Starting phenix.real_space_refine
on Wed Mar  5 21:33:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qx9_18715/03_2025/8qx9_18715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qx9_18715/03_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_18715/03_2025/8qx9_18715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qx9_18715/03_2025/8qx9_18715.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qx9_18715/03_2025/8qx9_18715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qx9_18715/03_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-5624/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: 1.46, per 1000 atoms: 0.40
  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: 0.81
  Conformation dependent library (CDL) restraints added in 504.7 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: 0.47
  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: 0.82

  Time building geometry restraints manager: 1.00 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: 0.05
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:             0.950
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.220
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.710
-------------------------------------------------------------------------------
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  : 0.383 
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: 0.1222
  time to fit residues: 26.6177
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  : 0.405 
-------------------------------------------------------------------------------
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 = 0.291142 restraints weight = 5000.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.5718 r_free = 0.5718 target = 0.293587 restraints weight = 3865.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5723 r_free = 0.5723 target = 0.294664 restraints weight = 3259.757|
|-----------------------------------------------------------------------------|
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  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.8089 (ttm) cc_final: 0.7888 (ttt)
REVERT: B  307 MET cc_start: 0.8095 (ttm) cc_final: 0.7889 (ttt)
REVERT: C  322 MET cc_start: 0.7294 (mtt) cc_final: 0.6892 (mtt)
REVERT: C  336 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7319 (tmm)
REVERT: C  339 MET cc_start: 0.7607 (mtp) cc_final: 0.7353 (mtp)
REVERT: C  346 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7503 (mm-40)
REVERT: D  322 MET cc_start: 0.7282 (mtt) cc_final: 0.6881 (mtt)
REVERT: D  336 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7328 (tmm)
REVERT: D  339 MET cc_start: 0.7611 (mtp) cc_final: 0.7342 (mtp)
REVERT: D  346 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7496 (mm-40)
REVERT: E  322 MET cc_start: 0.7851 (mpp) cc_final: 0.7256 (mmm)
REVERT: F  322 MET cc_start: 0.7848 (mpp) cc_final: 0.7258 (mmm)
REVERT: G  322 MET cc_start: 0.7429 (mtt) cc_final: 0.6799 (mtt)
REVERT: H  322 MET cc_start: 0.7400 (mtt) cc_final: 0.6777 (mtt)
REVERT: I  336 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7585 (tmm)
REVERT: I  337 MET cc_start: 0.7958 (mtp) cc_final: 0.7516 (mtp)
REVERT: J  336 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7593 (tmm)
REVERT: J  337 MET cc_start: 0.7966 (mtp) cc_final: 0.7522 (mtp)
REVERT: K  322 MET cc_start: 0.7936 (mpp) cc_final: 0.7514 (mtt)
REVERT: L  322 MET cc_start: 0.7935 (mpp) cc_final: 0.7526 (mtt)
  outliers start: 6
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1206
  time to fit residues: 24.1450
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  : 0.341 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 7 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0020
   chunk 47 optimal weight:    0.4980
   chunk 4 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   overall best weight:    0.8590

-------------------------------------------------------------------------------
