Starting phenix.real_space_refine
on Tue Feb  3 14:18:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qx9_18715/02_2026/8qx9_18715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qx9_18715/02_2026/8qx9_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_18715/02_2026/8qx9_18715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qx9_18715/02_2026/8qx9_18715.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qx9_18715/02_2026/8qx9_18715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qx9_18715/02_2026/8qx9_18715.cif"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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:
    B, C, D, E, F, G, H, I, J, K, L
  Time building chain proxies: 0.25, per 1000 atoms: 0.07
  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: 0.18
  Conformation dependent library (CDL) restraints added in 89.5 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: 0.07
  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: 0.27

  Time building geometry restraints manager: 0.24 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  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:             0.540
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     2.970
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:0.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    4.350
-------------------------------------------------------------------------------
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= 1.031
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 PHE   0.012   0.003   PHE L 316 
 TRP   0.046   0.010   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.01385 ( 3744)
  covalent geometry    : angle       2.17342 ( 4980)
  hydrogen bonds       : bond        0.22508 (   30)
  hydrogen bonds       : angle       7.60692 (   90)

*********************** 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  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 MET cc_start: 0.7376 (ttt) cc_final: 0.7017 (ttt)
REVERT: B  336 MET cc_start: 0.7397 (ttt) cc_final: 0.7029 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0500
  time to fit residues: 11.1862
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  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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
** 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 327 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 327 GLN
L 327 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5247 r_free = 0.5247 target = 0.393530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.5684 r_free = 0.5684 target = 0.291411 restraints weight = 5029.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.5720 r_free = 0.5720 target = 0.294164 restraints weight = 3760.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.5724 r_free = 0.5724 target = 0.295493 restraints weight = 3122.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.5726 r_free = 0.5726 target = 0.295907 restraints weight = 2795.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.5729 r_free = 0.5729 target = 0.297108 restraints weight = 2674.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.5115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.4075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3744  Z= 0.135
  Angle     :  0.625   5.019   4980  Z= 0.332
  Chirality :  0.040   0.113    480
  Planarity :  0.003   0.016    684
  Dihedral  :  5.553  16.774    528
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 27.30 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.60 (0.17), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.003   PHE G 313 
 TRP   0.016   0.003   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3744)
  covalent geometry    : angle       0.62514 ( 4980)
  hydrogen bonds       : bond        0.02657 (   30)
  hydrogen bonds       : angle       5.16530 (   90)

*********************** 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
  163 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 156
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  336 MET cc_start: 0.7483 (ttt) cc_final: 0.7150 (ttt)
REVERT: B  336 MET cc_start: 0.7485 (ttt) cc_final: 0.7152 (ttt)
REVERT: C  322 MET cc_start: 0.7274 (mtt) cc_final: 0.6886 (mtt)
REVERT: C  346 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7436 (mm-40)
REVERT: D  322 MET cc_start: 0.7263 (mtt) cc_final: 0.6853 (mtt)
REVERT: D  346 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7457 (mm-40)
REVERT: E  322 MET cc_start: 0.7799 (mpp) cc_final: 0.7169 (mmm)
REVERT: F  322 MET cc_start: 0.7799 (mpp) cc_final: 0.7174 (mmm)
REVERT: G  322 MET cc_start: 0.7336 (mtt) cc_final: 0.6659 (mtt)
REVERT: H  322 MET cc_start: 0.7322 (mtt) cc_final: 0.6649 (mtt)
REVERT: I  336 MET cc_start: 0.7567 (ttt) cc_final: 0.7349 (tmm)
REVERT: I  337 MET cc_start: 0.7372 (mtp) cc_final: 0.6905 (mtp)
REVERT: J  336 MET cc_start: 0.7568 (ttt) cc_final: 0.7342 (tmm)
REVERT: J  337 MET cc_start: 0.7383 (mtp) cc_final: 0.6908 (mtp)
REVERT: K  322 MET cc_start: 0.7892 (mpp) cc_final: 0.7519 (mtt)
REVERT: L  322 MET cc_start: 0.7891 (mpp) cc_final: 0.7525 (mtt)
  outliers start: 7
  outliers final: 2
  residues processed: 156
  average time/residue: 0.0399
  time to fit residues: 8.1354
Evaluate side-chains
  147 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 16 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    1.4582

