Starting phenix.real_space_refine
on Fri Oct 10 12:52:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qxb_18717/10_2025/8qxb_18717.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qxb_18717/10_2025/8qxb_18717.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qxb_18717/10_2025/8qxb_18717.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qxb_18717/10_2025/8qxb_18717.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qxb_18717/10_2025/8qxb_18717.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qxb_18717/10_2025/8qxb_18717.cif"
  }
  resolution = 3.86
  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=   0.002
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     126      5.16       5
     C    3348      2.51       5
     N     990      2.21       5
     O    1080      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5544
  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, M, N, O, P, Q, R
  Time building chain proxies: 0.60, per 1000 atoms: 0.11
  Number of scatterers: 5544
  At special positions: 0
  Unit cell: (109.2, 104, 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     126     16.00
     O    1080      8.00
     N     990      7.00
     C    3348      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: 0.33
  Conformation dependent library (CDL) restraints added in 178.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1332

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318
      removed outlier: 6.021A  pdb=" N   SER A 317 " --> pdb=" O   ILE D 318 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER D 317 " --> pdb=" O   ILE G 318 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER G 317 " --> pdb=" O   ILE J 318 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   SER J 317 " --> pdb=" O   ILE M 318 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER M 317 " --> pdb=" O   ILE P 318 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 331
      removed outlier: 5.905A  pdb=" N   ALA A 328 " --> pdb=" O   ALA D 329 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   GLN D 331 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU A 330 " --> pdb=" O   GLN D 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA D 328 " --> pdb=" O   ALA G 329 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   GLN G 331 " --> pdb=" O   ALA D 328 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU D 330 " --> pdb=" O   GLN G 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA G 328 " --> pdb=" O   ALA J 329 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLN J 331 " --> pdb=" O   ALA G 328 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   LEU G 330 " --> pdb=" O   GLN J 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA J 328 " --> pdb=" O   ALA M 329 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   GLN M 331 " --> pdb=" O   ALA J 328 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   LEU J 330 " --> pdb=" O   GLN M 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA M 328 " --> pdb=" O   ALA P 329 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   GLN P 331 " --> pdb=" O   ALA M 328 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   LEU M 330 " --> pdb=" O   GLN P 331 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 318
      removed outlier: 6.022A  pdb=" N   SER B 317 " --> pdb=" O   ILE E 318 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER E 317 " --> pdb=" O   ILE H 318 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER H 317 " --> pdb=" O   ILE K 318 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER K 317 " --> pdb=" O   ILE N 318 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER N 317 " --> pdb=" O   ILE Q 318 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 331
      removed outlier: 5.905A  pdb=" N   ALA B 328 " --> pdb=" O   ALA E 329 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   GLN E 331 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU B 330 " --> pdb=" O   GLN E 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA E 328 " --> pdb=" O   ALA H 329 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLN H 331 " --> pdb=" O   ALA E 328 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   LEU E 330 " --> pdb=" O   GLN H 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA H 328 " --> pdb=" O   ALA K 329 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLN K 331 " --> pdb=" O   ALA H 328 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU H 330 " --> pdb=" O   GLN K 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA K 328 " --> pdb=" O   ALA N 329 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   GLN N 331 " --> pdb=" O   ALA K 328 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU K 330 " --> pdb=" O   GLN N 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA N 328 " --> pdb=" O   ALA Q 329 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLN Q 331 " --> pdb=" O   ALA N 328 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU N 330 " --> pdb=" O   GLN Q 331 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 318
      removed outlier: 6.022A  pdb=" N   SER C 317 " --> pdb=" O   ILE F 318 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER F 317 " --> pdb=" O   ILE I 318 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER I 317 " --> pdb=" O   ILE L 318 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   SER L 317 " --> pdb=" O   ILE O 318 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER O 317 " --> pdb=" O   ILE R 318 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 331
      removed outlier: 5.905A  pdb=" N   ALA C 328 " --> pdb=" O   ALA F 329 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLN F 331 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU C 330 " --> pdb=" O   GLN F 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA F 328 " --> pdb=" O   ALA I 329 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLN I 331 " --> pdb=" O   ALA F 328 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU F 330 " --> pdb=" O   GLN I 331 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   ALA I 328 " --> pdb=" O   ALA L 329 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLN L 331 " --> pdb=" O   ALA I 328 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   LEU I 330 " --> pdb=" O   GLN L 331 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   ALA L 328 " --> pdb=" O   ALA O 329 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLN O 331 " --> pdb=" O   ALA L 328 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   LEU L 330 " --> pdb=" O   GLN O 331 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   ALA O 328 " --> pdb=" O   ALA R 329 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLN R 331 " --> pdb=" O   ALA O 328 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   LEU O 330 " --> pdb=" O   GLN R 331 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    No hydrogen bonds 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: 0.05

