.090: 151
       0.090 -    0.120: 24
       0.120 -    0.150: 18
  Chirality restraints: 1248
  Sorted by residual:
  chirality pdb=" CA  GLU C 254 "
            pdb=" N   GLU C 254 "
            pdb=" C   GLU C 254 "
            pdb=" CB  GLU C 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  GLU D 254 "
            pdb=" N   GLU D 254 "
            pdb=" C   GLU D 254 "
            pdb=" CB  GLU D 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  GLU B 254 "
            pdb=" N   GLU B 254 "
            pdb=" C   GLU B 254 "
            pdb=" CB  GLU B 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 1245 not shown)

  Planarity restraints: 1384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR D 284 "   -0.022 5.00e-02 4.00e+02   3.32e-02 1.77e+00
        pdb=" N   PRO D 285 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO D 285 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D 285 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 284 "   -0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO C 285 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO C 285 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 285 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 284 "    0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO A 285 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 285 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 285 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1381 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 974
        2.73 -     3.27: 8897
        3.27 -     3.81: 13274
        3.81 -     4.36: 15434
        4.36 -     4.90: 26126
  Nonbonded interactions: 64705
  Sorted by model distance:
  nonbonded pdb=" O   THR B 276 "
            pdb=" OG1 THR B 277 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   THR A 276 "
            pdb=" OG1 THR A 277 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   THR C 276 "
            pdb=" OG1 THR C 277 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   THR D 276 "
            pdb=" OG1 THR D 277 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OE1 GLU C 254 "
            pdb=" N   GLN C 286 "
     model   vdw
     2.202 3.120
  ... (remaining 64700 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     20.550
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
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      :  0.012   0.175   8448  Z= 0.807
  Angle     :  0.735   6.741  11436  Z= 0.413
  Chirality :  0.043   0.150   1248
  Planarity :  0.003   0.033   1384
  Dihedral  : 14.924  86.731   2924
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 26.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  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: -2.00 (0.24), residues: 984
  helix: -0.93 (0.15), residues: 808
  sheet:  None (None), residues: 0
  loop : -2.41 (0.50), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 269 
 HIS   0.002   0.001   HIS C 324 
 PHE   0.020   0.002   PHE C 142 
 TYR   0.012   0.002   TYR B 154 
 ARG   0.003   0.000   ARG B  75 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.6962 (ptmt) cc_final: 0.6505 (ptmm)
REVERT: A  204 GLN cc_start: 0.8762 (mm110) cc_final: 0.8499 (mm110)
REVERT: B   76 LYS cc_start: 0.6951 (ptmt) cc_final: 0.6472 (ptmm)
REVERT: B  204 GLN cc_start: 0.8757 (mm110) cc_final: 0.8481 (mm110)
REVERT: C  204 GLN cc_start: 0.8771 (mm110) cc_final: 0.8491 (mm110)
REVERT: D  144 ARG cc_start: 0.6476 (mtt-85) cc_final: 0.6274 (mtt-85)
REVERT: D  204 GLN cc_start: 0.8764 (mm110) cc_final: 0.8469 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2578
  time to fit residues: 71.2911
Evaluate side-chains
  189 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0050
   chunk 25 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    0.1980
   chunk 47 optimal weight:    0.6980
   chunk 58 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B 204 GLN
C 204 GLN
D 204 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.199674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.155977 restraints weight = 9458.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.26
r_work: 0.3191 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8448  Z= 0.222
  Angle     :  0.574   5.758  11436  Z= 0.299
  Chirality :  0.039   0.149   1248
  Planarity :  0.004   0.037   1384
  Dihedral  :  4.109  14.642   1124