-------------------------------------------------------------------------------
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
H 346 GLN
I 346 GLN
J 346 GLN
K 319 ASN
L 319 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5249 r_free = 0.5249 target = 0.384650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.5656 r_free = 0.5656 target = 0.277117 restraints weight = 5015.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5682 r_free = 0.5682 target = 0.279211 restraints weight = 4054.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.5685 r_free = 0.5685 target = 0.280091 restraints weight = 3524.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.5687 r_free = 0.5687 target = 0.280472 restraints weight = 3253.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5687 r_free = 0.5687 target = 0.280472 restraints weight = 3141.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.5084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.4769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3744  Z= 0.172
  Angle     :  0.680   6.724   4980  Z= 0.356
  Chirality :  0.040   0.108    480
  Planarity :  0.002   0.010    684
  Dihedral  :  5.586  19.550    528
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 25.86 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.62 (0.17), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.012   0.002   PHE G 313 
 TRP   0.026   0.004   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 3744)
  covalent geometry    : angle       0.67991 ( 4980)
  hydrogen bonds       : bond        0.02755 (   30)
  hydrogen bonds       : angle       5.61508 (   90)

*********************** 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
  157 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A  336 MET cc_start: 0.7538 (ttt) cc_final: 0.7270 (ttt)
REVERT: B  336 MET cc_start: 0.7526 (ttt) cc_final: 0.7264 (ttt)
REVERT: C  322 MET cc_start: 0.7428 (mtt) cc_final: 0.6789 (mtt)
REVERT: C  343 GLN cc_start: 0.8244 (mp10) cc_final: 0.8014 (mp10)
REVERT: D  322 MET cc_start: 0.7426 (mtt) cc_final: 0.6761 (mtt)
REVERT: D  343 GLN cc_start: 0.8257 (mp10) cc_final: 0.7989 (mp10)
REVERT: E  346 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7545 (mm-40)
REVERT: F  346 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7572 (mm-40)
REVERT: I  336 MET cc_start: 0.7807 (ttt) cc_final: 0.7366 (ttt)
REVERT: I  337 MET cc_start: 0.7638 (mtp) cc_final: 0.7398 (mtp)
REVERT: J  336 MET cc_start: 0.7807 (ttt) cc_final: 0.7369 (ttt)
REVERT: J  337 MET cc_start: 0.7648 (mtp) cc_final: 0.7405 (mtp)
REVERT: K  322 MET cc_start: 0.7951 (mpp) cc_final: 0.7615 (mtt)
REVERT: L  322 MET cc_start: 0.7954 (mpp) cc_final: 0.7629 (mtt)
  outliers start: 9
  outliers final: 1
  residues processed: 148
  average time/residue: 0.0419
  time to fit residues: 8.1542
Evaluate side-chains
  139 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  345 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0970
   chunk 45 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
C 327 GLN
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 346 GLN
D 327 GLN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 346 GLN
** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 346 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5211 r_free = 0.5211 target = 0.373448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.5591 r_free = 0.5591 target = 0.259918 restraints weight = 5073.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.5592 r_free = 0.5592 target = 0.260196 restraints weight = 4489.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5592 r_free = 0.5592 target = 0.260201 restraints weight = 4339.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5592 r_free = 0.5592 target = 0.260201 restraints weight = 4337.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5592 r_free = 0.5592 target = 0.260201 restraints weight = 4337.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.5015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.5491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   3744  Z= 0.293
  Angle     :  0.797   8.506   4980  Z= 0.420
  Chirality :  0.042   0.118    480
  Planarity :  0.003   0.013    684
  Dihedral  :  5.972  22.648    528
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  7.47 %
    Allowed  : 23.28 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.63 (0.17), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.013   0.003   PHE G 313 
 TRP   0.034   0.006   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 3744)
  covalent geometry    : angle       0.79736 ( 4980)
  hydrogen bonds       : bond        0.03612 (   30)
  hydrogen bonds       : angle       5.16117 (   90)