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 990
        1.32 -     1.44: 1440
        1.44 -     1.57: 2934
        1.57 -     1.69: 0
        1.69 -     1.82: 252
  Bond restraints: 5616
  Sorted by residual:
  bond pdb=" C   SER J 317 "
       pdb=" O   SER J 317 "
    ideal  model  delta    sigma   weight residual
    1.235  1.193  0.043 1.13e-02 7.83e+03 1.41e+01
  bond pdb=" C   SER C 317 "
       pdb=" O   SER C 317 "
    ideal  model  delta    sigma   weight residual
    1.235  1.193  0.042 1.13e-02 7.83e+03 1.41e+01
  bond pdb=" C   SER A 317 "
       pdb=" O   SER A 317 "
    ideal  model  delta    sigma   weight residual
    1.235  1.193  0.042 1.13e-02 7.83e+03 1.41e+01
  bond pdb=" C   SER M 317 "
       pdb=" O   SER M 317 "
    ideal  model  delta    sigma   weight residual
    1.235  1.193  0.042 1.13e-02 7.83e+03 1.41e+01
  bond pdb=" C   SER D 317 "
       pdb=" O   SER D 317 "
    ideal  model  delta    sigma   weight residual
    1.235  1.193  0.042 1.13e-02 7.83e+03 1.41e+01
  ... (remaining 5611 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 3956
        1.33 -     2.66: 1559
        2.66 -     3.99: 1205
        3.99 -     5.32: 601
        5.32 -     6.66: 149
  Bond angle restraints: 7470
  Sorted by residual:
  angle pdb=" N   GLN O 327 "
        pdb=" CA  GLN O 327 "
        pdb=" C   GLN O 327 "
      ideal   model   delta    sigma   weight residual
     111.07  104.91    6.16 1.07e+00 8.73e-01 3.32e+01
  angle pdb=" N   GLN H 327 "
        pdb=" CA  GLN H 327 "
        pdb=" C   GLN H 327 "
      ideal   model   delta    sigma   weight residual
     111.07  104.91    6.16 1.07e+00 8.73e-01 3.31e+01
  angle pdb=" N   GLN N 327 "
        pdb=" CA  GLN N 327 "
        pdb=" C   GLN N 327 "
      ideal   model   delta    sigma   weight residual
     111.07  104.91    6.16 1.07e+00 8.73e-01 3.31e+01
  angle pdb=" N   GLN J 327 "
        pdb=" CA  GLN J 327 "
        pdb=" C   GLN J 327 "
      ideal   model   delta    sigma   weight residual
     111.07  104.91    6.16 1.07e+00 8.73e-01 3.31e+01
  angle pdb=" N   GLN G 327 "
        pdb=" CA  GLN G 327 "
        pdb=" C   GLN G 327 "
      ideal   model   delta    sigma   weight residual
     111.07  104.92    6.15 1.07e+00 8.73e-01 3.30e+01
  ... (remaining 7465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.03 -    15.30: 2880
       15.30 -    30.56: 234
       30.56 -    45.83: 108
       45.83 -    61.10: 36
       61.10 -    76.36: 36
  Dihedral angle restraints: 3294
    sinusoidal: 1170
      harmonic: 2124
  Sorted by residual:
  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 -114.29   -8.31     0      2.50e+00 1.60e-01 1.10e+01
  dihedral pdb=" C   PHE F 316 "
           pdb=" N   PHE F 316 "
           pdb=" CA  PHE F 316 "
           pdb=" CB  PHE F 316 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.29   -8.31     0      2.50e+00 1.60e-01 1.10e+01
  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 -114.30   -8.30     0      2.50e+00 1.60e-01 1.10e+01
  ... (remaining 3291 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 242
       0.053 -    0.106: 208
       0.106 -    0.160: 162
       0.160 -    0.213: 54
       0.213 -    0.266: 54
  Chirality restraints: 720
  Sorted by residual:
  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    2.24    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  TRP M 334 "
            pdb=" N   TRP M 334 "
            pdb=" C   TRP M 334 "
            pdb=" CB  TRP M 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  TRP D 334 "
            pdb=" N   TRP D 334 "
            pdb=" C   TRP D 334 "
            pdb=" CB  TRP D 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 717 not shown)

  Planarity restraints: 1026
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO Q 320 "    0.014 2.00e-02 2.50e+03   3.00e-02 9.00e+00
        pdb=" C   PRO Q 320 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   PRO Q 320 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ALA Q 321 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO H 320 "    0.014 2.00e-02 2.50e+03   2.99e-02 8.94e+00
        pdb=" C   PRO H 320 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   PRO H 320 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ALA H 321 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO M 320 "   -0.014 2.00e-02 2.50e+03   2.99e-02 8.93e+00
        pdb=" C   PRO M 320 "    0.052 2.00e-02 2.50e+03
        pdb=" O   PRO M 320 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ALA M 321 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1023 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 2559
        2.99 -     3.47: 5265
        3.47 -     3.94: 9271
        3.94 -     4.42: 10560
        4.42 -     4.90: 20365
  Nonbonded interactions: 48020
  Sorted by model distance:
  nonbonded pdb=" N   PRO B 320 "
            pdb=" O   PRO B 320 "
     model   vdw
     2.508 2.496
  nonbonded pdb=" N   PRO A 320 "
            pdb=" O   PRO A 320 "
     model   vdw
     2.509 2.496
  nonbonded pdb=" N   PRO P 320 "
            pdb=" O   PRO P 320 "
     model   vdw
     2.509 2.496
  nonbonded pdb=" N   PRO C 320 "
            pdb=" O   PRO C 320 "
     model   vdw
     2.509 2.496
  nonbonded pdb=" N   PRO H 320 "
            pdb=" O   PRO H 320 "
     model   vdw
     2.509 2.496
  ... (remaining 48015 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: 0.02
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'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.880
  Find NCS groups from input model:        0.060
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
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   0.046   5616  Z= 1.055
  Angle     :  2.276   6.656   7470  Z= 1.679
  Chirality :  0.115   0.266    720
  Planarity :  0.010   0.030   1026
  Dihedral  : 18.192  76.362   1962
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.24 %
    Favored  : 82.76 %
  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 aren not related in a simple way.