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.07 %
    Favored  : 82.89 %
  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:  0.75 (0.26), residues: 984
  helix:  1.21 (0.17), residues: 828
  sheet:  None (None), residues: 0
  loop : -3.36 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 146 
 HIS   0.002   0.001   HIS C 328 
 PHE   0.008   0.001   PHE C  80 
 TYR   0.016   0.001   TYR B  74 
 ARG   0.006   0.001   ARG C 201 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 193
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A   89 ARG cc_start: 0.6465 (ptp-110) cc_final: 0.5351 (ptt-90)
REVERT: A  101 LEU cc_start: 0.8667 (mt) cc_final: 0.8410 (tt)
REVERT: B   89 ARG cc_start: 0.6443 (ptp-110) cc_final: 0.5319 (ptt-90)
REVERT: B  326 GLN cc_start: 0.6400 (mt0) cc_final: 0.6179 (tt0)
REVERT: C   89 ARG cc_start: 0.6402 (ptp-110) cc_final: 0.5289 (ptt-90)
REVERT: C  101 LEU cc_start: 0.8642 (mt) cc_final: 0.8383 (tt)
REVERT: D   89 ARG cc_start: 0.6375 (ptp-110) cc_final: 0.5290 (ptt-90)
REVERT: D  101 LEU cc_start: 0.8636 (mt) cc_final: 0.8382 (tt)
  outliers start: 17
  outliers final: 12
  residues processed: 196
  average time/residue: 0.2386
  time to fit residues: 60.9846
Evaluate side-chains
  184 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  118 TYR
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain C residue  115 ILE
Chi-restraints excluded: chain C residue  118 TYR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  118 TYR
Chi-restraints excluded: chain D residue  171 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0010
   chunk 86 optimal weight:   10.0000
   chunk 84 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 13 optimal weight:    7.9990
   chunk 73 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 204 GLN
B 323 GLN
C 204 GLN
D 323 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.207153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.158648 restraints weight = 9537.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.61
r_work: 0.3210 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8448  Z= 0.185
  Angle     :  0.523   6.075  11436  Z= 0.274
  Chirality :  0.036   0.145   1248
  Planarity :  0.004   0.031   1384
  Dihedral  :  3.788  12.874   1124
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.46 %
    Favored  : 80.02 %
  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:  1.80 (0.26), residues: 984
  helix:  2.00 (0.17), residues: 808
  sheet:  None (None), residues: 0
  loop : -2.84 (0.43), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 146 
 HIS   0.002   0.001   HIS D 328 
 PHE   0.016   0.001   PHE D 168 
 TYR   0.011   0.001   TYR A  74 
 ARG   0.006   0.001   ARG B 144 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7170 (ptmt) cc_final: 0.6704 (ptmm)
REVERT: A   78 GLN cc_start: 0.6947 (tm-30) cc_final: 0.6704 (tm-30)
REVERT: A  101 LEU cc_start: 0.8527 (mt) cc_final: 0.8180 (tt)
REVERT: A  120 LYS cc_start: 0.8716 (tppt) cc_final: 0.7793 (tmmt)
REVERT: A  165 ARG cc_start: 0.7359 (ttp80) cc_final: 0.7049 (ttp80)
REVERT: A  171 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7158 (tt)
REVERT: A  206 LEU cc_start: 0.8384 (mp) cc_final: 0.7792 (mp)
REVERT: A  320 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8789 (t)
REVERT: B   76 LYS cc_start: 0.7172 (ptmt) cc_final: 0.6703 (ptmm)
REVERT: B   78 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6782 (tm-30)
REVERT: B  101 LEU cc_start: 0.8491 (mt) cc_final: 0.8149 (tt)
REVERT: B  120 LYS cc_start: 0.8706 (tppt) cc_final: 0.7755 (tmmt)
REVERT: B  165 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7154 (ttt-90)
REVERT: B  206 LEU cc_start: 0.8359 (mp) cc_final: 0.7767 (mp)
REVERT: B  320 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8814 (t)
REVERT: C   76 LYS cc_start: 0.7142 (ptmt) cc_final: 0.6677 (ptmm)
REVERT: C   78 GLN cc_start: 0.6993 (tm-30) cc_final: 0.6744 (tm-30)
REVERT: C  101 LEU cc_start: 0.8571 (mt) cc_final: 0.8363 (tt)
REVERT: C  120 LYS cc_start: 0.8698 (tppt) cc_final: 0.7760 (tmmt)
REVERT: C  165 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7101 (ttt-90)
REVERT: C  206 LEU cc_start: 0.8380 (mp) cc_final: 0.7793 (mp)
REVERT: C  320 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8794 (t)
REVERT: D   76 LYS cc_start: 0.7152 (ptmt) cc_final: 0.6695 (ptmm)
REVERT: D   78 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6816 (tm-30)