*********************** 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
  176 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8256 (pt0)
REVERT: A  336 MET cc_start: 0.7828 (ttt) cc_final: 0.7578 (ttt)
REVERT: B  331 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8291 (pt0)
REVERT: B  336 MET cc_start: 0.7810 (ttt) cc_final: 0.7580 (ttt)
REVERT: C  322 MET cc_start: 0.7459 (mtt) cc_final: 0.6767 (mtt)
REVERT: C  343 GLN cc_start: 0.8342 (mp10) cc_final: 0.8129 (mp10)
REVERT: D  322 MET cc_start: 0.7439 (mtt) cc_final: 0.6799 (mtt)
REVERT: D  343 GLN cc_start: 0.8331 (mp10) cc_final: 0.8120 (mp10)
REVERT: I  327 GLN cc_start: 0.7524 (tp-100) cc_final: 0.7222 (tp-100)
REVERT: I  336 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7629 (ttt)
REVERT: J  327 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7228 (tp-100)
REVERT: J  336 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7630 (ttt)
REVERT: K  322 MET cc_start: 0.8098 (mpp) cc_final: 0.7733 (mtt)
REVERT: L  322 MET cc_start: 0.8103 (mpp) cc_final: 0.7744 (mtt)
  outliers start: 26
  outliers final: 12
  residues processed: 150
  average time/residue: 0.0312
  time to fit residues: 6.1368
Evaluate side-chains
  164 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  327 GLN
Chi-restraints excluded: chain C residue  345 ASN
Chi-restraints excluded: chain C residue  346 GLN
Chi-restraints excluded: chain D residue  327 GLN
Chi-restraints excluded: chain D 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
Chi-restraints excluded: chain I residue  336 MET
Chi-restraints excluded: chain J residue  336 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 13 optimal weight:    0.1980
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.5265 r_free = 0.5265 target = 0.388738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.5731 r_free = 0.5731 target = 0.277928 restraints weight = 5058.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5735 r_free = 0.5735 target = 0.279681 restraints weight = 4085.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.5782 r_free = 0.5782 target = 0.281778 restraints weight = 3559.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.5783 r_free = 0.5783 target = 0.282085 restraints weight = 3222.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.5783 r_free = 0.5783 target = 0.282105 restraints weight = 3122.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.5112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.5834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3744  Z= 0.132
  Angle     :  0.665   7.505   4980  Z= 0.339
  Chirality :  0.040   0.107    480
  Planarity :  0.002   0.008    684
  Dihedral  :  5.577  17.134    528
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 27.01 %
    Favored  : 67.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.58 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.13), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHE G 313 
 TRP   0.017   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3744)
  covalent geometry    : angle       0.66491 ( 4980)
  hydrogen bonds       : bond        0.02084 (   30)
  hydrogen bonds       : angle       4.67211 (   90)