  whole: -3.90 (0.18), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.14), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.003   PHE Q 313 
 TRP   0.047   0.010   TRP O 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.01418 ( 5616)
  covalent geometry    : angle       2.27580 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 321
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.8052 (ttt) cc_final: 0.7837 (ttp)
REVERT: A  323 MET cc_start: 0.6862 (ttm) cc_final: 0.6635 (ttt)
REVERT: A  334 TRP cc_start: 0.6777 (p90) cc_final: 0.5382 (m100)
REVERT: B  307 MET cc_start: 0.8224 (ttt) cc_final: 0.7900 (ttp)
REVERT: B  334 TRP cc_start: 0.6702 (p90) cc_final: 0.4991 (m100)
REVERT: C  334 TRP cc_start: 0.6713 (p90) cc_final: 0.4806 (m100)
REVERT: E  305 SER cc_start: 0.6314 (m) cc_final: 0.6098 (m)
REVERT: E  307 MET cc_start: 0.8478 (ttt) cc_final: 0.8097 (ttt)
REVERT: F  307 MET cc_start: 0.8411 (ttt) cc_final: 0.8178 (ttt)
REVERT: F  334 TRP cc_start: 0.6975 (p90) cc_final: 0.6637 (p90)
REVERT: H  307 MET cc_start: 0.8441 (ttt) cc_final: 0.8215 (ttm)
REVERT: I  305 SER cc_start: 0.6337 (m) cc_final: 0.6025 (m)
REVERT: K  305 SER cc_start: 0.6294 (m) cc_final: 0.6072 (m)
REVERT: L  307 MET cc_start: 0.8216 (ttt) cc_final: 0.7780 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 321
  average time/residue: 0.0525
  time to fit residues: 23.7356
Evaluate side-chains
  231 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 327 GLN
B 327 GLN
C 327 GLN
E 343 GLN
** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 344 GLN
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 343 GLN
I 344 GLN
** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 343 GLN
** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 343 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4930 r_free = 0.4930 target = 0.318428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.248375 restraints weight = 8534.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 89)----------------|
| r_work = 0.5064 r_free = 0.5064 target = 0.247265 restraints weight = 11521.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.5067 r_free = 0.5067 target = 0.246990 restraints weight = 10687.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5072 r_free = 0.5072 target = 0.247525 restraints weight = 9515.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5072 r_free = 0.5072 target = 0.247600 restraints weight = 8598.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.4480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6286
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5616  Z= 0.138
  Angle     :  0.683   7.134   7470  Z= 0.347
  Chirality :  0.039   0.122    720
  Planarity :  0.003   0.028   1026
  Dihedral  :  5.375  15.205    792
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 40.04 %
    Favored  : 57.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.03 (0.20), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.15), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.007   0.001   PHE L 313 
 TRP   0.019   0.003   TRP A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5616)
  covalent geometry    : angle       0.68304 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 251
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 MET cc_start: 0.7159 (mmt) cc_final: 0.6812 (ptt)
REVERT: A  323 MET cc_start: 0.7351 (ttm) cc_final: 0.6776 (ttt)
REVERT: B  339 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7654 (ptp)
REVERT: B  340 LEU cc_start: 0.8572 (tt) cc_final: 0.8364 (tt)
REVERT: C  340 LEU cc_start: 0.8560 (tt) cc_final: 0.8343 (tt)
REVERT: D  327 GLN cc_start: 0.8871 (tp40) cc_final: 0.7895 (tm-30)
REVERT: D  339 MET cc_start: 0.8391 (ptm) cc_final: 0.7851 (ptp)
REVERT: E  327 GLN cc_start: 0.8879 (tp40) cc_final: 0.7802 (tm-30)
REVERT: F  327 GLN cc_start: 0.8849 (tp40) cc_final: 0.8068 (tp40)
REVERT: F  339 MET cc_start: 0.8043 (ttp) cc_final: 0.7574 (mtt)
REVERT: F  346 GLN cc_start: 0.8798 (mt0) cc_final: 0.7997 (mt0)
REVERT: G  311 MET cc_start: 0.8072 (ptp) cc_final: 0.7683 (ptp)
REVERT: G  322 MET cc_start: 0.6074 (mtt) cc_final: 0.4073 (ptp)
REVERT: G  327 GLN cc_start: 0.8865 (tp40) cc_final: 0.8087 (tm-30)
REVERT: H  322 MET cc_start: 0.7292 (mmt) cc_final: 0.7066 (mmt)
REVERT: H  327 GLN cc_start: 0.8777 (tp40) cc_final: 0.7687 (tp40)
REVERT: H  346 GLN cc_start: 0.8802 (mt0) cc_final: 0.7447 (mt0)
REVERT: I  305 SER cc_start: 0.7764 (m) cc_final: 0.7512 (p)
REVERT: I  311 MET cc_start: 0.8371 (ptp) cc_final: 0.8104 (ptp)
REVERT: I  322 MET cc_start: 0.7403 (mmt) cc_final: 0.6877 (mmt)
REVERT: I  327 GLN cc_start: 0.8606 (tp40) cc_final: 0.7952 (tm-30)
REVERT: J  327 GLN cc_start: 0.8477 (tp40) cc_final: 0.7825 (tm-30)
REVERT: J  345 ASN cc_start: 0.8204 (m110) cc_final: 0.7794 (m110)
REVERT: K  327 GLN cc_start: 0.8772 (tp40) cc_final: 0.7862 (tm-30)
REVERT: L  327 GLN cc_start: 0.8574 (tp40) cc_final: 0.8016 (tm-30)
REVERT: M  327 GLN cc_start: 0.8468 (tp40) cc_final: 0.8002 (tm-30)
REVERT: M  334 TRP cc_start: 0.8076 (p90) cc_final: 0.7848 (p90)
REVERT: M  336 MET cc_start: 0.7269 (ttp) cc_final: 0.6248 (ttp)
REVERT: N  327 GLN cc_start: 0.8903 (tp40) cc_final: 0.7895 (tp40)
REVERT: N  339 MET cc_start: 0.8297 (ptm) cc_final: 0.7816 (ptp)
REVERT: N  346 GLN cc_start: 0.8257 (mt0) cc_final: 0.7966 (mt0)
REVERT: O  311 MET cc_start: 0.7998 (ptp) cc_final: 0.7587 (ptp)
REVERT: O  322 MET cc_start: 0.7030 (mmm) cc_final: 0.6616 (mmt)
REVERT: O  327 GLN cc_start: 0.8851 (tp40) cc_final: 0.8489 (tm-30)
REVERT: O  334 TRP cc_start: 0.7940 (p90) cc_final: 0.7550 (p90)
REVERT: P  311 MET cc_start: 0.8416 (ptp) cc_final: 0.7950 (ptp)
REVERT: P  336 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6967 (ttt)
REVERT: Q  311 MET cc_start: 0.8445 (ptp) cc_final: 0.8200 (ptp)
REVERT: Q  313 PHE cc_start: 0.7918 (m-10) cc_final: 0.7642 (m-10)
REVERT: Q  337 MET cc_start: 0.7210 (mmt) cc_final: 0.6620 (mtt)
REVERT: Q  339 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7662 (tpt)
REVERT: R  311 MET cc_start: 0.8465 (ptp) cc_final: 0.8218 (ptp)
REVERT: R  313 PHE cc_start: 0.7991 (m-10) cc_final: 0.7672 (m-10)
  outliers start: 15
  outliers final: 5
  residues processed: 253
  average time/residue: 0.0517
  time to fit residues: 18.3268
Evaluate side-chains
  229 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 221
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain J residue  305 SER
Chi-restraints excluded: chain P residue  305 SER
Chi-restraints excluded: chain P residue  336 MET
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain Q residue  339 MET
Chi-restraints excluded: chain R residue  305 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0070
   chunk 40 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0470
   chunk 64 optimal weight:    0.0370
   chunk 6 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0470
   chunk 12 optimal weight:    9.9990
   overall best weight:    0.2274

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 344 GLN
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 344 GLN
** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.243698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.156151 restraints weight = 7312.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.161136 restraints weight = 4057.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.163865 restraints weight = 2795.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.165792 restraints weight = 2255.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.166822 restraints weight = 1965.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.4459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6080
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5616  Z= 0.097
  Angle     :  0.621   7.348   7470  Z= 0.300
  Chirality :  0.039   0.128    720
  Planarity :  0.002   0.031   1026
  Dihedral  :  4.895  16.309    792
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 37.55 %
    Favored  : 58.24 %
  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 aren not related in a simple way.