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 = 0.5255 r_free = 0.5255 target = 0.392010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.5709 r_free = 0.5709 target = 0.287421 restraints weight = 4949.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.5733 r_free = 0.5733 target = 0.289680 restraints weight = 3946.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5738 r_free = 0.5738 target = 0.290548 restraints weight = 3387.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.5103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.4766

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= 0.198
  Angle     :  0.627   7.379   4980  Z= 0.323
  Chirality :  0.039   0.108    480
  Planarity :  0.002   0.009    684
  Dihedral  :  5.469  19.838    528
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 11.74
  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: -4.46 (0.17), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.004   TRP D 334 
 PHE   0.013   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  : 0.386 
Fit side-chains
REVERT: A  307 MET cc_start: 0.8084 (ttm) cc_final: 0.7843 (ttt)
REVERT: B  307 MET cc_start: 0.8083 (ttm) cc_final: 0.7842 (ttt)
REVERT: C  322 MET cc_start: 0.7093 (mtt) cc_final: 0.6480 (mtt)
REVERT: C  343 GLN cc_start: 0.8259 (mp10) cc_final: 0.8011 (mp10)
REVERT: C  346 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7721 (mm-40)
REVERT: D  322 MET cc_start: 0.7130 (mtt) cc_final: 0.6494 (mtt)
REVERT: D  343 GLN cc_start: 0.8253 (mp10) cc_final: 0.8011 (mp10)
REVERT: E  346 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7547 (mm-40)
REVERT: F  346 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7558 (mm-40)
REVERT: G  322 MET cc_start: 0.7098 (mtt) cc_final: 0.6659 (mtt)
REVERT: G  346 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7668 (mm-40)
REVERT: H  322 MET cc_start: 0.7072 (mtt) cc_final: 0.6633 (mtt)
REVERT: H  346 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7671 (mm-40)
REVERT: I  307 MET cc_start: 0.8532 (ttm) cc_final: 0.8307 (ttp)
REVERT: I  337 MET cc_start: 0.7955 (mtp) cc_final: 0.7751 (mtt)
REVERT: J  307 MET cc_start: 0.8526 (ttm) cc_final: 0.8305 (ttp)
REVERT: J  337 MET cc_start: 0.7959 (mtp) cc_final: 0.7757 (mtt)
REVERT: K  322 MET cc_start: 0.7953 (mpp) cc_final: 0.7665 (mtt)
REVERT: L  322 MET cc_start: 0.7953 (mpp) cc_final: 0.7686 (mtt)
  outliers start: 10
  outliers final: 4
  residues processed: 148
  average time/residue: 0.1172
  time to fit residues: 22.1852
Evaluate side-chains
  141 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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 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:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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 = 0.5219 r_free = 0.5219 target = 0.377502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.5482 r_free = 0.5482 target = 0.259956 restraints weight = 5149.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5465 r_free = 0.5465 target = 0.260707 restraints weight = 7434.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.5464 r_free = 0.5464 target = 0.261067 restraints weight = 7412.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.5000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.5503

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= 0.404
  Angle     :  0.782   8.845   4980  Z= 0.413
  Chirality :  0.042   0.113    480
  Planarity :  0.003   0.013    684
  Dihedral  :  5.999  22.292    528
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 16.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 25.00 %
    Favored  : 69.25 %
  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: -4.52 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.006   TRP C 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
  166 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A  307 MET cc_start: 0.8455 (ttm) cc_final: 0.8170 (ttt)
REVERT: A  331 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8063 (pt0)
REVERT: B  307 MET cc_start: 0.8458 (ttm) cc_final: 0.8172 (ttt)
REVERT: B  331 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8167 (pt0)
REVERT: C  322 MET cc_start: 0.7508 (mtt) cc_final: 0.6679 (mtt)
REVERT: C  336 MET cc_start: 0.8035 (tmm) cc_final: 0.7387 (tmm)
REVERT: D  322 MET cc_start: 0.7423 (mtt) cc_final: 0.6701 (mtt)
REVERT: D  336 MET cc_start: 0.8033 (tmm) cc_final: 0.7385 (tmm)