REVERT: D  101 LEU cc_start: 0.8565 (mt) cc_final: 0.8237 (tt)
REVERT: D  120 LYS cc_start: 0.8690 (tppt) cc_final: 0.7742 (tmmt)
REVERT: D  165 ARG cc_start: 0.7428 (ttp80) cc_final: 0.7121 (ttp80)
REVERT: D  171 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.7070 (tt)
REVERT: D  206 LEU cc_start: 0.8343 (mp) cc_final: 0.7754 (mp)
REVERT: D  320 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8776 (t)
  outliers start: 21
  outliers final: 7
  residues processed: 199
  average time/residue: 0.2454
  time to fit residues: 63.3812
Evaluate side-chains
  182 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  118 TYR
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   93 PHE
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   93 PHE
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain D residue   93 PHE
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  320 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0070
   chunk 13 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
C 323 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.207096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.157717 restraints weight = 9460.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.65
r_work: 0.3218 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8448  Z= 0.181
  Angle     :  0.505   7.972  11436  Z= 0.259
  Chirality :  0.035   0.145   1248
  Planarity :  0.003   0.029   1384
  Dihedral  :  3.663  11.866   1124
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 18.18 %
    Favored  : 77.99 %
  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:  2.34 (0.26), residues: 984
  helix:  2.35 (0.17), residues: 812
  sheet:  None (None), residues: 0
  loop : -2.65 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 146 
 HIS   0.002   0.001   HIS B 328 
 PHE   0.013   0.001   PHE A 168 
 TYR   0.009   0.001   TYR D 284 
 ARG   0.004   0.000   ARG D 213 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 175
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7251 (ptmt) cc_final: 0.6770 (ptmm)
REVERT: A   78 GLN cc_start: 0.7085 (tm-30) cc_final: 0.6720 (tm-30)
REVERT: A  101 LEU cc_start: 0.8618 (mt) cc_final: 0.8298 (tt)
REVERT: A  120 LYS cc_start: 0.8754 (tppt) cc_final: 0.7845 (tmmt)
REVERT: A  127 TYR cc_start: 0.6873 (t80) cc_final: 0.6071 (m-80)
REVERT: A  165 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7156 (ttt-90)
REVERT: A  206 LEU cc_start: 0.8365 (mp) cc_final: 0.7789 (mp)
REVERT: A  320 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8792 (t)
REVERT: B   76 LYS cc_start: 0.7237 (ptmt) cc_final: 0.6855 (pttt)
REVERT: B   78 GLN cc_start: 0.7065 (tm-30) cc_final: 0.6682 (tm-30)
REVERT: B   86 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6474 (mm-30)
REVERT: B  101 LEU cc_start: 0.8560 (mt) cc_final: 0.8239 (tt)
REVERT: B  120 LYS cc_start: 0.8727 (tppt) cc_final: 0.7817 (tmmt)
REVERT: B  127 TYR cc_start: 0.6836 (t80) cc_final: 0.6067 (m-80)
REVERT: B  158 ARG cc_start: 0.6434 (tpt170) cc_final: 0.6158 (mtp85)
REVERT: B  165 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7110 (ttp80)
REVERT: B  206 LEU cc_start: 0.8334 (mp) cc_final: 0.7756 (mp)
REVERT: B  213 ARG cc_start: 0.7910 (ttt180) cc_final: 0.7630 (ttt180)
REVERT: B  320 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8785 (t)
REVERT: C   76 LYS cc_start: 0.7213 (ptmt) cc_final: 0.6731 (ptmm)
REVERT: C   78 GLN cc_start: 0.7044 (tm-30) cc_final: 0.6677 (tm-30)
REVERT: C   86 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6386 (mm-30)
REVERT: C  101 LEU cc_start: 0.8609 (mt) cc_final: 0.8303 (tt)
REVERT: C  120 LYS cc_start: 0.8703 (tppt) cc_final: 0.7810 (tmmt)
REVERT: C  127 TYR cc_start: 0.6817 (t80) cc_final: 0.5987 (m-80)
REVERT: C  165 ARG cc_start: 0.7390 (ttp80) cc_final: 0.7142 (ttt-90)
REVERT: C  206 LEU cc_start: 0.8350 (mp) cc_final: 0.7774 (mp)
REVERT: C  213 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7659 (ttt180)
REVERT: C  320 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8751 (t)
REVERT: D   76 LYS cc_start: 0.7238 (ptmt) cc_final: 0.6755 (ptmm)
REVERT: D   78 GLN cc_start: 0.7094 (tm-30) cc_final: 0.6717 (tm-30)
REVERT: D  101 LEU cc_start: 0.8576 (mt) cc_final: 0.8280 (tt)
REVERT: D  120 LYS cc_start: 0.8709 (tppt) cc_final: 0.7797 (tmmt)
REVERT: D  127 TYR cc_start: 0.6851 (t80) cc_final: 0.6071 (m-80)
