Starting phenix.real_space_refine
on Mon Jan 13 19:14:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qx9_18715/01_2025/8qx9_18715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qx9_18715/01_2025/8qx9_18715.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qx9_18715/01_2025/8qx9_18715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qx9_18715/01_2025/8qx9_18715.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qx9_18715/01_2025/8qx9_18715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qx9_18715/01_2025/8qx9_18715.cif"
  }
  resolution = 3.76
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      84      5.16       5
     C    2232      2.51       5
     N     660      2.21       5
     O     720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3696
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 308
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 1.65, per 1000 atoms: 0.45
  Number of scatterers: 3696
  At special positions: 0
  Unit cell: (102.96, 84.24, 46.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      84     16.00
     O     720      8.00
     N     660      7.00
     C    2232      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 469.4 milliseconds
  

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  888

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 312
    Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 323
    Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 334
      removed outlier: 6.592A  pdb=" N   ALA A 329 " --> pdb=" O   LEU C 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER C 332 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN A 331 " --> pdb=" O   SER C 332 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   TRP C 334 " --> pdb=" O   GLN A 331 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER A 333 " --> pdb=" O   TRP C 334 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA C 329 " --> pdb=" O   LEU E 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER E 332 " --> pdb=" O   ALA C 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN C 331 " --> pdb=" O   SER E 332 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   TRP E 334 " --> pdb=" O   GLN C 331 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   SER C 333 " --> pdb=" O   TRP E 334 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA E 329 " --> pdb=" O   LEU G 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER G 332 " --> pdb=" O   ALA E 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN E 331 " --> pdb=" O   SER G 332 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   TRP G 334 " --> pdb=" O   GLN E 331 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER E 333 " --> pdb=" O   TRP G 334 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA G 329 " --> pdb=" O   LEU I 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER I 332 " --> pdb=" O   ALA G 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN G 331 " --> pdb=" O   SER I 332 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   TRP I 334 " --> pdb=" O   GLN G 331 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   SER G 333 " --> pdb=" O   TRP I 334 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA I 329 " --> pdb=" O   LEU K 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER K 332 " --> pdb=" O   ALA I 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN I 331 " --> pdb=" O   SER K 332 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   TRP K 334 " --> pdb=" O   GLN I 331 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   SER I 333 " --> pdb=" O   TRP K 334 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 312
    Processing sheet with id=AA5, first strand: chain 'B' and resid 321 through 323
    Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 334
      removed outlier: 6.592A  pdb=" N   ALA B 329 " --> pdb=" O   LEU D 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER D 332 " --> pdb=" O   ALA B 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN B 331 " --> pdb=" O   SER D 332 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   TRP D 334 " --> pdb=" O   GLN B 331 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER B 333 " --> pdb=" O   TRP D 334 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA D 329 " --> pdb=" O   LEU F 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER F 332 " --> pdb=" O   ALA D 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN D 331 " --> pdb=" O   SER F 332 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   TRP F 334 " --> pdb=" O   GLN D 331 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   SER D 333 " --> pdb=" O   TRP F 334 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA F 329 " --> pdb=" O   LEU H 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER H 332 " --> pdb=" O   ALA F 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN F 331 " --> pdb=" O   SER H 332 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   TRP H 334 " --> pdb=" O   GLN F 331 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER F 333 " --> pdb=" O   TRP H 334 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA H 329 " --> pdb=" O   LEU J 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER J 332 " --> pdb=" O   ALA H 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN H 331 " --> pdb=" O   SER J 332 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   TRP J 334 " --> pdb=" O   GLN H 331 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   SER H 333 " --> pdb=" O   TRP J 334 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA J 329 " --> pdb=" O   LEU L 330 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   SER L 332 " --> pdb=" O   ALA J 329 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN J 331 " --> pdb=" O   SER L 332 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   TRP L 334 " --> pdb=" O   GLN J 331 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   SER J 333 " --> pdb=" O   TRP L 334 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    30 hydrogen bonds defined for protein.