REVERT: I  327 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7320 (tp-100)
REVERT: I  336 MET cc_start: 0.8126 (tmm) cc_final: 0.7509 (tmm)
REVERT: I  337 MET cc_start: 0.8324 (mtp) cc_final: 0.7707 (mtp)
REVERT: J  327 GLN cc_start: 0.7643 (tp-100) cc_final: 0.7316 (tp-100)
REVERT: J  336 MET cc_start: 0.8118 (tmm) cc_final: 0.7502 (tmm)
REVERT: J  337 MET cc_start: 0.8335 (mtp) cc_final: 0.7715 (mtp)
REVERT: K  322 MET cc_start: 0.8015 (mpp) cc_final: 0.7696 (mtt)
REVERT: L  322 MET cc_start: 0.8016 (mpp) cc_final: 0.7707 (mtt)
  outliers start: 20
  outliers final: 13
  residues processed: 146
  average time/residue: 0.1274
  time to fit residues: 23.8555
Evaluate side-chains
  157 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
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 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 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 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:    4.9990
   chunk 16 optimal weight:    9.9990
   chunk 31 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 44 optimal weight:    0.1980
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
D 346 GLN
E 327 GLN
E 346 GLN
F 327 GLN
F 346 GLN
G 346 GLN
H 346 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5246 r_free = 0.5246 target = 0.384180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.5664 r_free = 0.5664 target = 0.273525 restraints weight = 5131.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5667 r_free = 0.5667 target = 0.274643 restraints weight = 4395.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.5668 r_free = 0.5668 target = 0.275041 restraints weight = 3964.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.5059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.5798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3744  Z= 0.235
  Angle     :  0.689   7.743   4980  Z= 0.354
  Chirality :  0.039   0.106    480
  Planarity :  0.002   0.008    684
  Dihedral  :  5.771  20.352    528
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 27.87 %
    Favored  : 66.09 %
  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: -4.53 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP C 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
  170 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  307 MET cc_start: 0.8129 (ttm) cc_final: 0.7877 (ttt)
REVERT: A  331 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7875 (pt0)
REVERT: A  336 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7132 (tmm)
REVERT: A  337 MET cc_start: 0.8217 (mtp) cc_final: 0.7331 (mtp)
REVERT: B  307 MET cc_start: 0.8133 (ttm) cc_final: 0.7877 (ttt)
REVERT: B  331 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8006 (pt0)
REVERT: B  336 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7143 (tmm)
REVERT: B  337 MET cc_start: 0.8220 (mtp) cc_final: 0.7356 (mtp)
REVERT: C  322 MET cc_start: 0.7394 (mtt) cc_final: 0.6322 (mtt)
REVERT: C  336 MET cc_start: 0.7790 (tmm) cc_final: 0.7225 (tmm)
REVERT: C  346 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7596 (tp40)
REVERT: D  322 MET cc_start: 0.7250 (mtt) cc_final: 0.6333 (mtt)
REVERT: D  336 MET cc_start: 0.7808 (tmm) cc_final: 0.7235 (tmm)
REVERT: G  343 GLN cc_start: 0.8398 (mp10) cc_final: 0.8120 (mp10)
REVERT: H  343 GLN cc_start: 0.8397 (mp10) cc_final: 0.8110 (mp10)
REVERT: I  307 MET cc_start: 0.8478 (ttm) cc_final: 0.8226 (ttp)
REVERT: I  336 MET cc_start: 0.7945 (tmm) cc_final: 0.7311 (tmm)
REVERT: I  337 MET cc_start: 0.8278 (mtp) cc_final: 0.7708 (mtp)
REVERT: J  307 MET cc_start: 0.8475 (ttm) cc_final: 0.8219 (ttp)
REVERT: J  336 MET cc_start: 0.7934 (tmm) cc_final: 0.7300 (tmm)
REVERT: J  337 MET cc_start: 0.8284 (mtp) cc_final: 0.7708 (mtp)
REVERT: K  322 MET cc_start: 0.8021 (mpp) cc_final: 0.7718 (mtt)
REVERT: L  322 MET cc_start: 0.8014 (mpp) cc_final: 0.7705 (mtt)
  outliers start: 21
  outliers final: 15
  residues processed: 149
  average time/residue: 0.1132
  time to fit residues: 21.5533
Evaluate side-chains
  168 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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 D residue  346 GLN