*********************** 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
  167 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7848 (pt0)
REVERT: A  336 MET cc_start: 0.7811 (ttt) cc_final: 0.7342 (ttt)
REVERT: B  331 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8022 (pt0)
REVERT: B  336 MET cc_start: 0.7833 (ttt) cc_final: 0.7415 (ttt)
REVERT: C  322 MET cc_start: 0.7308 (mtt) cc_final: 0.6643 (mmt)
REVERT: C  343 GLN cc_start: 0.8311 (mp10) cc_final: 0.8083 (mp10)
REVERT: D  322 MET cc_start: 0.7316 (mtt) cc_final: 0.6345 (mtt)
REVERT: D  327 GLN cc_start: 0.7657 (mt0) cc_final: 0.7370 (mt0)
REVERT: D  336 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6803 (tmt)
REVERT: D  343 GLN cc_start: 0.8313 (mp10) cc_final: 0.8102 (mp10)
REVERT: E  346 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7618 (tp-100)
REVERT: F  346 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7619 (tp-100)
REVERT: G  336 MET cc_start: 0.7509 (ttp) cc_final: 0.7302 (ttm)
REVERT: H  312 ASN cc_start: 0.7992 (t0) cc_final: 0.7765 (t0)
REVERT: J  336 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7582 (ttt)
REVERT: K  322 MET cc_start: 0.8032 (mpp) cc_final: 0.7686 (mtt)
REVERT: L  322 MET cc_start: 0.8031 (mpp) cc_final: 0.7691 (mtt)
  outliers start: 19
  outliers final: 8
  residues processed: 148
  average time/residue: 0.0423
  time to fit residues: 8.2466
Evaluate side-chains
  160 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  346 GLN
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue  345 ASN
Chi-restraints excluded: chain F residue  345 ASN
Chi-restraints excluded: chain G residue  345 ASN
Chi-restraints excluded: chain G residue  346 GLN
Chi-restraints excluded: chain H residue  345 ASN
Chi-restraints excluded: chain H residue  346 GLN
Chi-restraints excluded: chain J residue  323 MET
Chi-restraints excluded: chain J residue  336 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 46 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
C 327 GLN
** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 346 GLN
** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 346 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5227 r_free = 0.5227 target = 0.379126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.5651 r_free = 0.5651 target = 0.262302 restraints weight = 5143.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5653 r_free = 0.5653 target = 0.263442 restraints weight = 4439.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5656 r_free = 0.5656 target = 0.264869 restraints weight = 4037.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.5708 r_free = 0.5708 target = 0.266320 restraints weight = 3705.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.5709 r_free = 0.5709 target = 0.266689 restraints weight = 3519.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.5060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.6146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3744  Z= 0.249
  Angle     :  0.749   8.315   4980  Z= 0.394
  Chirality :  0.041   0.107    480
  Planarity :  0.002   0.010    684
  Dihedral  :  5.732  19.940    528
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 31.03 %
    Favored  : 64.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 PHE   0.016   0.002   PHE H 313 
 TRP   0.025   0.005   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 3744)
  covalent geometry    : angle       0.74884 ( 4980)
  hydrogen bonds       : bond        0.03051 (   30)
  hydrogen bonds       : angle       4.83006 (   90)

*********************** 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
  166 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8231 (pt0)
REVERT: A  336 MET cc_start: 0.7881 (ttt) cc_final: 0.7428 (ttt)
REVERT: B  331 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8311 (pt0)
REVERT: B  336 MET cc_start: 0.7927 (ttt) cc_final: 0.7535 (ttt)
REVERT: C  322 MET cc_start: 0.7414 (mtt) cc_final: 0.6552 (mtt)
REVERT: C  343 GLN cc_start: 0.8287 (mp10) cc_final: 0.7974 (mp10)
REVERT: D  322 MET cc_start: 0.7529 (mtt) cc_final: 0.6760 (mtt)
REVERT: D  343 GLN cc_start: 0.8313 (mp10) cc_final: 0.8016 (mp10)
REVERT: G  343 GLN cc_start: 0.8344 (mp10) cc_final: 0.8035 (mp10)
REVERT: H  343 GLN cc_start: 0.8358 (mp10) cc_final: 0.8035 (mp10)
REVERT: J  336 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7741 (ttt)
REVERT: K  322 MET cc_start: 0.8113 (mpp) cc_final: 0.7757 (mtt)
REVERT: L  322 MET cc_start: 0.8110 (mpp) cc_final: 0.7764 (mtt)
  outliers start: 14
  outliers final: 8
  residues processed: 152
  average time/residue: 0.0396
  time to fit residues: 7.9324
Evaluate side-chains
  161 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  327 GLN
Chi-restraints excluded: chain C residue  346 GLN
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 H residue  344 GLN
Chi-restraints excluded: chain J residue  336 MET
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 8 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   chunk 41 optimal weight:    0.4980
   chunk 18 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    0.9584

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5273 r_free = 0.5273 target = 0.388455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.5732 r_free = 0.5732 target = 0.274775 restraints weight = 5263.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.5756 r_free = 0.5756 target = 0.276828 restraints weight = 4431.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5759 r_free = 0.5759 target = 0.277803 restraints weight = 3908.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.5762 r_free = 0.5762 target = 0.278777 restraints weight = 3616.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5799 r_free = 0.5799 target = 0.279879 restraints weight = 3395.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.5114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.6477