  whole: -4.00 (0.21), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.16), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.001   PHE D 313 
 TRP   0.015   0.002   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5616)
  covalent geometry    : angle       0.62111 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 253
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 MET cc_start: 0.6634 (ttm) cc_final: 0.6307 (ttt)
REVERT: B  307 MET cc_start: 0.8633 (ttm) cc_final: 0.8322 (tpp)
REVERT: B  311 MET cc_start: 0.8505 (ptp) cc_final: 0.7774 (ptp)
REVERT: B  319 ASN cc_start: 0.8579 (m110) cc_final: 0.8343 (m110)
REVERT: B  323 MET cc_start: 0.6437 (ttt) cc_final: 0.5903 (ttm)
REVERT: B  339 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7566 (ttm)
REVERT: D  322 MET cc_start: 0.6907 (ptp) cc_final: 0.6185 (mtt)
REVERT: E  346 GLN cc_start: 0.8944 (mt0) cc_final: 0.8597 (tt0)
REVERT: F  339 MET cc_start: 0.8121 (ttp) cc_final: 0.7721 (mtt)
REVERT: G  327 GLN cc_start: 0.8756 (tp40) cc_final: 0.8150 (tm-30)
REVERT: G  336 MET cc_start: 0.7617 (ttp) cc_final: 0.7067 (ttt)
REVERT: H  322 MET cc_start: 0.7241 (mmt) cc_final: 0.6445 (mmt)
REVERT: H  327 GLN cc_start: 0.8728 (tp40) cc_final: 0.7691 (tp40)
REVERT: H  336 MET cc_start: 0.7579 (ttp) cc_final: 0.7306 (ttt)
REVERT: H  346 GLN cc_start: 0.8782 (mt0) cc_final: 0.7393 (mt0)
REVERT: I  305 SER cc_start: 0.7490 (m) cc_final: 0.7252 (p)
REVERT: I  311 MET cc_start: 0.8168 (ptp) cc_final: 0.7925 (ptp)
REVERT: I  313 PHE cc_start: 0.8077 (m-10) cc_final: 0.7441 (m-10)
REVERT: I  322 MET cc_start: 0.7239 (mmt) cc_final: 0.6362 (mmt)
REVERT: J  322 MET cc_start: 0.7083 (mmt) cc_final: 0.6448 (mmt)
REVERT: J  327 GLN cc_start: 0.8368 (tp40) cc_final: 0.7675 (tm-30)
REVERT: J  336 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6486 (ttt)
REVERT: J  339 MET cc_start: 0.8830 (ptm) cc_final: 0.8536 (ptp)
REVERT: K  327 GLN cc_start: 0.8676 (tp40) cc_final: 0.7812 (tm-30)
REVERT: K  337 MET cc_start: 0.7205 (mmt) cc_final: 0.6868 (mmt)
REVERT: L  327 GLN cc_start: 0.8511 (tp40) cc_final: 0.8100 (tm-30)
REVERT: M  327 GLN cc_start: 0.8536 (tp40) cc_final: 0.8020 (tp40)
REVERT: N  327 GLN cc_start: 0.8861 (tp40) cc_final: 0.7896 (tp40)
REVERT: N  346 GLN cc_start: 0.8334 (mt0) cc_final: 0.7925 (mt0)
REVERT: O  322 MET cc_start: 0.7136 (mmt) cc_final: 0.6454 (mmt)
REVERT: O  327 GLN cc_start: 0.8927 (tp40) cc_final: 0.8491 (tm-30)
REVERT: O  334 TRP cc_start: 0.7749 (p90) cc_final: 0.7432 (p90)
REVERT: O  336 MET cc_start: 0.6948 (ttt) cc_final: 0.6728 (ttt)
REVERT: P  311 MET cc_start: 0.8404 (ptp) cc_final: 0.8164 (ptp)
REVERT: Q  311 MET cc_start: 0.8519 (ptp) cc_final: 0.8218 (ptp)
REVERT: Q  339 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7436 (mmp)
REVERT: R  311 MET cc_start: 0.8551 (ptp) cc_final: 0.8344 (ptp)
REVERT: R  336 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6762 (ttt)
  outliers start: 22
  outliers final: 11
  residues processed: 258
  average time/residue: 0.0524
  time to fit residues: 19.0771
Evaluate side-chains
  242 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 227
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue  336 MET
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain J residue  305 SER
Chi-restraints excluded: chain J residue  336 MET
Chi-restraints excluded: chain L residue  305 SER
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain M residue  344 GLN
Chi-restraints excluded: chain N residue  305 SER
Chi-restraints excluded: chain P residue  305 SER
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain Q residue  339 MET
Chi-restraints excluded: chain R residue  305 SER
Chi-restraints excluded: chain R residue  336 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 343 GLN
** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 343 GLN
** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.234249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.140897 restraints weight = 7317.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.145815 restraints weight = 4221.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.148666 restraints weight = 2997.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.150292 restraints weight = 2440.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.151245 restraints weight = 2165.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.4307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.5345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5616  Z= 0.138
  Angle     :  0.645   7.590   7470  Z= 0.309
  Chirality :  0.038   0.120    720
  Planarity :  0.004   0.041   1026
  Dihedral  :  4.992  15.424    792
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 36.78 %
    Favored  : 59.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.98 (0.20), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.15), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.012   0.001   PHE D 313 
 TRP   0.017   0.003   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5616)
  covalent geometry    : angle       0.64512 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 235
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  322 MET cc_start: 0.5213 (mmt) cc_final: 0.4963 (pmm)
REVERT: C  322 MET cc_start: 0.5741 (mmt) cc_final: 0.4673 (ptp)
REVERT: D  322 MET cc_start: 0.5625 (ptp) cc_final: 0.5368 (mtt)
REVERT: D  323 MET cc_start: 0.6891 (ttt) cc_final: 0.6517 (ttt)
REVERT: D  339 MET cc_start: 0.7951 (ptm) cc_final: 0.7535 (ptp)
REVERT: E  322 MET cc_start: 0.6772 (mmt) cc_final: 0.6551 (mmt)
REVERT: E  344 GLN cc_start: 0.7888 (mt0) cc_final: 0.7674 (mt0)
REVERT: G  327 GLN cc_start: 0.8933 (tp40) cc_final: 0.8337 (tm-30)
REVERT: G  336 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7004 (ttp)
REVERT: G  337 MET cc_start: 0.8004 (mmt) cc_final: 0.7320 (mmt)
REVERT: H  322 MET cc_start: 0.7508 (mmt) cc_final: 0.7299 (mmt)
REVERT: H  327 GLN cc_start: 0.8898 (tp40) cc_final: 0.7789 (tp40)
REVERT: H  346 GLN cc_start: 0.8549 (mt0) cc_final: 0.7408 (mt0)
REVERT: I  327 GLN cc_start: 0.8787 (tp40) cc_final: 0.7903 (tp40)
REVERT: J  322 MET cc_start: 0.7230 (mmt) cc_final: 0.6997 (mmt)
REVERT: J  327 GLN cc_start: 0.8726 (tp40) cc_final: 0.7966 (tm-30)
REVERT: J  336 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7635 (ttt)
REVERT: K  322 MET cc_start: 0.7115 (mmt) cc_final: 0.6914 (mmt)
REVERT: K  327 GLN cc_start: 0.8924 (tp40) cc_final: 0.8039 (tm-30)
REVERT: L  327 GLN cc_start: 0.8723 (tp40) cc_final: 0.8348 (tm-30)
REVERT: L  336 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7873 (ttp)
REVERT: M  327 GLN cc_start: 0.8530 (tp40) cc_final: 0.8087 (tp40)
REVERT: M  336 MET cc_start: 0.8041 (ttt) cc_final: 0.7808 (ttt)
REVERT: N  327 GLN cc_start: 0.9008 (tp40) cc_final: 0.8081 (tp40)