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  345 ASN
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
Chi-restraints excluded: chain I residue  323 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 2 optimal weight:    0.0980
   chunk 44 optimal weight:    9.9990
   chunk 47 optimal weight:    0.0870
   chunk 29 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0970
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.2560

-------------------------------------------------------------------------------
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 = 0.5239 r_free = 0.5239 target = 0.385193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.5654 r_free = 0.5654 target = 0.274213 restraints weight = 5139.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5656 r_free = 0.5656 target = 0.275175 restraints weight = 4492.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5656 r_free = 0.5656 target = 0.275175 restraints weight = 4109.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.5048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.6038

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= 0.241
  Angle     :  0.680   7.390   4980  Z= 0.354
  Chirality :  0.039   0.106    480
  Planarity :  0.002   0.010    684
  Dihedral  :  5.668  20.050    528
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 32.76 %
    Favored  : 61.49 %
  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: -4.52 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   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
  170 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  307 MET cc_start: 0.8142 (ttm) cc_final: 0.7902 (ttt)
REVERT: A  331 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7897 (pt0)
REVERT: A  337 MET cc_start: 0.8217 (mtp) cc_final: 0.7867 (mtt)
REVERT: B  307 MET cc_start: 0.8149 (ttm) cc_final: 0.7906 (ttt)
REVERT: B  331 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8047 (pt0)
REVERT: B  337 MET cc_start: 0.8232 (mtp) cc_final: 0.7878 (mtt)
REVERT: C  322 MET cc_start: 0.7398 (mtt) cc_final: 0.6255 (mtt)
REVERT: C  336 MET cc_start: 0.7675 (tmm) cc_final: 0.6891 (tmm)
REVERT: D  322 MET cc_start: 0.7291 (mtt) cc_final: 0.6351 (mtt)
REVERT: D  336 MET cc_start: 0.7688 (tmm) cc_final: 0.6890 (tmm)
REVERT: E  322 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7083 (mmt)
REVERT: G  343 GLN cc_start: 0.8384 (mp10) cc_final: 0.8070 (mp10)
REVERT: H  336 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7434 (tmm)
REVERT: H  343 GLN cc_start: 0.8384 (mp10) cc_final: 0.8065 (mp10)
REVERT: I  336 MET cc_start: 0.7884 (tmm) cc_final: 0.7313 (tmm)
REVERT: I  337 MET cc_start: 0.8277 (mtp) cc_final: 0.7660 (mtp)
REVERT: J  336 MET cc_start: 0.7858 (tmm) cc_final: 0.7292 (tmm)
REVERT: J  337 MET cc_start: 0.8286 (mtp) cc_final: 0.7663 (mtp)
REVERT: K  322 MET cc_start: 0.8044 (mpp) cc_final: 0.7740 (mtt)
REVERT: L  322 MET cc_start: 0.8046 (mpp) cc_final: 0.7735 (mtt)
  outliers start: 20
  outliers final: 12
  residues processed: 150
  average time/residue: 0.1163
  time to fit residues: 22.3071
Evaluate side-chains
  162 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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 D residue  345 ASN
Chi-restraints excluded: chain E residue  322 MET
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  336 MET
Chi-restraints excluded: chain H residue  345 ASN
Chi-restraints excluded: chain H residue  346 GLN
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:    8.9990
   chunk 46 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.5204 r_free = 0.5204 target = 0.382406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.5677 r_free = 0.5677 target = 0.267826 restraints weight = 5224.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5679 r_free = 0.5679 target = 0.268772 restraints weight = 4570.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.5680 r_free = 0.5680 target = 0.269085 restraints weight = 4202.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.5027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.6410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3744  Z= 0.341