    90 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: 0.80

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 648
        1.31 -     1.44: 972
        1.44 -     1.56: 1956
        1.56 -     1.69: 0
        1.69 -     1.81: 168
  Bond restraints: 3744
  Sorted by residual:
  bond pdb=" C   PRO E 320 "
       pdb=" O   PRO E 320 "
    ideal  model  delta    sigma   weight residual
    1.233  1.189  0.044 1.16e-02 7.43e+03 1.42e+01
  bond pdb=" C   PRO F 320 "
       pdb=" O   PRO F 320 "
    ideal  model  delta    sigma   weight residual
    1.233  1.189  0.044 1.16e-02 7.43e+03 1.42e+01
  bond pdb=" C   PRO D 320 "
       pdb=" O   PRO D 320 "
    ideal  model  delta    sigma   weight residual
    1.233  1.189  0.044 1.16e-02 7.43e+03 1.42e+01
  bond pdb=" C   PRO C 320 "
       pdb=" O   PRO C 320 "
    ideal  model  delta    sigma   weight residual
    1.233  1.189  0.044 1.16e-02 7.43e+03 1.42e+01
  bond pdb=" C   PRO J 320 "
       pdb=" O   PRO J 320 "
    ideal  model  delta    sigma   weight residual
    1.233  1.189  0.044 1.16e-02 7.43e+03 1.41e+01
  ... (remaining 3739 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 2984
        1.54 -     3.09: 1048
        3.09 -     4.63: 716
        4.63 -     6.18: 187
        6.18 -     7.72: 45
  Bond angle restraints: 4980
  Sorted by residual:
  angle pdb=" N   GLN E 327 "
        pdb=" CA  GLN E 327 "
        pdb=" C   GLN E 327 "
      ideal   model   delta    sigma   weight residual
     111.36  105.16    6.20 1.09e+00 8.42e-01 3.24e+01
  angle pdb=" N   GLN I 327 "
        pdb=" CA  GLN I 327 "
        pdb=" C   GLN I 327 "
      ideal   model   delta    sigma   weight residual
     111.36  105.16    6.20 1.09e+00 8.42e-01 3.23e+01
  angle pdb=" N   GLN J 327 "
        pdb=" CA  GLN J 327 "
        pdb=" C   GLN J 327 "
      ideal   model   delta    sigma   weight residual
     111.36  105.16    6.20 1.09e+00 8.42e-01 3.23e+01
  angle pdb=" N   GLN K 327 "
        pdb=" CA  GLN K 327 "
        pdb=" C   GLN K 327 "
      ideal   model   delta    sigma   weight residual
     111.36  105.17    6.19 1.09e+00 8.42e-01 3.23e+01
  angle pdb=" N   GLN L 327 "
        pdb=" CA  GLN L 327 "
        pdb=" C   GLN L 327 "
      ideal   model   delta    sigma   weight residual
     111.36  105.17    6.19 1.09e+00 8.42e-01 3.23e+01
  ... (remaining 4975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 1858
       16.26 -    32.51: 218
       32.51 -    48.76: 84
       48.76 -    65.02: 12
       65.02 -    81.27: 24
  Dihedral angle restraints: 2196
    sinusoidal: 780
      harmonic: 1416
  Sorted by residual:
  dihedral pdb=" C   PHE K 316 "
           pdb=" N   PHE K 316 "
           pdb=" CA  PHE K 316 "
           pdb=" CB  PHE K 316 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.64   -7.96     0      2.50e+00 1.60e-01 1.01e+01
  dihedral pdb=" C   PHE L 316 "
           pdb=" N   PHE L 316 "
           pdb=" CA  PHE L 316 "
           pdb=" CB  PHE L 316 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.64   -7.96     0      2.50e+00 1.60e-01 1.01e+01
  dihedral pdb=" C   PHE G 316 "
           pdb=" N   PHE G 316 "
           pdb=" CA  PHE G 316 "
           pdb=" CB  PHE G 316 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.65   -7.95     0      2.50e+00 1.60e-01 1.01e+01
  ... (remaining 2193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.004 -    0.056: 182
       0.056 -    0.107: 142
       0.107 -    0.159: 84
       0.159 -    0.210: 58
       0.210 -    0.262: 14
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  TRP A 334 "
            pdb=" N   TRP A 334 "
            pdb=" C   TRP A 334 "
            pdb=" CB  TRP A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CA  TRP B 334 "
            pdb=" N   TRP B 334 "
            pdb=" C   TRP B 334 "
            pdb=" CB  TRP B 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CA  TRP G 334 "
            pdb=" N   TRP G 334 "
            pdb=" C   TRP G 334 "
            pdb=" CB  TRP G 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 477 not shown)

  Planarity restraints: 684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 334 "    0.028 2.00e-02 2.50e+03   1.75e-02 7.63e+00
        pdb=" CG  TRP C 334 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 334 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 334 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 334 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 334 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 334 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 334 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 334 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 334 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 334 "    0.028 2.00e-02 2.50e+03   1.75e-02 7.63e+00
        pdb=" CG  TRP D 334 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 334 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 334 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 334 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 334 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 334 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 334 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 334 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 334 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L 334 "    0.028 2.00e-02 2.50e+03   1.75e-02 7.63e+00