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= 0.155
  Angle     :  0.715   8.031   4980  Z= 0.363
  Chirality :  0.039   0.105    480
  Planarity :  0.002   0.011    684
  Dihedral  :  5.551  19.800    528
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 33.05 %
    Favored  : 62.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.68 (0.18), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.56 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.002   PHE H 313 
 TRP   0.016   0.003   TRP H 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3744)
  covalent geometry    : angle       0.71453 ( 4980)
  hydrogen bonds       : bond        0.02429 (   30)
  hydrogen bonds       : angle       4.73628 (   90)

*********************** 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
  163 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8083 (pt0)
REVERT: A  336 MET cc_start: 0.7629 (ttt) cc_final: 0.7401 (ttt)
REVERT: B  331 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8256 (pt0)
REVERT: B  336 MET cc_start: 0.7788 (ttt) cc_final: 0.7493 (ttt)
REVERT: C  322 MET cc_start: 0.7286 (mtt) cc_final: 0.6381 (mtt)
REVERT: C  343 GLN cc_start: 0.8211 (mp10) cc_final: 0.7940 (mp10)
REVERT: D  322 MET cc_start: 0.7361 (mtt) cc_final: 0.6703 (mtt)
REVERT: D  336 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7067 (tmt)
REVERT: D  343 GLN cc_start: 0.8217 (mp10) cc_final: 0.7962 (mp10)
REVERT: G  343 GLN cc_start: 0.8370 (mp10) cc_final: 0.8050 (mp10)
REVERT: H  343 GLN cc_start: 0.8382 (mp10) cc_final: 0.8033 (mp10)
REVERT: K  322 MET cc_start: 0.8026 (mpp) cc_final: 0.7654 (mtt)
REVERT: L  312 ASN cc_start: 0.7534 (t0) cc_final: 0.6925 (t0)
REVERT: L  322 MET cc_start: 0.8088 (mpp) cc_final: 0.7729 (mtt)
  outliers start: 14
  outliers final: 5
  residues processed: 149
  average time/residue: 0.0408
  time to fit residues: 7.9890
Evaluate side-chains
  151 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain D residue  336 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.5220 r_free = 0.5220 target = 0.386585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.5733 r_free = 0.5733 target = 0.269217 restraints weight = 5306.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.5736 r_free = 0.5736 target = 0.270372 restraints weight = 4554.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5768 r_free = 0.5768 target = 0.271938 restraints weight = 4150.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.5768 r_free = 0.5768 target = 0.272002 restraints weight = 3875.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5768 r_free = 0.5768 target = 0.272002 restraints weight = 3851.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.5053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.6691

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= 0.213
  Angle     :  0.821   8.478   4980  Z= 0.409
  Chirality :  0.040   0.105    480
  Planarity :  0.002   0.010    684
  Dihedral  :  5.727  21.733    528
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 34.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.73 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.60 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHE G 313 
 TRP   0.021   0.004   TRP E 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 3744)
  covalent geometry    : angle       0.82135 ( 4980)
  hydrogen bonds       : bond        0.02883 (   30)
  hydrogen bonds       : angle       4.93005 (   90)