REVERT: D  165 ARG cc_start: 0.7423 (ttp80) cc_final: 0.7103 (ttp80)
REVERT: D  171 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.7135 (tt)
REVERT: D  206 LEU cc_start: 0.8320 (mp) cc_final: 0.7760 (mp)
REVERT: D  213 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7549 (ttt180)
REVERT: D  320 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8708 (t)
  outliers start: 32
  outliers final: 11
  residues processed: 195
  average time/residue: 0.2299
  time to fit residues: 59.2916
Evaluate side-chains
  186 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue   93 PHE
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  213 ARG
Chi-restraints excluded: chain D residue  231 GLU
Chi-restraints excluded: chain D residue  296 THR
Chi-restraints excluded: chain D residue  320 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0060
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B  96 HIS
B 204 GLN
C 204 GLN
D  96 HIS
D 204 GLN
D 323 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.201792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.158166 restraints weight = 9275.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.32
r_work: 0.3221 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8448  Z= 0.181
  Angle     :  0.485   7.316  11436  Z= 0.248
  Chirality :  0.035   0.140   1248
  Planarity :  0.003   0.027   1384
  Dihedral  :  3.619  15.252   1124
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.02 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.68 (0.27), residues: 984
  helix:  2.56 (0.17), residues: 812
  sheet:  None (None), residues: 0
  loop : -2.37 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 146 
 HIS   0.002   0.001   HIS B 328 
 PHE   0.009   0.001   PHE D 168 
 TYR   0.009   0.001   TYR D 284 
 ARG   0.003   0.000   ARG D 213 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 168
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7256 (ptmt) cc_final: 0.6794 (ptmm)
REVERT: A   78 GLN cc_start: 0.6937 (tm-30) cc_final: 0.6654 (tm-30)
REVERT: A  101 LEU cc_start: 0.8500 (mt) cc_final: 0.8210 (tt)
REVERT: A  120 LYS cc_start: 0.8714 (tppt) cc_final: 0.7812 (tmmt)
REVERT: A  127 TYR cc_start: 0.6890 (t80) cc_final: 0.6107 (m-80)
REVERT: A  206 LEU cc_start: 0.8354 (mp) cc_final: 0.7809 (mp)
REVERT: A  320 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8783 (t)
REVERT: B   76 LYS cc_start: 0.7259 (ptmt) cc_final: 0.6892 (pttt)
REVERT: B   78 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6680 (tm-30)
REVERT: B   86 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6449 (mm-30)
REVERT: B  101 LEU cc_start: 0.8495 (mt) cc_final: 0.8211 (tt)
REVERT: B  120 LYS cc_start: 0.8686 (tppt) cc_final: 0.7795 (tmmt)
REVERT: B  127 TYR cc_start: 0.6774 (t80) cc_final: 0.6015 (m-80)
REVERT: B  158 ARG cc_start: 0.6399 (tpt170) cc_final: 0.6130 (mtp85)
REVERT: B  165 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7137 (ttp80)
REVERT: B  206 LEU cc_start: 0.8359 (mp) cc_final: 0.7802 (mp)
REVERT: B  213 ARG cc_start: 0.7868 (ttt180) cc_final: 0.7620 (ttt180)
REVERT: B  320 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8653 (t)
REVERT: C   76 LYS cc_start: 0.7221 (ptmt) cc_final: 0.6825 (pttt)
REVERT: C   78 GLN cc_start: 0.7012 (tm-30) cc_final: 0.6717 (tm-30)
REVERT: C   86 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6436 (mm-30)
REVERT: C  101 LEU cc_start: 0.8455 (mt) cc_final: 0.8174 (tt)
REVERT: C  120 LYS cc_start: 0.8681 (tppt) cc_final: 0.7808 (tmmt)
REVERT: C  127 TYR cc_start: 0.6771 (t80) cc_final: 0.6005 (m-80)
REVERT: C  165 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7228 (ttt-90)
REVERT: C  206 LEU cc_start: 0.8343 (mp) cc_final: 0.7795 (mp)
REVERT: C  213 ARG cc_start: 0.7897 (ttt180) cc_final: 0.7622 (ttt180)
REVERT: C  320 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8693 (t)
REVERT: D   76 LYS cc_start: 0.7231 (ptmt) cc_final: 0.6877 (pttt)
REVERT: D   78 GLN cc_start: 0.7005 (tm-30) cc_final: 0.6723 (tm-30)
REVERT: D  120 LYS cc_start: 0.8673 (tppt) cc_final: 0.7793 (tmmt)
REVERT: D  127 TYR cc_start: 0.6896 (t80) cc_final: 0.6117 (m-80)
REVERT: D  165 ARG cc_start: 0.7477 (ttp80) cc_final: 0.7151 (ttp80)
REVERT: D  206 LEU cc_start: 0.8336 (mp) cc_final: 0.7790 (mp)
REVERT: D  320 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8728 (t)
  outliers start: 28
  outliers final: 17
  residues processed: 185