        pdb=" CG  TRP L 334 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP L 334 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP L 334 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP L 334 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP L 334 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP L 334 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L 334 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L 334 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP L 334 "    0.001 2.00e-02 2.50e+03
  ... (remaining 681 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1576
        2.98 -     3.46: 3594
        3.46 -     3.94: 6298
        3.94 -     4.42: 6843
        4.42 -     4.90: 13577
  Nonbonded interactions: 31888
  Sorted by model distance:
  nonbonded pdb=" N   ILE A 318 "
            pdb=" O   ILE A 318 "
     model   vdw
     2.496 2.496
  nonbonded pdb=" N   ILE B 318 "
            pdb=" O   ILE B 318 "
     model   vdw
     2.496 2.496
  nonbonded pdb=" N   ILE J 318 "
            pdb=" O   ILE J 318 "
     model   vdw
     2.496 2.496
  nonbonded pdb=" N   ILE I 318 "
            pdb=" O   ILE I 318 "
     model   vdw
     2.496 2.496
  nonbonded pdb=" N   ILE H 318 "
            pdb=" O   ILE H 318 "
     model   vdw
     2.496 2.496
  ... (remaining 31883 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.840
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
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      :  0.014   0.044   3744  Z= 0.915
  Angle     :  2.173   7.720   4980  Z= 1.625
  Chirality :  0.110   0.262    480
  Planarity :  0.010   0.025    684
  Dihedral  : 18.791  81.271   1308
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 27.59 %
    Favored  : 72.41 %
  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: -4.75 (0.17), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.61 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.010   TRP C 334 
 PHE   0.012   0.003   PHE L 316 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  337 MET cc_start: 0.7608 (mtp) cc_final: 0.6965 (mtp)
REVERT: J  337 MET cc_start: 0.7626 (mtp) cc_final: 0.6969 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1258
  time to fit residues: 27.1517
Evaluate side-chains
  160 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 331 GLN
B 331 GLN
** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 331 GLN
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 331 GLN
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 319 ASN
K 327 GLN
L 319 ASN
L 327 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5260 r_free = 0.5260 target = 0.395199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.5692 r_free = 0.5692 target = 0.291128 restraints weight = 5000.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.5722 r_free = 0.5722 target = 0.293590 restraints weight = 3866.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5726 r_free = 0.5726 target = 0.294611 restraints weight = 3259.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.5117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.4150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3744  Z= 0.211
  Angle     :  0.665   7.790   4980  Z= 0.342
  Chirality :  0.039   0.110    480
  Planarity :  0.003   0.016    684
  Dihedral  :  5.747  21.137    528
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 26.15 %
    Favored  : 72.13 %
  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: -4.55 (0.17), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.46 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP D 334 
 PHE   0.009   0.003   PHE G 313 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 158
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.8091 (ttm) cc_final: 0.7889 (ttt)
REVERT: B  307 MET cc_start: 0.8094 (ttm) cc_final: 0.7889 (ttt)
REVERT: C  322 MET cc_start: 0.7288 (mtt) cc_final: 0.6885 (mtt)
REVERT: C  336 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7318 (tmm)
REVERT: C  339 MET cc_start: 0.7609 (mtp) cc_final: 0.7356 (mtp)
REVERT: C  346 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7511 (mm-40)
REVERT: D  322 MET cc_start: 0.7280 (mtt) cc_final: 0.6877 (mtt)
REVERT: D  336 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7324 (tmm)
REVERT: D  339 MET cc_start: 0.7609 (mtp) cc_final: 0.7341 (mtp)
REVERT: D  346 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7502 (mm-40)
REVERT: E  322 MET cc_start: 0.7849 (mpp) cc_final: 0.7257 (mmm)
REVERT: F  322 MET cc_start: 0.7847 (mpp) cc_final: 0.7258 (mmm)
REVERT: G  322 MET cc_start: 0.7427 (mtt) cc_final: 0.6800 (mtt)
REVERT: H  322 MET cc_start: 0.7394 (mtt) cc_final: 0.6777 (mtt)
REVERT: I  336 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7587 (tmm)
REVERT: I  337 MET cc_start: 0.7962 (mtp) cc_final: 0.7520 (mtp)
REVERT: J  336 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7589 (tmm)