  Angle     :  0.740   8.231   4980  Z= 0.390
  Chirality :  0.040   0.104    480
  Planarity :  0.002   0.010    684
  Dihedral  :  5.928  21.772    528
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 35.34 %
    Favored  : 59.48 %
  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: -4.65 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.005   TRP D 334 
 PHE   0.011   0.002   PHE H 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
  170 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.8436 (ttm) cc_final: 0.8133 (ttt)
REVERT: A  331 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8174 (pt0)
REVERT: A  337 MET cc_start: 0.8190 (mtp) cc_final: 0.7849 (mtp)
REVERT: B  307 MET cc_start: 0.8470 (ttm) cc_final: 0.8145 (ttt)
REVERT: B  331 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8279 (pt0)
REVERT: B  337 MET cc_start: 0.8198 (mtp) cc_final: 0.7854 (mtp)
REVERT: C  322 MET cc_start: 0.7539 (mtt) cc_final: 0.6593 (mtt)
REVERT: C  336 MET cc_start: 0.7917 (tmm) cc_final: 0.7203 (tmm)
REVERT: D  322 MET cc_start: 0.7579 (mtt) cc_final: 0.6777 (mtt)
REVERT: D  336 MET cc_start: 0.7920 (tmm) cc_final: 0.7207 (tmm)
REVERT: E  322 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7014 (mmt)
REVERT: F  322 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7021 (mmt)
REVERT: G  343 GLN cc_start: 0.8461 (mp10) cc_final: 0.8087 (mp10)
REVERT: H  336 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7625 (tmm)
REVERT: H  343 GLN cc_start: 0.8458 (mp10) cc_final: 0.8077 (mp10)
REVERT: I  336 MET cc_start: 0.8018 (tmm) cc_final: 0.7274 (tmm)
REVERT: J  336 MET cc_start: 0.8018 (tmm) cc_final: 0.7290 (tmm)
REVERT: K  322 MET cc_start: 0.8050 (mpp) cc_final: 0.7705 (mtt)
REVERT: L  322 MET cc_start: 0.8060 (mpp) cc_final: 0.7730 (mtt)
REVERT: L  346 GLN cc_start: 0.6556 (mm110) cc_final: 0.6319 (mm-40)
  outliers start: 18
  outliers final: 10
  residues processed: 152
  average time/residue: 0.1174
  time to fit residues: 22.9047
Evaluate side-chains
  165 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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  322 MET
Chi-restraints excluded: chain F residue  322 MET
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain G residue  344 GLN
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  344 GLN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5247 r_free = 0.5247 target = 0.395975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.5777 r_free = 0.5777 target = 0.281811 restraints weight = 5313.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5780 r_free = 0.5780 target = 0.283493 restraints weight = 4453.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5788 r_free = 0.5788 target = 0.285125 restraints weight = 3927.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.5079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.6676

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= 0.220
  Angle     :  0.705   8.705   4980  Z= 0.362
  Chirality :  0.039   0.107    480
  Planarity :  0.002   0.011    684
  Dihedral  :  5.712  22.624    528
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 34.20 %
    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: -4.53 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.45 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP G 334 
 PHE   0.013   0.002   PHE H 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
  169 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 155
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  307 MET cc_start: 0.8152 (ttm) cc_final: 0.7896 (ttt)
REVERT: A  331 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7660 (pt0)
REVERT: A  337 MET cc_start: 0.8121 (mtp) cc_final: 0.7897 (mtt)
REVERT: B  307 MET cc_start: 0.8151 (ttm) cc_final: 0.7895 (ttt)
REVERT: B  331 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8084 (pt0)
REVERT: B  337 MET cc_start: 0.8133 (mtp) cc_final: 0.7908 (mtt)
REVERT: C  322 MET cc_start: 0.7333 (mtt) cc_final: 0.6503 (mmt)
REVERT: C  336 MET cc_start: 0.7526 (tmm) cc_final: 0.6955 (tmm)
REVERT: C  346 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7619 (tp40)
REVERT: D  322 MET cc_start: 0.7293 (mtt) cc_final: 0.6386 (mtt)