REVERT: N  346 GLN cc_start: 0.8485 (mt0) cc_final: 0.7960 (mt0)
REVERT: O  327 GLN cc_start: 0.8998 (tp40) cc_final: 0.8554 (tm-30)
REVERT: P  311 MET cc_start: 0.8698 (ptp) cc_final: 0.8409 (ptp)
REVERT: Q  311 MET cc_start: 0.8746 (ptp) cc_final: 0.8442 (ptp)
REVERT: Q  339 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7356 (mmp)
  outliers start: 20
  outliers final: 14
  residues processed: 240
  average time/residue: 0.0554
  time to fit residues: 18.6184
Evaluate side-chains
  240 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 222
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue  336 MET
Chi-restraints excluded: chain E residue  339 MET
Chi-restraints excluded: chain G residue  336 MET
Chi-restraints excluded: chain J residue  305 SER
Chi-restraints excluded: chain J residue  336 MET
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain L residue  305 SER
Chi-restraints excluded: chain L residue  336 MET
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain N residue  305 SER
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain P residue  305 SER
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain Q residue  334 TRP
Chi-restraints excluded: chain Q residue  339 MET
Chi-restraints excluded: chain R residue  305 SER
Chi-restraints excluded: chain R residue  334 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 327 GLN
D 345 ASN
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 343 GLN
** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 343 GLN
** P 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.138336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.101841 restraints weight = 7472.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.105041 restraints weight = 4666.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.107063 restraints weight = 3471.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.108102 restraints weight = 2891.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.108939 restraints weight = 2609.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.6067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.040   5616  Z= 0.360
  Angle     :  0.802   6.337   7470  Z= 0.416
  Chirality :  0.041   0.133    720
  Planarity :  0.004   0.028   1026
  Dihedral  :  6.077  16.191    792
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 19.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 33.72 %
    Favored  : 61.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.63 (0.15), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.11), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.016   0.003   PHE P 316 
 TRP   0.024   0.004   TRP G 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00784 ( 5616)
  covalent geometry    : angle       0.80237 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 210
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 GLN cc_start: 0.6705 (tm-30) cc_final: 0.6453 (tm-30)
REVERT: B  311 MET cc_start: 0.9113 (ptp) cc_final: 0.8532 (ptp)
REVERT: B  327 GLN cc_start: 0.6604 (tm-30) cc_final: 0.6313 (tm-30)
REVERT: D  307 MET cc_start: 0.9221 (ttt) cc_final: 0.8816 (ttm)
REVERT: D  322 MET cc_start: 0.6123 (ptp) cc_final: 0.5222 (mmt)
REVERT: D  327 GLN cc_start: 0.8776 (tp40) cc_final: 0.8310 (tp40)
REVERT: D  339 MET cc_start: 0.8190 (ptm) cc_final: 0.7938 (ptm)
REVERT: E  322 MET cc_start: 0.7553 (mmt) cc_final: 0.4771 (ptp)
REVERT: E  327 GLN cc_start: 0.8858 (tp40) cc_final: 0.8573 (tp40)
REVERT: E  346 GLN cc_start: 0.8585 (mt0) cc_final: 0.7924 (tp40)
REVERT: F  307 MET cc_start: 0.8651 (ttt) cc_final: 0.8206 (ttt)
REVERT: G  336 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7754 (ttp)
REVERT: G  337 MET cc_start: 0.8013 (mmt) cc_final: 0.7493 (mmt)
REVERT: H  327 GLN cc_start: 0.8842 (tp40) cc_final: 0.7971 (tp40)
REVERT: H  336 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8112 (ttt)
REVERT: H  346 GLN cc_start: 0.8577 (mt0) cc_final: 0.7417 (mt0)
REVERT: I  322 MET cc_start: 0.7089 (mmt) cc_final: 0.4070 (ptp)
REVERT: I  327 GLN cc_start: 0.8703 (tp40) cc_final: 0.7822 (tp40)
REVERT: J  322 MET cc_start: 0.7114 (mmt) cc_final: 0.6592 (mmt)
REVERT: J  336 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7779 (ttt)
REVERT: L  322 MET cc_start: 0.7613 (mmt) cc_final: 0.7256 (mmt)
REVERT: M  327 GLN cc_start: 0.8497 (tp40) cc_final: 0.7914 (tp40)
REVERT: M  336 MET cc_start: 0.8535 (ttt) cc_final: 0.8236 (ttt)
REVERT: N  327 GLN cc_start: 0.8948 (tp40) cc_final: 0.8031 (tp40)
REVERT: N  346 GLN cc_start: 0.8579 (mt0) cc_final: 0.7868 (mt0)
REVERT: O  327 GLN cc_start: 0.8932 (tp40) cc_final: 0.8624 (tm-30)
REVERT: P  322 MET cc_start: 0.5202 (mtt) cc_final: 0.4484 (mtt)
REVERT: Q  339 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7657 (mmp)
REVERT: R  322 MET cc_start: 0.5726 (mtt) cc_final: 0.5190 (mtt)
  outliers start: 25
  outliers final: 16
  residues processed: 219
  average time/residue: 0.0543
  time to fit residues: 16.5964
Evaluate side-chains
  222 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 202
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue  336 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  336 MET
Chi-restraints excluded: chain H residue  336 MET
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain J residue  305 SER
Chi-restraints excluded: chain J residue  336 MET
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain L residue  305 SER
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain N residue  305 SER
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain P residue  305 SER
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain Q residue  334 TRP
Chi-restraints excluded: chain Q residue  339 MET
Chi-restraints excluded: chain R residue  305 SER
Chi-restraints excluded: chain R residue  334 TRP
Chi-restraints excluded: chain R residue  347 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 44 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.235229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.131976 restraints weight = 7269.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.136397 restraints weight = 4271.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.139071 restraints weight = 3080.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.140575 restraints weight = 2528.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.141769 restraints weight = 2255.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.6338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5616  Z= 0.135
  Angle     :  0.648   7.541   7470  Z= 0.309
  Chirality :  0.038   0.113    720
  Planarity :  0.003   0.022   1026
  Dihedral  :  5.141  16.520    792
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 34.29 %
    Favored  : 61.69 %
  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 aren not related in a simple way.