REVERT: J  337 MET cc_start: 0.7972 (mtp) cc_final: 0.7524 (mtp)
REVERT: K  322 MET cc_start: 0.7934 (mpp) cc_final: 0.7515 (mtt)
REVERT: L  322 MET cc_start: 0.7932 (mpp) cc_final: 0.7525 (mtt)
  outliers start: 6
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1250
  time to fit residues: 25.0927
Evaluate side-chains
  148 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  336 MET
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain I residue  336 MET
Chi-restraints excluded: chain J residue  336 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0870
   chunk 43 optimal weight:    0.0070
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 47 optimal weight:    0.0570
   chunk 4 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.8298

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

Flipped N/Q/H residues before XYZ refinement:
C 346 GLN
D 346 GLN
** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.392248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.5699 r_free = 0.5699 target = 0.287550 restraints weight = 4946.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5702 r_free = 0.5702 target = 0.289405 restraints weight = 3962.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.5747 r_free = 0.5747 target = 0.291527 restraints weight = 3391.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.5108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.4759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3744  Z= 0.195
  Angle     :  0.628   7.347   4980  Z= 0.323
  Chirality :  0.039   0.108    480
  Planarity :  0.002   0.009    684
  Dihedral  :  5.478  19.982    528
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.72 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.47 (0.17), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.004   TRP D 334 
 PHE   0.012   0.002   PHE G 313 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.8079 (ttm) cc_final: 0.7841 (ttt)
REVERT: B  307 MET cc_start: 0.8081 (ttm) cc_final: 0.7842 (ttt)
REVERT: C  322 MET cc_start: 0.7114 (mtt) cc_final: 0.6519 (mtt)
REVERT: C  343 GLN cc_start: 0.8263 (mp10) cc_final: 0.8012 (mp10)
REVERT: C  346 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7688 (mm-40)
REVERT: D  322 MET cc_start: 0.7124 (mtt) cc_final: 0.6489 (mtt)
REVERT: D  343 GLN cc_start: 0.8257 (mp10) cc_final: 0.8007 (mp10)
REVERT: D  346 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7683 (mm-40)
REVERT: E  346 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7520 (mm-40)
REVERT: F  346 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7530 (mm-40)
REVERT: G  322 MET cc_start: 0.7070 (mtt) cc_final: 0.6665 (mtt)
REVERT: G  346 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7572 (mm-40)
REVERT: H  322 MET cc_start: 0.7046 (mtt) cc_final: 0.6644 (mtt)
REVERT: H  346 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7577 (mm-40)
REVERT: I  307 MET cc_start: 0.8534 (ttm) cc_final: 0.8253 (ttp)
REVERT: I  337 MET cc_start: 0.7953 (mtp) cc_final: 0.7751 (mtt)
REVERT: J  307 MET cc_start: 0.8530 (ttm) cc_final: 0.8253 (ttp)
REVERT: K  322 MET cc_start: 0.7947 (mpp) cc_final: 0.7663 (mtt)
REVERT: L  322 MET cc_start: 0.7950 (mpp) cc_final: 0.7689 (mtt)
  outliers start: 10
  outliers final: 4
  residues processed: 148
  average time/residue: 0.1321
  time to fit residues: 24.6891
Evaluate side-chains
  144 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 138
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain C residue  346 GLN
Chi-restraints excluded: chain D residue  346 GLN
Chi-restraints excluded: chain I residue  345 ASN
Chi-restraints excluded: chain J residue  345 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 8 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 346 GLN
D 346 GLN
** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5194 r_free = 0.5194 target = 0.370423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.5547 r_free = 0.5547 target = 0.253513 restraints weight = 5177.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.5547 r_free = 0.5547 target = 0.253513 restraints weight = 4748.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5547 r_free = 0.5547 target = 0.253513 restraints weight = 4748.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.5722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.040   3744  Z= 0.506
  Angle     :  0.826   5.577   4980  Z= 0.453
  Chirality :  0.045   0.137    480
  Planarity :  0.004   0.015    684
  Dihedral  :  6.370  24.950    528
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 27.30 %
    Favored  : 66.38 %
  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: -4.56 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.007   TRP D 334 
 PHE   0.013   0.003   PHE G 313 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.8458 (ttm) cc_final: 0.8140 (ttt)
REVERT: A  331 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8072 (pt0)
REVERT: A  336 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7557 (tmm)
REVERT: B  307 MET cc_start: 0.8464 (ttm) cc_final: 0.8146 (ttt)
REVERT: B  331 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8180 (pt0)