REVERT: D  336 MET cc_start: 0.7522 (tmm) cc_final: 0.6922 (tmm)
REVERT: D  346 GLN cc_start: 0.8169 (tp40) cc_final: 0.7754 (tp-100)
REVERT: G  339 MET cc_start: 0.7808 (mtp) cc_final: 0.7576 (mtt)
REVERT: G  343 GLN cc_start: 0.8354 (mp10) cc_final: 0.7968 (mp10)
REVERT: H  343 GLN cc_start: 0.8355 (mp10) cc_final: 0.7971 (mp10)
REVERT: H  346 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7815 (tp40)
REVERT: I  337 MET cc_start: 0.8329 (mtp) cc_final: 0.7736 (mtt)
REVERT: J  336 MET cc_start: 0.7725 (tmm) cc_final: 0.7509 (ttt)
REVERT: J  337 MET cc_start: 0.8323 (mtp) cc_final: 0.7710 (mtt)
REVERT: K  322 MET cc_start: 0.8002 (mpp) cc_final: 0.7651 (mtt)
REVERT: L  322 MET cc_start: 0.8035 (mpp) cc_final: 0.7662 (mtt)
  outliers start: 14
  outliers final: 6
  residues processed: 155
  average time/residue: 0.1131
  time to fit residues: 22.4830
Evaluate side-chains
  156 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  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 G residue  345 ASN
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:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 37 optimal weight:    0.4980
   chunk 13 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.8586

-------------------------------------------------------------------------------
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**
C 344 GLN
D 327 GLN
D 346 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 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5204 r_free = 0.5204 target = 0.378861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.5653 r_free = 0.5653 target = 0.255449 restraints weight = 5294.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.5653 r_free = 0.5653 target = 0.255449 restraints weight = 4829.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5653 r_free = 0.5653 target = 0.255449 restraints weight = 4829.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.4994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.6898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3744  Z= 0.430
  Angle     :  0.821   8.465   4980  Z= 0.434
  Chirality :  0.043   0.118    480
  Planarity :  0.003   0.010    684
  Dihedral  :  6.264  24.359    528
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 33.33 %
    Favored  : 62.36 %
  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 (0.20), 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   0.026   0.006   TRP I 334 
 PHE   0.012   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
  165 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  307 MET cc_start: 0.8506 (ttm) cc_final: 0.8168 (ttt)
REVERT: A  331 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8219 (pt0)
REVERT: A  337 MET cc_start: 0.8193 (mtp) cc_final: 0.7892 (mtt)
REVERT: B  307 MET cc_start: 0.8508 (ttm) cc_final: 0.8177 (ttt)
REVERT: B  331 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8402 (pt0)
REVERT: B  337 MET cc_start: 0.8199 (mtp) cc_final: 0.7915 (mtt)
REVERT: C  322 MET cc_start: 0.7587 (mtt) cc_final: 0.6940 (mtt)
REVERT: C  336 MET cc_start: 0.8059 (tmm) cc_final: 0.7261 (tmm)
REVERT: D  322 MET cc_start: 0.7608 (mtt) cc_final: 0.6996 (mtt)
REVERT: D  336 MET cc_start: 0.8091 (tmm) cc_final: 0.7342 (tmm)
REVERT: G  343 GLN cc_start: 0.8371 (mp10) cc_final: 0.7960 (mp10)
REVERT: H  312 ASN cc_start: 0.7980 (t0) cc_final: 0.7762 (t0)
REVERT: H  343 GLN cc_start: 0.8387 (mp10) cc_final: 0.7991 (mp10)
REVERT: I  337 MET cc_start: 0.8481 (mtp) cc_final: 0.8003 (mtt)
REVERT: J  307 MET cc_start: 0.8687 (ttm) cc_final: 0.8381 (ttm)
REVERT: J  336 MET cc_start: 0.8274 (tmm) cc_final: 0.7516 (tmm)
REVERT: J  337 MET cc_start: 0.8504 (mtp) cc_final: 0.7699 (mtp)
REVERT: K  322 MET cc_start: 0.8166 (mpp) cc_final: 0.7833 (mpp)
REVERT: L  322 MET cc_start: 0.8213 (mpp) cc_final: 0.7870 (mpp)
  outliers start: 15
  outliers final: 9
  residues processed: 150
  average time/residue: 0.1242
  time to fit residues: 24.0081
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  : 0.341 
-------------------------------------------------------------------------------
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 D residue  345 ASN