  average time/residue: 0.2377
  time to fit residues: 57.5148
Evaluate side-chains
  186 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  213 ARG
Chi-restraints excluded: chain D residue  231 GLU
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  296 THR
Chi-restraints excluded: chain D residue  320 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 84 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0060
   overall best weight:    0.8798

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

Flipped N/Q/H residues before XYZ refinement:
A  96 HIS
B 204 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.200851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.154328 restraints weight = 9215.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.37
r_work: 0.3212 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8448  Z= 0.197
  Angle     :  0.483   7.589  11436  Z= 0.248
  Chirality :  0.035   0.129   1248
  Planarity :  0.003   0.030   1384
  Dihedral  :  3.586  14.508   1124
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.98 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.83 (0.27), residues: 984
  helix:  2.64 (0.17), residues: 812
  sheet:  None (None), residues: 0
  loop : -2.16 (0.50), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 146 
 HIS   0.002   0.001   HIS C 328 
 PHE   0.008   0.001   PHE C 297 
 TYR   0.009   0.001   TYR D 284 
 ARG   0.006   0.000   ARG A 213 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 170
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7301 (ptmt) cc_final: 0.6961 (pttt)
REVERT: A   78 GLN cc_start: 0.6950 (tm-30) cc_final: 0.6651 (tm-30)
REVERT: A  120 LYS cc_start: 0.8706 (tppt) cc_final: 0.7796 (tmmt)
REVERT: A  127 TYR cc_start: 0.6849 (t80) cc_final: 0.6109 (m-80)
REVERT: A  158 ARG cc_start: 0.6416 (tpt170) cc_final: 0.6062 (mtp85)
REVERT: A  206 LEU cc_start: 0.8299 (mp) cc_final: 0.7767 (mp)
REVERT: A  320 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8740 (t)
REVERT: B   76 LYS cc_start: 0.7313 (ptmt) cc_final: 0.6951 (pttt)
REVERT: B   78 GLN cc_start: 0.6871 (tm-30) cc_final: 0.6573 (tm-30)
REVERT: B  120 LYS cc_start: 0.8662 (tppt) cc_final: 0.7797 (tmmt)
REVERT: B  127 TYR cc_start: 0.6924 (t80) cc_final: 0.6120 (m-80)
REVERT: B  158 ARG cc_start: 0.6363 (tpt170) cc_final: 0.6128 (mtp85)
REVERT: B  206 LEU cc_start: 0.8326 (mp) cc_final: 0.7780 (mp)
REVERT: B  320 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8629 (t)
REVERT: C   76 LYS cc_start: 0.7258 (ptmt) cc_final: 0.6888 (pttt)
REVERT: C   78 GLN cc_start: 0.6952 (tm-30) cc_final: 0.6647 (tm-30)
REVERT: C  120 LYS cc_start: 0.8666 (tppt) cc_final: 0.7820 (tmmt)
REVERT: C  127 TYR cc_start: 0.6759 (t80) cc_final: 0.6031 (m-80)
REVERT: C  165 ARG cc_start: 0.7479 (ttp80) cc_final: 0.7257 (ttt-90)
REVERT: C  206 LEU cc_start: 0.8285 (mp) cc_final: 0.7757 (mp)
REVERT: C  320 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8636 (t)
REVERT: D   76 LYS cc_start: 0.7273 (ptmt) cc_final: 0.6923 (pttt)
REVERT: D   78 GLN cc_start: 0.6955 (tm-30) cc_final: 0.6641 (tm-30)
REVERT: D  120 LYS cc_start: 0.8665 (tppt) cc_final: 0.7762 (tmmt)
REVERT: D  127 TYR cc_start: 0.6842 (t80) cc_final: 0.6103 (m-80)
REVERT: D  206 LEU cc_start: 0.8312 (mp) cc_final: 0.7773 (mp)
REVERT: D  320 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8609 (t)
  outliers start: 27
  outliers final: 16
  residues processed: 189
  average time/residue: 0.2169
  time to fit residues: 54.7308
Evaluate side-chains
  179 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  231 GLU
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  296 THR
Chi-restraints excluded: chain D residue  320 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 90 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0970
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
C 204 GLN
D 204 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.203253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.156507 restraints weight = 9316.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.35
r_work: 0.3248 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8448  Z= 0.168
  Angle     :  0.472   7.220  11436  Z= 0.242
  Chirality :  0.034   0.119   1248
  Planarity :  0.003   0.033   1384
  Dihedral  :  3.509  15.308   1124
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.86 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.03 (0.27), residues: 984