REVERT: B  336 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7579 (tmm)
REVERT: C  322 MET cc_start: 0.7572 (mtt) cc_final: 0.6773 (mtt)
REVERT: D  322 MET cc_start: 0.7595 (mtt) cc_final: 0.6858 (mtt)
REVERT: I  327 GLN cc_start: 0.7414 (tp-100) cc_final: 0.7093 (tp-100)
REVERT: I  336 MET cc_start: 0.8241 (tmm) cc_final: 0.7582 (tmm)
REVERT: I  337 MET cc_start: 0.8448 (mtp) cc_final: 0.7871 (mtp)
REVERT: J  327 GLN cc_start: 0.7415 (tp-100) cc_final: 0.7097 (tp-100)
REVERT: K  322 MET cc_start: 0.8132 (mpp) cc_final: 0.7806 (mpp)
REVERT: L  322 MET cc_start: 0.8137 (mpp) cc_final: 0.7807 (mpp)
  outliers start: 22
  outliers final: 15
  residues processed: 150
  average time/residue: 0.1211
  time to fit residues: 23.0513
Evaluate side-chains
  165 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain B residue  336 MET
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain C residue  345 ASN
Chi-restraints excluded: chain C residue  346 GLN
Chi-restraints excluded: chain D residue  345 ASN
Chi-restraints excluded: chain D residue  346 GLN
Chi-restraints excluded: chain E residue  345 ASN
Chi-restraints excluded: chain F residue  345 ASN
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain G residue  345 ASN
Chi-restraints excluded: chain H residue  323 MET
Chi-restraints excluded: chain H residue  345 ASN
Chi-restraints excluded: chain J residue  337 MET
Chi-restraints excluded: chain K residue  323 MET
Chi-restraints excluded: chain L residue  323 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0050
   overall best weight:    1.3198

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

Flipped N/Q/H residues before XYZ refinement:
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 327 GLN
** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 346 GLN
F 327 GLN
** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 346 GLN
** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 346 GLN
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 346 GLN
** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5230 r_free = 0.5230 target = 0.381402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.5638 r_free = 0.5638 target = 0.269166 restraints weight = 5147.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5641 r_free = 0.5641 target = 0.270484 restraints weight = 4441.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.5684 r_free = 0.5684 target = 0.272164 restraints weight = 3997.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.5057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.6001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3744  Z= 0.254
  Angle     :  0.702   8.281   4980  Z= 0.363
  Chirality :  0.039   0.105    480
  Planarity :  0.002   0.010    684
  Dihedral  :  5.863  18.630    528
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 27.01 %
    Favored  : 66.38 %
  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: -4.54 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.45 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.004   TRP D 334 
 PHE   0.014   0.002   PHE G 313 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A  307 MET cc_start: 0.8434 (ttm) cc_final: 0.8159 (ttt)
REVERT: A  331 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7978 (pt0)
REVERT: B  307 MET cc_start: 0.8444 (ttm) cc_final: 0.8175 (ttt)
REVERT: B  331 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8112 (pt0)
REVERT: C  322 MET cc_start: 0.7314 (mtt) cc_final: 0.6335 (mtt)
REVERT: C  336 MET cc_start: 0.7757 (tmm) cc_final: 0.7102 (tmm)
REVERT: D  322 MET cc_start: 0.7406 (mtt) cc_final: 0.6541 (mtt)
REVERT: D  336 MET cc_start: 0.7723 (tmm) cc_final: 0.7149 (tmm)
REVERT: G  343 GLN cc_start: 0.8396 (mp10) cc_final: 0.8090 (mp10)
REVERT: H  343 GLN cc_start: 0.8401 (mp10) cc_final: 0.8098 (mp10)
REVERT: I  336 MET cc_start: 0.7898 (tmm) cc_final: 0.7310 (tmm)
REVERT: I  337 MET cc_start: 0.8265 (mtp) cc_final: 0.7645 (mtp)
REVERT: J  307 MET cc_start: 0.8576 (ttm) cc_final: 0.8326 (ttp)
REVERT: K  322 MET cc_start: 0.8054 (mpp) cc_final: 0.7701 (mtt)
REVERT: L  322 MET cc_start: 0.8054 (mpp) cc_final: 0.7715 (mtt)
  outliers start: 23
  outliers final: 12
  residues processed: 152
  average time/residue: 0.1234
  time to fit residues: 23.7577
Evaluate side-chains
  166 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain E residue  327 GLN
Chi-restraints excluded: chain E residue  346 GLN
Chi-restraints excluded: chain F residue  327 GLN
Chi-restraints excluded: chain F residue  346 GLN
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain G residue  345 ASN
Chi-restraints excluded: chain G residue  346 GLN
Chi-restraints excluded: chain H residue  323 MET
Chi-restraints excluded: chain H residue  345 ASN
Chi-restraints excluded: chain H residue  346 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 2 optimal weight:    0.0870
   chunk 44 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0670
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.8300

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

Flipped N/Q/H residues before XYZ refinement:
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5219 r_free = 0.5219 target = 0.380319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.5633 r_free = 0.5633 target = 0.265013 restraints weight = 5165.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.5636 r_free = 0.5636 target = 0.265593 restraints weight = 4653.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5637 r_free = 0.5637 target = 0.265836 restraints weight = 4375.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.4657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.6255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3744  Z= 0.303
  Angle     :  0.725   7.364   4980  Z= 0.378
  Chirality :  0.040   0.106    480
  Planarity :  0.002   0.012    684
  Dihedral  :  5.902  20.156    528
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 31.61 %
    Favored  : 62.07 %
  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: -4.60 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP D 334 
 PHE   0.012   0.002   PHE G 313 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.8372 (ttm) cc_final: 0.7919 (ttt)
REVERT: A  331 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7755 (pt0)
REVERT: B  307 MET cc_start: 0.8395 (ttm) cc_final: 0.7943 (ttt)
REVERT: B  331 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7952 (pt0)
REVERT: C  322 MET cc_start: 0.7567 (mtt) cc_final: 0.6175 (mtt)
REVERT: C  336 MET cc_start: 0.8158 (tmm) cc_final: 0.7114 (tmm)
REVERT: D  322 MET cc_start: 0.7715 (mtt) cc_final: 0.6527 (mtt)
REVERT: D  336 MET cc_start: 0.8154 (tmm) cc_final: 0.7109 (tmm)
REVERT: E  322 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6958 (mtt)
REVERT: E  336 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7476 (tmm)
REVERT: F  322 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6945 (mtt)
REVERT: F  336 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7449 (tmm)
REVERT: G  336 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7692 (ttt)
REVERT: G  339 MET cc_start: 0.7674 (mtp) cc_final: 0.7296 (mtt)
REVERT: G  343 GLN cc_start: 0.8286 (mp10) cc_final: 0.7749 (mp10)
REVERT: H  336 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7641 (ttt)
REVERT: H  343 GLN cc_start: 0.8261 (mp10) cc_final: 0.7709 (mp10)
REVERT: I  336 MET cc_start: 0.8251 (tmm) cc_final: 0.7105 (tmm)
REVERT: K  322 MET cc_start: 0.8319 (mpp) cc_final: 0.7700 (mtt)
REVERT: L  322 MET cc_start: 0.8321 (mpp) cc_final: 0.7711 (mtt)
  outliers start: 22
  outliers final: 9
  residues processed: 150
  average time/residue: 0.1183
  time to fit residues: 22.6210
Evaluate side-chains
  163 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain D residue  323 MET
Chi-restraints excluded: chain E residue  322 MET
Chi-restraints excluded: chain E residue  336 MET
Chi-restraints excluded: chain F residue  322 MET
Chi-restraints excluded: chain F residue  336 MET
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain G residue  336 MET
Chi-restraints excluded: chain G residue  345 ASN
Chi-restraints excluded: chain H residue  323 MET
Chi-restraints excluded: chain H residue  336 MET
Chi-restraints excluded: chain H residue  345 ASN
Chi-restraints excluded: chain K residue  323 MET
Chi-restraints excluded: chain L residue  323 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 46 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5244 r_free = 0.5244 target = 0.393488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.5763 r_free = 0.5763 target = 0.278930 restraints weight = 5252.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5788 r_free = 0.5788 target = 0.281003 restraints weight = 4427.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5793 r_free = 0.5793 target = 0.282024 restraints weight = 3929.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.5078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.6529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3744  Z= 0.206
  Angle     :  0.677   6.893   4980  Z= 0.350
  Chirality :  0.039   0.107    480
  Planarity :  0.002   0.010    684
  Dihedral  :  5.638  19.615    528
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 33.91 %
    Favored  : 61.21 %
  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: -4.58 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP H 334 
 PHE   0.012   0.002   PHE G 313 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  307 MET cc_start: 0.8265 (ttm) cc_final: 0.7978 (ttt)
REVERT: A  331 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7771 (pt0)
REVERT: B  307 MET cc_start: 0.8189 (ttm) cc_final: 0.7870 (ttt)
REVERT: B  331 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8211 (pt0)
REVERT: C  322 MET cc_start: 0.7241 (mtt) cc_final: 0.6533 (mmt)
REVERT: C  336 MET cc_start: 0.7580 (tmm) cc_final: 0.7128 (tmm)
REVERT: D  322 MET cc_start: 0.7389 (mtt) cc_final: 0.6506 (mtt)
REVERT: D  336 MET cc_start: 0.7552 (tmm) cc_final: 0.7165 (tmm)
REVERT: E  337 MET cc_start: 0.7433 (mtp) cc_final: 0.7055 (mtp)
REVERT: F  337 MET cc_start: 0.7632 (mtp) cc_final: 0.7129 (mtp)
REVERT: G  339 MET cc_start: 0.7806 (mtp) cc_final: 0.7555 (mtt)
REVERT: G  343 GLN cc_start: 0.8407 (mp10) cc_final: 0.7996 (mp10)
REVERT: G  346 GLN cc_start: 0.8237 (tp-100) cc_final: 0.8010 (tp40)