  whole: -4.34 (0.16), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.12), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.001   PHE D 313 
 TRP   0.013   0.002   TRP A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5616)
  covalent geometry    : angle       0.64780 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 222
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  327 GLN cc_start: 0.8701 (tp40) cc_final: 0.8232 (tp40)
REVERT: D  336 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8104 (ttp)
REVERT: E  327 GLN cc_start: 0.8750 (tp40) cc_final: 0.8496 (tp40)
REVERT: E  346 GLN cc_start: 0.8718 (mt0) cc_final: 0.7874 (tp40)
REVERT: F  307 MET cc_start: 0.8566 (ttt) cc_final: 0.8249 (ttt)
REVERT: G  322 MET cc_start: 0.6890 (mmm) cc_final: 0.4694 (ptp)
REVERT: G  336 MET cc_start: 0.8413 (ttp) cc_final: 0.7269 (ttp)
REVERT: G  337 MET cc_start: 0.7953 (mmt) cc_final: 0.7417 (mmt)
REVERT: H  327 GLN cc_start: 0.8824 (tp40) cc_final: 0.7844 (tp40)
REVERT: H  336 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7693 (ttt)
REVERT: H  346 GLN cc_start: 0.8354 (mt0) cc_final: 0.6974 (mt0)
REVERT: I  322 MET cc_start: 0.7087 (mmt) cc_final: 0.4883 (ptp)
REVERT: I  327 GLN cc_start: 0.8646 (tp40) cc_final: 0.7740 (tp40)
REVERT: J  322 MET cc_start: 0.6931 (mmt) cc_final: 0.6565 (mmt)
REVERT: J  327 GLN cc_start: 0.8669 (tp40) cc_final: 0.7838 (tp40)
REVERT: J  336 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7883 (ttt)
REVERT: K  327 GLN cc_start: 0.8967 (tp40) cc_final: 0.7978 (tp40)
REVERT: L  322 MET cc_start: 0.7386 (mmt) cc_final: 0.7017 (mmt)
REVERT: L  323 MET cc_start: 0.7405 (ttt) cc_final: 0.7095 (ttt)
REVERT: L  327 GLN cc_start: 0.8693 (tp40) cc_final: 0.8316 (tp40)
REVERT: L  336 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7550 (ttp)
REVERT: M  327 GLN cc_start: 0.8471 (tp40) cc_final: 0.7846 (tp40)
REVERT: N  327 GLN cc_start: 0.8893 (tp40) cc_final: 0.7988 (tp40)
REVERT: N  337 MET cc_start: 0.7607 (mtt) cc_final: 0.7339 (mtt)
REVERT: N  346 GLN cc_start: 0.8445 (mt0) cc_final: 0.7465 (mt0)
REVERT: O  327 GLN cc_start: 0.8945 (tp40) cc_final: 0.8584 (tm-30)
REVERT: O  337 MET cc_start: 0.8059 (mmt) cc_final: 0.7839 (mmm)
REVERT: P  322 MET cc_start: 0.5079 (mtt) cc_final: 0.4666 (mtt)
REVERT: Q  307 MET cc_start: 0.8307 (ttt) cc_final: 0.7830 (ttp)
REVERT: Q  339 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7459 (mmp)
REVERT: R  322 MET cc_start: 0.5382 (mtt) cc_final: 0.4853 (mtt)
  outliers start: 21
  outliers final: 13
  residues processed: 226
  average time/residue: 0.0566
  time to fit residues: 17.8119
Evaluate side-chains
  233 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 215
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 GLN
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue  336 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain H residue  336 MET
Chi-restraints excluded: chain J residue  305 SER
Chi-restraints excluded: chain J residue  336 MET
Chi-restraints excluded: chain L residue  305 SER
Chi-restraints excluded: chain L residue  336 MET
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain N residue  305 SER
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain P residue  305 SER
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain Q residue  334 TRP
Chi-restraints excluded: chain Q residue  339 MET
Chi-restraints excluded: chain R residue  305 SER
Chi-restraints excluded: chain R residue  334 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   chunk 4 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 54 optimal weight:    7.9990
   chunk 70 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0060
   chunk 0 optimal weight:   10.0000
   chunk 71 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.5174

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.239515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.139535 restraints weight = 7311.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.144099 restraints weight = 4263.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.146627 restraints weight = 3059.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.148704 restraints weight = 2522.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.149883 restraints weight = 2204.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.4435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6272
moved from start:          0.6583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5616  Z= 0.101
  Angle     :  0.631   8.824   7470  Z= 0.290
  Chirality :  0.038   0.117    720
  Planarity :  0.002   0.018   1026
  Dihedral  :  4.650  18.194    792
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 34.48 %
    Favored  : 61.88 %
  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 aren not related in a simple way.