  helix:  2.76 (0.17), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.99 (0.51), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 146 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.012   0.001   PHE A 168 
 TYR   0.008   0.001   TYR D 284 
 ARG   0.006   0.000   ARG D 144 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7332 (ptmt) cc_final: 0.6986 (pttt)
REVERT: A   78 GLN cc_start: 0.6875 (tm-30) cc_final: 0.6589 (tm-30)
REVERT: A  120 LYS cc_start: 0.8697 (tppt) cc_final: 0.7776 (tmmt)
REVERT: A  127 TYR cc_start: 0.6865 (t80) cc_final: 0.6125 (m-80)
REVERT: A  158 ARG cc_start: 0.6300 (tpt170) cc_final: 0.5974 (mtp85)
REVERT: A  206 LEU cc_start: 0.8264 (mp) cc_final: 0.7758 (mp)
REVERT: A  320 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8730 (t)
REVERT: B   76 LYS cc_start: 0.7362 (ptmt) cc_final: 0.7010 (pttt)
REVERT: B   78 GLN cc_start: 0.6864 (tm-30) cc_final: 0.6560 (tm-30)
REVERT: B  120 LYS cc_start: 0.8647 (tppt) cc_final: 0.7780 (tmmt)
REVERT: B  127 TYR cc_start: 0.7023 (t80) cc_final: 0.6126 (m-80)
REVERT: B  158 ARG cc_start: 0.6332 (tpt170) cc_final: 0.6100 (mtp85)
REVERT: B  206 LEU cc_start: 0.8303 (mp) cc_final: 0.7818 (mp)
REVERT: C   76 LYS cc_start: 0.7320 (ptmt) cc_final: 0.6939 (pttt)
REVERT: C   78 GLN cc_start: 0.6841 (tm-30) cc_final: 0.6554 (tm-30)
REVERT: C  120 LYS cc_start: 0.8627 (tppt) cc_final: 0.7767 (tmmt)
REVERT: C  127 TYR cc_start: 0.6996 (t80) cc_final: 0.6170 (m-80)
REVERT: C  158 ARG cc_start: 0.6367 (tpt170) cc_final: 0.6049 (mtp85)
REVERT: C  206 LEU cc_start: 0.8286 (mp) cc_final: 0.7803 (mp)
REVERT: C  320 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8557 (t)
REVERT: D   76 LYS cc_start: 0.7302 (ptmt) cc_final: 0.6955 (pttt)
REVERT: D   78 GLN cc_start: 0.6845 (tm-30) cc_final: 0.6542 (tm-30)
REVERT: D  120 LYS cc_start: 0.8646 (tppt) cc_final: 0.7758 (tmmt)
REVERT: D  127 TYR cc_start: 0.6890 (t80) cc_final: 0.6122 (m-80)
REVERT: D  206 LEU cc_start: 0.8278 (mp) cc_final: 0.7766 (mp)
  outliers start: 28
  outliers final: 17
  residues processed: 185
  average time/residue: 0.2184
  time to fit residues: 54.0282
Evaluate side-chains
  186 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  231 GLU
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  296 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.200837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.156570 restraints weight = 9289.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.33
r_work: 0.3200 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8448  Z= 0.236
  Angle     :  0.521   6.959  11436  Z= 0.266
  Chirality :  0.037   0.144   1248
  Planarity :  0.003   0.026   1384
  Dihedral  :  3.535  13.658   1124
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 19.14 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.02 (0.27), residues: 984
  helix:  2.74 (0.17), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.94 (0.51), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 146 
 HIS   0.002   0.001   HIS D 228 
 PHE   0.015   0.001   PHE A 168 
 TYR   0.010   0.001   TYR D 284 
 ARG   0.007   0.000   ARG A 213 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 171
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7368 (ptmt) cc_final: 0.7017 (pttt)
REVERT: A   78 GLN cc_start: 0.6928 (tm-30) cc_final: 0.6613 (tm-30)
REVERT: A  120 LYS cc_start: 0.8692 (tppt) cc_final: 0.7792 (tmmt)
REVERT: A  127 TYR cc_start: 0.6910 (t80) cc_final: 0.6159 (m-80)
REVERT: A  158 ARG cc_start: 0.6372 (tpt170) cc_final: 0.6063 (mtp85)
REVERT: A  206 LEU cc_start: 0.8296 (mp) cc_final: 0.7772 (mp)
REVERT: A  320 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8766 (t)
REVERT: B   76 LYS cc_start: 0.7357 (ptmt) cc_final: 0.6996 (pttt)
REVERT: B   78 GLN cc_start: 0.6962 (tm-30) cc_final: 0.6635 (tm-30)
REVERT: B   93 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.6707 (t80)
REVERT: B  120 LYS cc_start: 0.8677 (tppt) cc_final: 0.7830 (tmmt)
REVERT: B  127 TYR cc_start: 0.7066 (t80) cc_final: 0.6177 (m-80)
REVERT: B  158 ARG cc_start: 0.6378 (tpt170) cc_final: 0.6152 (mtp85)
REVERT: B  206 LEU cc_start: 0.8342 (mp) cc_final: 0.7827 (mp)
REVERT: C   76 LYS cc_start: 0.7313 (ptmt) cc_final: 0.6925 (pttt)
REVERT: C   78 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6613 (tm-30)
REVERT: C   93 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6634 (t80)