REVERT: H  336 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7273 (tmm)
REVERT: H  343 GLN cc_start: 0.8440 (mp10) cc_final: 0.8015 (mp10)
REVERT: H  346 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7924 (tp-100)
REVERT: I  336 MET cc_start: 0.7752 (tmm) cc_final: 0.7528 (ttt)
REVERT: I  337 MET cc_start: 0.8246 (mtp) cc_final: 0.7686 (mtt)
REVERT: J  343 GLN cc_start: 0.8222 (mp10) cc_final: 0.7985 (mp10)
REVERT: K  322 MET cc_start: 0.8028 (mpp) cc_final: 0.7628 (mtt)
REVERT: K  346 GLN cc_start: 0.6565 (mm110) cc_final: 0.6170 (mm-40)
REVERT: L  322 MET cc_start: 0.8077 (mpp) cc_final: 0.7695 (mtt)
REVERT: L  336 MET cc_start: 0.7054 (tpp) cc_final: 0.6793 (tpp)
REVERT: L  346 GLN cc_start: 0.6539 (mm110) cc_final: 0.6068 (mm-40)
  outliers start: 17
  outliers final: 5
  residues processed: 151
  average time/residue: 0.1202
  time to fit residues: 23.0521
Evaluate side-chains
  154 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain G residue  344 GLN
Chi-restraints excluded: chain H residue  323 MET
Chi-restraints excluded: chain H residue  336 MET
Chi-restraints excluded: chain H residue  344 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0570
   chunk 15 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0020
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.4906

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

Flipped N/Q/H residues before XYZ refinement:
D 331 GLN
F 331 GLN
H 331 GLN
J 331 GLN
** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5324 r_free = 0.5324 target = 0.418730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.5901 r_free = 0.5901 target = 0.302747 restraints weight = 5611.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5903 r_free = 0.5903 target = 0.303520 restraints weight = 4775.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.5945 r_free = 0.5945 target = 0.305429 restraints weight = 4422.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.5147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.6796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3744  Z= 0.208
  Angle     :  0.751  12.936   4980  Z= 0.369
  Chirality :  0.039   0.107    480
  Planarity :  0.002   0.011    684
  Dihedral  :  5.608  25.785    528
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 35.06 %
    Favored  : 61.78 %
  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: -4.57 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP G 334 
 PHE   0.011   0.002   PHE F 313 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7592 (pt0)
REVERT: B  307 MET cc_start: 0.8081 (ttm) cc_final: 0.7854 (ttt)
REVERT: B  331 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8041 (pt0)
REVERT: C  322 MET cc_start: 0.6956 (mtt) cc_final: 0.6437 (mmt)
REVERT: D  322 MET cc_start: 0.7046 (mtt) cc_final: 0.6296 (mtt)
REVERT: E  336 MET cc_start: 0.7553 (tmm) cc_final: 0.7201 (tmt)
REVERT: G  343 GLN cc_start: 0.8404 (mp10) cc_final: 0.8003 (mp10)
REVERT: H  343 GLN cc_start: 0.8365 (mp10) cc_final: 0.7998 (mp10)
REVERT: I  336 MET cc_start: 0.8135 (tmm) cc_final: 0.7414 (tmm)
REVERT: I  337 MET cc_start: 0.8267 (mtp) cc_final: 0.7497 (mtp)
REVERT: J  343 GLN cc_start: 0.8223 (mp10) cc_final: 0.8004 (mp10)
REVERT: K  322 MET cc_start: 0.8058 (mpp) cc_final: 0.7838 (mpp)
REVERT: K  346 GLN cc_start: 0.6533 (mm110) cc_final: 0.6049 (mm-40)
REVERT: L  322 MET cc_start: 0.8058 (mpp) cc_final: 0.7834 (mpp)
  outliers start: 11
  outliers final: 4
  residues processed: 151
  average time/residue: 0.1209
  time to fit residues: 23.1552
Evaluate side-chains
  150 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 144
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain G residue  344 GLN
Chi-restraints excluded: chain H residue  323 MET
Chi-restraints excluded: chain H residue  344 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 344 GLN
H 344 GLN
** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5211 r_free = 0.5211 target = 0.377746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.5666 r_free = 0.5666 target = 0.255261 restraints weight = 5250.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.5669 r_free = 0.5669 target = 0.255819 restraints weight = 4821.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5671 r_free = 0.5671 target = 0.256465 restraints weight = 4600.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.5011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.6958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   3744  Z= 0.397
  Angle     :  0.855  10.448   4980  Z= 0.437
  Chirality :  0.043   0.154    480
  Planarity :  0.003   0.011    684
  Dihedral  :  6.241  27.184    528
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 33.62 %
    Favored  : 62.64 %
  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: -4.84 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.69 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.005   TRP D 334 
 PHE   0.009   0.002   PHE G 313 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8454 (pt0)
REVERT: B  307 MET cc_start: 0.8513 (ttm) cc_final: 0.8192 (ttt)
REVERT: B  331 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8539 (pt0)