  whole: -4.26 (0.17), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.13), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHE D 313 
 TRP   0.013   0.002   TRP I 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 5616)
  covalent geometry    : angle       0.63094 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 225
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  319 ASN cc_start: 0.8767 (m110) cc_final: 0.8565 (m110)
REVERT: B  322 MET cc_start: 0.5767 (ptp) cc_final: 0.4528 (pmm)
REVERT: C  307 MET cc_start: 0.8655 (tpp) cc_final: 0.8034 (tpt)
REVERT: C  322 MET cc_start: 0.5768 (ptp) cc_final: 0.4695 (pmm)
REVERT: D  327 GLN cc_start: 0.8553 (tp40) cc_final: 0.8152 (tp40)
REVERT: E  327 GLN cc_start: 0.8689 (tp40) cc_final: 0.8455 (tp40)
REVERT: E  346 GLN cc_start: 0.9042 (mt0) cc_final: 0.8002 (tp40)
REVERT: G  322 MET cc_start: 0.7293 (mmm) cc_final: 0.4454 (ptp)
REVERT: G  336 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6191 (ttp)
REVERT: G  337 MET cc_start: 0.7825 (mmt) cc_final: 0.7121 (mmt)
REVERT: H  327 GLN cc_start: 0.8655 (tp40) cc_final: 0.7791 (tp40)
REVERT: H  346 GLN cc_start: 0.8760 (mt0) cc_final: 0.7359 (mt0)
REVERT: I  322 MET cc_start: 0.6908 (mmt) cc_final: 0.4458 (ptp)
REVERT: I  327 GLN cc_start: 0.8514 (tp40) cc_final: 0.7659 (tp40)
REVERT: J  322 MET cc_start: 0.6858 (mmt) cc_final: 0.6582 (mmt)
REVERT: J  327 GLN cc_start: 0.8472 (tp40) cc_final: 0.7671 (tp40)
REVERT: J  336 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7166 (ttt)
REVERT: K  327 GLN cc_start: 0.8784 (tp40) cc_final: 0.7853 (tp40)
REVERT: L  322 MET cc_start: 0.7047 (mmt) cc_final: 0.6839 (mmt)
REVERT: L  327 GLN cc_start: 0.8566 (tp40) cc_final: 0.8205 (tp40)
REVERT: L  336 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6149 (ttp)
REVERT: L  337 MET cc_start: 0.7983 (mmt) cc_final: 0.7445 (mmt)
REVERT: L  339 MET cc_start: 0.8844 (ptp) cc_final: 0.8615 (ptt)
REVERT: M  327 GLN cc_start: 0.8527 (tp40) cc_final: 0.7853 (tp40)
REVERT: M  337 MET cc_start: 0.8362 (mtt) cc_final: 0.7416 (mtt)
REVERT: N  327 GLN cc_start: 0.8823 (tp40) cc_final: 0.7935 (tp40)
REVERT: N  337 MET cc_start: 0.7795 (mtt) cc_final: 0.7405 (mtt)
REVERT: O  327 GLN cc_start: 0.8834 (tp40) cc_final: 0.8233 (tm-30)
REVERT: P  322 MET cc_start: 0.3989 (mtt) cc_final: 0.3698 (mtt)
REVERT: Q  307 MET cc_start: 0.7557 (ttt) cc_final: 0.7093 (ttp)
REVERT: Q  323 MET cc_start: 0.6262 (ttt) cc_final: 0.6018 (ttm)
REVERT: Q  339 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7222 (mmp)
REVERT: R  322 MET cc_start: 0.4542 (mtt) cc_final: 0.4168 (mtt)
  outliers start: 19
  outliers final: 12
  residues processed: 228
  average time/residue: 0.0549
  time to fit residues: 17.5525
Evaluate side-chains
  232 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 216
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue  336 MET
Chi-restraints excluded: chain G residue  336 MET
Chi-restraints excluded: chain J residue  305 SER
Chi-restraints excluded: chain J residue  336 MET
Chi-restraints excluded: chain K residue  305 SER
Chi-restraints excluded: chain L residue  305 SER
Chi-restraints excluded: chain L residue  336 MET
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain N residue  305 SER
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain P residue  305 SER
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain Q residue  334 TRP
Chi-restraints excluded: chain Q residue  339 MET
Chi-restraints excluded: chain R residue  305 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0870
   chunk 43 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 1 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   overall best weight:    1.2960

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

Flipped N/Q/H residues before XYZ refinement:
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 346 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 = 0.4680 r_free = 0.4680 target = 0.238155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.132312 restraints weight = 7140.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.136714 restraints weight = 4224.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.139542 restraints weight = 3061.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.141312 restraints weight = 2504.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.142108 restraints weight = 2208.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.6692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5616  Z= 0.169
  Angle     :  0.671   7.790   7470  Z= 0.318
  Chirality :  0.038   0.117    720
  Planarity :  0.002   0.018   1026
  Dihedral  :  4.990  17.816    792
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 34.29 %
    Favored  : 61.88 %
  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 aren not related in a simple way.