REVERT: C  120 LYS cc_start: 0.8659 (tppt) cc_final: 0.7813 (tmmt)
REVERT: C  127 TYR cc_start: 0.6990 (t80) cc_final: 0.6174 (m-80)
REVERT: C  158 ARG cc_start: 0.6371 (tpt170) cc_final: 0.6043 (mtp85)
REVERT: C  206 LEU cc_start: 0.8312 (mp) cc_final: 0.7809 (mp)
REVERT: C  320 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8704 (t)
REVERT: D   76 LYS cc_start: 0.7329 (ptmt) cc_final: 0.6969 (pttt)
REVERT: D   78 GLN cc_start: 0.6885 (tm-30) cc_final: 0.6569 (tm-30)
REVERT: D   93 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6652 (t80)
REVERT: D  120 LYS cc_start: 0.8627 (tppt) cc_final: 0.7761 (tmmt)
REVERT: D  127 TYR cc_start: 0.6895 (t80) cc_final: 0.6155 (m-80)
REVERT: D  206 LEU cc_start: 0.8288 (mp) cc_final: 0.7769 (mp)
  outliers start: 34
  outliers final: 21
  residues processed: 194
  average time/residue: 0.2214
  time to fit residues: 57.1834
Evaluate side-chains
  193 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   93 PHE
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue   93 PHE
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain D residue   93 PHE
Chi-restraints excluded: chain D residue   95 TYR
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  231 GLU
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  296 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.201779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.157807 restraints weight = 9462.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.36
r_work: 0.3208 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8448  Z= 0.215
  Angle     :  0.545  10.738  11436  Z= 0.274
  Chirality :  0.039   0.342   1248
  Planarity :  0.003   0.026   1384
  Dihedral  :  3.513  13.608   1124
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 18.90 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.95 (0.27), residues: 984
  helix:  2.67 (0.17), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.82 (0.53), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 146 
 HIS   0.002   0.001   HIS D 328 
 PHE   0.020   0.001   PHE B 316 
 TYR   0.010   0.001   TYR C  74 
 ARG   0.005   0.000   ARG C 213 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.7407 (ptmt) cc_final: 0.7032 (pttt)
REVERT: A   78 GLN cc_start: 0.6890 (tm-30) cc_final: 0.6585 (tm-30)
REVERT: A  120 LYS cc_start: 0.8686 (tppt) cc_final: 0.7815 (tmmt)
REVERT: A  127 TYR cc_start: 0.6853 (t80) cc_final: 0.6092 (m-80)
REVERT: A  158 ARG cc_start: 0.6356 (tpt170) cc_final: 0.6046 (mtp85)
REVERT: A  206 LEU cc_start: 0.8296 (mp) cc_final: 0.7795 (mp)
REVERT: A  320 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8763 (t)
REVERT: B   76 LYS cc_start: 0.7358 (ptmt) cc_final: 0.6989 (pttt)
REVERT: B   78 GLN cc_start: 0.6965 (tm-30) cc_final: 0.6626 (tm-30)
REVERT: B   93 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6678 (t80)
REVERT: B  120 LYS cc_start: 0.8668 (tppt) cc_final: 0.7829 (tmmt)
REVERT: B  127 TYR cc_start: 0.7050 (t80) cc_final: 0.6168 (m-80)
REVERT: B  158 ARG cc_start: 0.6371 (tpt170) cc_final: 0.6142 (mtp85)
REVERT: B  206 LEU cc_start: 0.8323 (mp) cc_final: 0.7813 (mp)
REVERT: C   76 LYS cc_start: 0.7355 (ptmt) cc_final: 0.6965 (pttt)
REVERT: C   78 GLN cc_start: 0.6919 (tm-30) cc_final: 0.6599 (tm-30)
REVERT: C  120 LYS cc_start: 0.8656 (tppt) cc_final: 0.7813 (tmmt)
REVERT: C  127 TYR cc_start: 0.6978 (t80) cc_final: 0.6187 (m-80)
REVERT: C  158 ARG cc_start: 0.6386 (tpt170) cc_final: 0.6057 (mtp85)
REVERT: C  206 LEU cc_start: 0.8293 (mp) cc_final: 0.7796 (mp)
REVERT: D   76 LYS cc_start: 0.7362 (ptmt) cc_final: 0.7009 (pttt)
REVERT: D   78 GLN cc_start: 0.6919 (tm-30) cc_final: 0.6596 (tm-30)
REVERT: D   93 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6602 (t80)
REVERT: D  120 LYS cc_start: 0.8623 (tppt) cc_final: 0.7763 (tmmt)
REVERT: D  127 TYR cc_start: 0.7005 (t80) cc_final: 0.6172 (m-80)
REVERT: D  206 LEU cc_start: 0.8279 (mp) cc_final: 0.7762 (mp)
  outliers start: 32
  outliers final: 21
  residues processed: 190
  average time/residue: 0.2130
  time to fit residues: 54.3629
Evaluate side-chains
  189 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain B residue   93 PHE
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain D residue   93 PHE
Chi-restraints excluded: chain D residue   95 TYR
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  231 GLU