REVERT: C  322 MET cc_start: 0.7616 (mtt) cc_final: 0.7101 (mtt)
REVERT: D  322 MET cc_start: 0.7640 (mtt) cc_final: 0.7209 (mtt)
REVERT: F  336 MET cc_start: 0.8066 (tmm) cc_final: 0.7292 (tmt)
REVERT: G  343 GLN cc_start: 0.8381 (mp10) cc_final: 0.7984 (mp10)
REVERT: H  336 MET cc_start: 0.8120 (tmm) cc_final: 0.7784 (ttp)
REVERT: H  343 GLN cc_start: 0.8387 (mp10) cc_final: 0.7975 (mp10)
REVERT: H  346 GLN cc_start: 0.8200 (tp40) cc_final: 0.7982 (tp40)
REVERT: I  336 MET cc_start: 0.8231 (tmm) cc_final: 0.7433 (tmm)
REVERT: J  343 GLN cc_start: 0.8270 (mp10) cc_final: 0.8020 (mp10)
REVERT: K  322 MET cc_start: 0.8145 (mpp) cc_final: 0.7836 (mpp)
REVERT: K  346 GLN cc_start: 0.6814 (mm110) cc_final: 0.6343 (mm-40)
REVERT: L  322 MET cc_start: 0.8189 (mpp) cc_final: 0.7871 (mpp)
  outliers start: 13
  outliers final: 8
  residues processed: 148
  average time/residue: 0.1256
  time to fit residues: 23.7020
Evaluate side-chains
  155 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  345 ASN
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain G residue  337 MET
Chi-restraints excluded: chain G residue  344 GLN
Chi-restraints excluded: chain H residue  323 MET
Chi-restraints excluded: chain H residue  344 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 36 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 47 optimal weight:    0.3980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 344 GLN
** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 344 GLN
H 344 GLN
** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 344 GLN
** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5268 r_free = 0.5268 target = 0.392432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.5794 r_free = 0.5794 target = 0.274732 restraints weight = 5232.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.5797 r_free = 0.5797 target = 0.275800 restraints weight = 4651.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.5836 r_free = 0.5836 target = 0.277269 restraints weight = 4314.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.5101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.7136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3744  Z= 0.232
  Angle     :  0.760  10.324   4980  Z= 0.385
  Chirality :  0.040   0.114    480
  Planarity :  0.002   0.011    684
  Dihedral  :  5.836  24.092    528
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 35.63 %
    Favored  : 61.21 %
  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: -4.75 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.61 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP J 334 
 PHE   0.011   0.002   PHE E 313 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7757 (pt0)
REVERT: B  307 MET cc_start: 0.8324 (ttm) cc_final: 0.8040 (ttt)
REVERT: B  331 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8201 (pt0)
REVERT: C  322 MET cc_start: 0.7062 (mtt) cc_final: 0.6483 (mmt)
REVERT: D  322 MET cc_start: 0.7291 (mtt) cc_final: 0.6503 (mtt)
REVERT: F  336 MET cc_start: 0.7874 (tmm) cc_final: 0.7291 (tmt)
REVERT: G  343 GLN cc_start: 0.8336 (mp10) cc_final: 0.7884 (mp10)
REVERT: H  343 GLN cc_start: 0.8351 (mp10) cc_final: 0.7884 (mp10)
REVERT: H  346 GLN cc_start: 0.7996 (tp40) cc_final: 0.7771 (tp40)
REVERT: I  336 MET cc_start: 0.7805 (tmm) cc_final: 0.7595 (ttt)
REVERT: I  337 MET cc_start: 0.8369 (mtp) cc_final: 0.7804 (mtt)
REVERT: J  343 GLN cc_start: 0.8195 (mp10) cc_final: 0.7776 (mp10)
REVERT: K  346 GLN cc_start: 0.6293 (mm110) cc_final: 0.5732 (mm-40)
  outliers start: 11
  outliers final: 7
  residues processed: 148
  average time/residue: 0.1247
  time to fit residues: 23.4144
Evaluate side-chains
  154 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  345 ASN
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain G residue  344 GLN
Chi-restraints excluded: chain H residue  323 MET
Chi-restraints excluded: chain H residue  344 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 344 GLN
H 344 GLN
** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5261 r_free = 0.5261 target = 0.391944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.5779 r_free = 0.5779 target = 0.274248 restraints weight = 5275.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5782 r_free = 0.5782 target = 0.275465 restraints weight = 4687.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5809 r_free = 0.5809 target = 0.276771 restraints weight = 4302.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.5091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.7229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3744  Z= 0.243
  Angle     :  0.750  10.067   4980  Z= 0.380
  Chirality :  0.039   0.106    480
  Planarity :  0.002   0.012    684
  Dihedral  :  5.799  24.464    528
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 35.34 %
    Favored  : 61.78 %
  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: -4.78 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.63 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP H 334 
 PHE   0.011   0.002   PHE H 313 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1539.93 seconds
wall clock time: 28 minutes 14.12 seconds (1694.12 seconds total)