Chi-restraints excluded: chain D residue  346 GLN
Chi-restraints excluded: chain G residue  323 MET
Chi-restraints excluded: chain G residue  344 GLN
Chi-restraints excluded: chain G residue  345 ASN
Chi-restraints excluded: chain H residue  323 MET
Chi-restraints excluded: chain H residue  344 GLN
Chi-restraints excluded: chain I residue  323 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 327 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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5240 r_free = 0.5240 target = 0.391536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.5750 r_free = 0.5750 target = 0.272737 restraints weight = 5247.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.5753 r_free = 0.5753 target = 0.273815 restraints weight = 4645.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.5794 r_free = 0.5794 target = 0.275488 restraints weight = 4277.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.5067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.7047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3744  Z= 0.240
  Angle     :  0.730   9.178   4980  Z= 0.380
  Chirality :  0.039   0.106    480
  Planarity :  0.002   0.011    684
  Dihedral  :  5.790  21.762    528
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 33.91 %
    Favored  : 62.36 %
  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: -4.71 (0.20), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.58 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP H 334 
 PHE   0.015   0.002   PHE H 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
  164 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  307 MET cc_start: 0.8466 (ttm) cc_final: 0.8190 (ttt)
REVERT: A  331 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7771 (pt0)
REVERT: B  307 MET cc_start: 0.8471 (ttm) cc_final: 0.8187 (ttt)
REVERT: B  331 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8157 (pt0)
REVERT: C  322 MET cc_start: 0.7139 (mtt) cc_final: 0.6577 (mmt)
REVERT: D  322 MET cc_start: 0.7333 (mtt) cc_final: 0.6505 (mtt)
REVERT: G  343 GLN cc_start: 0.8306 (mp10) cc_final: 0.7976 (mp10)
REVERT: H  343 GLN cc_start: 0.8332 (mp10) cc_final: 0.8023 (mp10)
REVERT: I  337 MET cc_start: 0.8167 (mtp) cc_final: 0.7939 (mtt)
REVERT: J  336 MET cc_start: 0.7857 (tmm) cc_final: 0.7614 (ttt)
REVERT: J  337 MET cc_start: 0.8372 (mtp) cc_final: 0.7801 (mtt)
REVERT: K  322 MET cc_start: 0.8053 (mpp) cc_final: 0.7595 (mtt)
REVERT: L  322 MET cc_start: 0.8136 (mpp) cc_final: 0.7859 (mpp)
  outliers start: 13
  outliers final: 7
  residues processed: 151
  average time/residue: 0.1214
  time to fit residues: 23.3667
Evaluate side-chains
  155 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain H residue  345 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0170
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0010
   chunk 3 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    0.5024

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

Flipped N/Q/H residues before XYZ refinement:
C 331 GLN
E 331 GLN
G 331 GLN
I 331 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.396812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.5798 r_free = 0.5798 target = 0.280423 restraints weight = 5293.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5800 r_free = 0.5800 target = 0.281315 restraints weight = 4615.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.5802 r_free = 0.5802 target = 0.282430 restraints weight = 4262.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.5090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.7193

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= 0.218
  Angle     :  0.712   9.646   4980  Z= 0.369
  Chirality :  0.039   0.107    480
  Planarity :  0.002   0.011    684
  Dihedral  :  5.513  21.263    528
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 33.33 %
    Favored  : 64.08 %
  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: -4.69 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 334 
 PHE   0.014   0.002   PHE H 313 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1556.31 seconds
wall clock time: 27 minutes 33.04 seconds (1653.04 seconds total)