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  296 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 91 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.208419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.169174 restraints weight = 9423.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 2.31
r_work: 0.3327 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8448  Z= 0.200
  Angle     :  0.535   9.627  11436  Z= 0.269
  Chirality :  0.038   0.332   1248
  Planarity :  0.003   0.025   1384
  Dihedral  :  3.470  13.752   1124
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.50 %
    Favored  : 77.39 %
  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:  2.97 (0.27), residues: 984
  helix:  2.66 (0.17), residues: 808
  sheet:  None (None), residues: 0
  loop : -1.59 (0.53), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 146 
 HIS   0.002   0.001   HIS B 328 
 PHE   0.024   0.001   PHE B 316 
 TYR   0.018   0.001   TYR C  82 
 ARG   0.004   0.000   ARG D 144 

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7551 (ptmt) cc_final: 0.7180 (pttt)
REVERT: A   78 GLN cc_start: 0.7029 (tm-30) cc_final: 0.6725 (tm-30)
REVERT: A  120 LYS cc_start: 0.8685 (tppt) cc_final: 0.7822 (tmmt)
REVERT: A  127 TYR cc_start: 0.6763 (t80) cc_final: 0.6064 (m-80)
REVERT: A  158 ARG cc_start: 0.6466 (tpt170) cc_final: 0.6174 (mtp85)
REVERT: A  206 LEU cc_start: 0.8410 (mp) cc_final: 0.7906 (mp)
REVERT: B   76 LYS cc_start: 0.7465 (ptmt) cc_final: 0.7069 (pttt)
REVERT: B   78 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6756 (tm-30)
REVERT: B   93 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6749 (t80)
REVERT: B  120 LYS cc_start: 0.8662 (tppt) cc_final: 0.7805 (tmmt)
REVERT: B  127 TYR cc_start: 0.7034 (t80) cc_final: 0.6197 (m-80)
REVERT: B  206 LEU cc_start: 0.8408 (mp) cc_final: 0.7918 (mp)
REVERT: C   76 LYS cc_start: 0.7439 (ptmt) cc_final: 0.7035 (pttt)
REVERT: C   78 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6668 (tm-30)
REVERT: C   93 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6664 (t80)
REVERT: C  120 LYS cc_start: 0.8663 (tppt) cc_final: 0.7825 (tmmt)
REVERT: C  127 TYR cc_start: 0.7144 (t80) cc_final: 0.6226 (m-80)
REVERT: C  158 ARG cc_start: 0.6489 (tpt170) cc_final: 0.6190 (mtp85)
REVERT: C  206 LEU cc_start: 0.8405 (mp) cc_final: 0.7915 (mp)
REVERT: D   76 LYS cc_start: 0.7448 (ptmt) cc_final: 0.7059 (pttt)
REVERT: D   78 GLN cc_start: 0.7078 (tm-30) cc_final: 0.6759 (tm-30)
REVERT: D   93 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6673 (t80)
REVERT: D  120 LYS cc_start: 0.8650 (tppt) cc_final: 0.7782 (tmmt)
REVERT: D  127 TYR cc_start: 0.6966 (t80) cc_final: 0.6134 (m-80)
REVERT: D  206 LEU cc_start: 0.8400 (mp) cc_final: 0.7906 (mp)
  outliers start: 26
  outliers final: 21
  residues processed: 189
  average time/residue: 0.2222
  time to fit residues: 55.4897
Evaluate side-chains
  189 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   93 PHE
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue   93 PHE
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  296 THR
Chi-restraints excluded: chain D residue   93 PHE
Chi-restraints excluded: chain D residue   95 TYR
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  231 GLU
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  296 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 204 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.206817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.165431 restraints weight = 9544.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.31
r_work: 0.3273 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8448  Z= 0.246
  Angle     :  0.550   9.255  11436  Z= 0.278
  Chirality :  0.039   0.324   1248
  Planarity :  0.003   0.025   1384
  Dihedral  :  3.479  12.281   1124
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.14 %
    Favored  : 77.39 %
  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:  2.97 (0.27), residues: 984
  helix:  2.67 (0.17), residues: 808
  sheet:  None (None), residues: 0
  loop : -1.62 (0.53), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 146 
 HIS   0.001   0.001   HIS A 328 
 PHE   0.028   0.001   PHE C 316 
 TYR   0.017   0.001   TYR C  82 
 ARG   0.004   0.000   ARG D 144 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4085.01 seconds
wall clock time: 71 minutes 29.27 seconds (4289.27 seconds total)