*********************** 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: 12
    poor density    : 150
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8146 (pt0)
REVERT: A  336 MET cc_start: 0.7688 (ttt) cc_final: 0.7414 (ttt)
REVERT: B  331 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8378 (pt0)
REVERT: B  336 MET cc_start: 0.7806 (ttt) cc_final: 0.7499 (ttt)
REVERT: C  322 MET cc_start: 0.7442 (mtt) cc_final: 0.6584 (mtt)
REVERT: C  343 GLN cc_start: 0.8271 (mp10) cc_final: 0.7969 (mp10)
REVERT: D  322 MET cc_start: 0.7401 (mtt) cc_final: 0.6768 (mtt)
REVERT: D  336 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7106 (tmt)
REVERT: D  343 GLN cc_start: 0.8249 (mp10) cc_final: 0.7988 (mp10)
REVERT: F  307 MET cc_start: 0.7922 (ttt) cc_final: 0.7691 (ttt)
REVERT: G  343 GLN cc_start: 0.8301 (mp10) cc_final: 0.8005 (mp10)
REVERT: G  346 GLN cc_start: 0.8095 (tp40) cc_final: 0.7645 (tp40)
REVERT: H  343 GLN cc_start: 0.8311 (mp10) cc_final: 0.7975 (mp10)
REVERT: H  346 GLN cc_start: 0.8030 (tp40) cc_final: 0.7573 (tp40)
REVERT: K  322 MET cc_start: 0.8149 (mpp) cc_final: 0.7731 (mpp)
REVERT: L  312 ASN cc_start: 0.7475 (t0) cc_final: 0.7269 (t0)
REVERT: L  322 MET cc_start: 0.8152 (mpp) cc_final: 0.7725 (mpp)
  outliers start: 12
  outliers final: 5
  residues processed: 150
  average time/residue: 0.0468
  time to fit residues: 9.2258
Evaluate side-chains
  153 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 145
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  345 ASN
Chi-restraints excluded: chain D residue  336 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 12 optimal weight:    0.0970
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.5278 r_free = 0.5278 target = 0.411514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.5832 r_free = 0.5832 target = 0.292483 restraints weight = 5590.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.5832 r_free = 0.5832 target = 0.292483 restraints weight = 4909.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5832 r_free = 0.5832 target = 0.292483 restraints weight = 4909.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5832 r_free = 0.5832 target = 0.292483 restraints weight = 4909.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5832 r_free = 0.5832 target = 0.292483 restraints weight = 4909.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.5066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.6920

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= 0.174
  Angle     :  0.826  10.055   4980  Z= 0.406
  Chirality :  0.039   0.105    480
  Planarity :  0.002   0.010    684
  Dihedral  :  5.737  21.690    528
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 32.47 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.77 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.63 (0.14), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHE H 313 
 TRP   0.016   0.003   TRP F 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3744)
  covalent geometry    : angle       0.82588 ( 4980)
  hydrogen bonds       : bond        0.02699 (   30)
  hydrogen bonds       : angle       4.72692 (   90)

*********************** 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
  162 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8070 (pt0)
REVERT: A  336 MET cc_start: 0.7672 (ttt) cc_final: 0.7432 (ttt)
REVERT: B  331 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8237 (pt0)
REVERT: B  336 MET cc_start: 0.7734 (ttt) cc_final: 0.7478 (ttt)
REVERT: C  322 MET cc_start: 0.7179 (mtt) cc_final: 0.6791 (mmt)
REVERT: C  343 GLN cc_start: 0.8251 (mp10) cc_final: 0.7946 (mp10)
REVERT: D  322 MET cc_start: 0.7291 (mtt) cc_final: 0.6586 (mtt)
REVERT: D  336 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7757 (tmm)
REVERT: D  343 GLN cc_start: 0.8244 (mp10) cc_final: 0.8015 (mp10)
REVERT: G  343 GLN cc_start: 0.8313 (mp10) cc_final: 0.7943 (mp10)
REVERT: H  343 GLN cc_start: 0.8308 (mp10) cc_final: 0.7907 (mp10)
REVERT: H  346 GLN cc_start: 0.7976 (tp40) cc_final: 0.7762 (tp-100)
REVERT: K  322 MET cc_start: 0.8085 (mpp) cc_final: 0.7732 (mpp)
REVERT: L  311 MET cc_start: 0.7271 (ptt) cc_final: 0.7009 (ptt)
REVERT: L  322 MET cc_start: 0.8098 (mpp) cc_final: 0.7741 (mpp)
  outliers start: 11
  outliers final: 7
  residues processed: 151
  average time/residue: 0.0419
  time to fit residues: 8.3391
Evaluate side-chains
  156 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  345 ASN
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain D 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 19 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    0.3980
   chunk 2 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.8386

-------------------------------------------------------------------------------
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 = 0.5232 r_free = 0.5232 target = 0.385874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.5724 r_free = 0.5724 target = 0.266794 restraints weight = 5426.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.5724 r_free = 0.5724 target = 0.266797 restraints weight = 4812.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5724 r_free = 0.5724 target = 0.266797 restraints weight = 4811.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5724 r_free = 0.5724 target = 0.266797 restraints weight = 4811.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5724 r_free = 0.5724 target = 0.266797 restraints weight = 4811.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.5033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.7050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3744  Z= 0.221
  Angle     :  0.866   9.402   4980  Z= 0.429
  Chirality :  0.040   0.105    480
  Planarity :  0.002   0.011    684
  Dihedral  :  5.827  24.590    528
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 34.48 %
    Favored  : 62.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.88 (0.19), residues: 516
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.15), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.016   0.002   PHE H 313 
 TRP   0.023   0.004   TRP E 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 3744)
  covalent geometry    : angle       0.86607 ( 4980)
  hydrogen bonds       : bond        0.03113 (   30)
  hydrogen bonds       : angle       4.89448 (   90)

********************** 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
  156 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 147
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  331 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8085 (pt0)
REVERT: A  336 MET cc_start: 0.7674 (ttt) cc_final: 0.7389 (ttt)
REVERT: B  331 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8156 (pt0)
REVERT: B  336 MET cc_start: 0.7752 (ttt) cc_final: 0.7461 (ttt)
REVERT: C  322 MET cc_start: 0.7480 (mtt) cc_final: 0.6519 (mtt)
REVERT: C  343 GLN cc_start: 0.8255 (mp10) cc_final: 0.7969 (mp10)
REVERT: D  322 MET cc_start: 0.7480 (mtt) cc_final: 0.6601 (mtt)
REVERT: D  336 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7133 (tmt)
REVERT: D  343 GLN cc_start: 0.8255 (mp10) cc_final: 0.8023 (mp10)
REVERT: F  307 MET cc_start: 0.8001 (ttt) cc_final: 0.7602 (ttt)
REVERT: G  343 GLN cc_start: 0.8302 (mp10) cc_final: 0.7951 (mp10)
REVERT: G  346 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7931 (tp40)
REVERT: H  343 GLN cc_start: 0.8299 (mp10) cc_final: 0.7897 (mp10)
REVERT: I  344 GLN cc_start: 0.8527 (mp10) cc_final: 0.8226 (mp10)
REVERT: J  344 GLN cc_start: 0.8534 (mp10) cc_final: 0.8237 (mp10)
REVERT: K  322 MET cc_start: 0.8148 (mpp) cc_final: 0.7837 (mpp)
REVERT: L  311 MET cc_start: 0.7217 (ptt) cc_final: 0.6971 (ptt)
REVERT: L  322 MET cc_start: 0.8148 (mpp) cc_final: 0.7829 (mpp)
  outliers start: 9
  outliers final: 5
  residues processed: 147
  average time/residue: 0.0472
  time to fit residues: 9.0917
Evaluate side-chains
  153 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 145
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
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 D residue  336 MET
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 0 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C 344 GLN
D 344 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5262 r_free = 0.5262 target = 0.394139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.5786 r_free = 0.5786 target = 0.278383 restraints weight = 5355.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.5788 r_free = 0.5788 target = 0.279095 restraints weight = 4711.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.5832 r_free = 0.5832 target = 0.280990 restraints weight = 4416.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.5832 r_free = 0.5832 target = 0.281016 restraints weight = 4100.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5832 r_free = 0.5832 target = 0.281016 restraints weight = 4090.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.5095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.7194

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= 0.152
  Angle     :  0.780   7.581   4980  Z= 0.391
  Chirality :  0.039   0.104    480
  Planarity :  0.002   0.011    684
  Dihedral  :  5.604  23.274    528
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 35.92 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.86 (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
 PHE   0.016   0.002   PHE H 313 
 TRP   0.016   0.003   TRP H 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3744)
  covalent geometry    : angle       0.77956 ( 4980)
  hydrogen bonds       : bond        0.02712 (   30)
  hydrogen bonds       : angle       4.85394 (   90)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 669.83 seconds
wall clock time: 12 minutes 9.75 seconds (729.75 seconds total)