  whole: -4.35 (0.17), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.13), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.002   PHE D 313 
 TRP   0.016   0.003   TRP L 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 5616)
  covalent geometry    : angle       0.67104 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 214
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: B  322 MET cc_start: 0.5336 (ptp) cc_final: 0.4359 (pmm)
REVERT: C  307 MET cc_start: 0.8706 (tpp) cc_final: 0.8162 (tpt)
REVERT: D  327 GLN cc_start: 0.8592 (tp40) cc_final: 0.8262 (tp40)
REVERT: E  346 GLN cc_start: 0.8801 (mt0) cc_final: 0.7972 (tp40)
REVERT: F  323 MET cc_start: 0.7242 (ttt) cc_final: 0.6879 (ttt)
REVERT: G  322 MET cc_start: 0.6795 (mmm) cc_final: 0.4506 (ptp)
REVERT: G  327 GLN cc_start: 0.8841 (tp40) cc_final: 0.8045 (tp40)
REVERT: G  336 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7476 (ttp)
REVERT: G  337 MET cc_start: 0.8028 (mmt) cc_final: 0.7352 (mmt)
REVERT: H  327 GLN cc_start: 0.8826 (tp40) cc_final: 0.7824 (tp40)
REVERT: H  346 GLN cc_start: 0.8428 (mt0) cc_final: 0.6939 (mt0)
REVERT: I  322 MET cc_start: 0.7055 (mmt) cc_final: 0.4757 (ptp)
REVERT: I  327 GLN cc_start: 0.8685 (tp40) cc_final: 0.7834 (tp40)
REVERT: J  327 GLN cc_start: 0.8717 (tp40) cc_final: 0.8317 (tp40)
REVERT: J  336 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7713 (ttt)
REVERT: K  327 GLN cc_start: 0.8841 (tp40) cc_final: 0.8042 (tp40)
REVERT: L  322 MET cc_start: 0.7385 (mmt) cc_final: 0.6975 (mmt)
REVERT: L  327 GLN cc_start: 0.8707 (tp40) cc_final: 0.8258 (tp40)
REVERT: M  327 GLN cc_start: 0.8534 (tp40) cc_final: 0.7871 (tp-100)
REVERT: N  327 GLN cc_start: 0.8826 (tp40) cc_final: 0.8130 (tp40)
REVERT: N  337 MET cc_start: 0.8063 (mtt) cc_final: 0.7731 (mtt)
REVERT: O  327 GLN cc_start: 0.8908 (tp40) cc_final: 0.8452 (tm-30)
REVERT: P  322 MET cc_start: 0.4499 (mtt) cc_final: 0.4123 (mtt)
REVERT: Q  307 MET cc_start: 0.8316 (ttt) cc_final: 0.7838 (ttp)
REVERT: Q  339 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7442 (mmp)
REVERT: R  322 MET cc_start: 0.5060 (mtt) cc_final: 0.4523 (mtt)
  outliers start: 20
  outliers final: 15
  residues processed: 216
  average time/residue: 0.0528
  time to fit residues: 16.0069
Evaluate side-chains
  228 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 210
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 GLN
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue  322 MET
Chi-restraints excluded: chain E residue  336 MET
Chi-restraints excluded: chain G residue  336 MET
Chi-restraints excluded: chain J residue  305 SER
Chi-restraints excluded: chain J residue  336 MET
Chi-restraints excluded: chain L residue  305 SER
Chi-restraints excluded: chain L residue  336 MET
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain N residue  305 SER
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain P residue  305 SER
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain Q residue  334 TRP
Chi-restraints excluded: chain Q residue  339 MET
Chi-restraints excluded: chain R residue  305 SER
Chi-restraints excluded: chain R residue  334 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 16 optimal weight:    0.3980
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 346 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 = 0.4679 r_free = 0.4679 target = 0.234800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.133508 restraints weight = 7186.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.137852 restraints weight = 4311.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.140534 restraints weight = 3142.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.142221 restraints weight = 2591.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.143209 restraints weight = 2306.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.6833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5616  Z= 0.145
  Angle     :  0.670   8.012   7470  Z= 0.312
  Chirality :  0.038   0.116    720
  Planarity :  0.002   0.016   1026
  Dihedral  :  4.904  18.897    792
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 33.72 %
    Favored  : 62.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.40 (0.17), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.13), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHE D 313 
 TRP   0.014   0.003   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5616)
  covalent geometry    : angle       0.67037 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 213
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: B  322 MET cc_start: 0.5321 (ptp) cc_final: 0.4368 (pmm)
REVERT: C  307 MET cc_start: 0.8670 (tpp) cc_final: 0.8162 (tpt)
REVERT: C  322 MET cc_start: 0.5299 (ptp) cc_final: 0.4343 (pmm)
REVERT: D  327 GLN cc_start: 0.8609 (tp40) cc_final: 0.8210 (tp40)
REVERT: E  327 GLN cc_start: 0.8253 (tp40) cc_final: 0.7953 (tm-30)
REVERT: F  323 MET cc_start: 0.7235 (ttt) cc_final: 0.6896 (ttt)
REVERT: G  322 MET cc_start: 0.6802 (mmm) cc_final: 0.4481 (ptt)
REVERT: G  327 GLN cc_start: 0.8850 (tp40) cc_final: 0.7978 (tp40)
REVERT: G  336 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7430 (ttp)
REVERT: G  337 MET cc_start: 0.8032 (mmt) cc_final: 0.7289 (mmt)
REVERT: H  327 GLN cc_start: 0.8858 (tp40) cc_final: 0.7508 (tp40)
REVERT: H  346 GLN cc_start: 0.8453 (mt0) cc_final: 0.6864 (mt0)
REVERT: I  322 MET cc_start: 0.7164 (mmt) cc_final: 0.5013 (ptp)
REVERT: I  327 GLN cc_start: 0.8691 (tp40) cc_final: 0.7837 (tp40)
REVERT: J  322 MET cc_start: 0.6694 (mmt) cc_final: 0.6366 (mmt)
REVERT: J  327 GLN cc_start: 0.8746 (tp40) cc_final: 0.7969 (tp40)
REVERT: J  336 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7904 (ttt)
REVERT: K  327 GLN cc_start: 0.8848 (tp40) cc_final: 0.8085 (tp40)
REVERT: L  322 MET cc_start: 0.7370 (mmt) cc_final: 0.7159 (mmt)
REVERT: L  327 GLN cc_start: 0.8722 (tp40) cc_final: 0.8303 (tp40)
REVERT: M  327 GLN cc_start: 0.8557 (tp40) cc_final: 0.7921 (tp40)
REVERT: N  327 GLN cc_start: 0.8670 (tp40) cc_final: 0.8111 (tp40)
REVERT: N  337 MET cc_start: 0.8114 (mtt) cc_final: 0.7809 (mtt)
REVERT: O  327 GLN cc_start: 0.8913 (tp40) cc_final: 0.8550 (tm-30)
REVERT: P  322 MET cc_start: 0.4689 (mtt) cc_final: 0.4414 (mtt)
REVERT: Q  307 MET cc_start: 0.8264 (ttt) cc_final: 0.7784 (ttp)
REVERT: Q  339 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7622 (mmp)
REVERT: R  322 MET cc_start: 0.4692 (mtt) cc_final: 0.4189 (mtt)
  outliers start: 21
  outliers final: 17
  residues processed: 217
  average time/residue: 0.0557
  time to fit residues: 16.9669
Evaluate side-chains
  229 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 209
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue  322 MET
Chi-restraints excluded: chain E residue  336 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  336 MET
Chi-restraints excluded: chain H residue  344 GLN
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain J residue  305 SER
Chi-restraints excluded: chain J residue  336 MET
Chi-restraints excluded: chain L residue  305 SER
Chi-restraints excluded: chain L residue  336 MET
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain N residue  305 SER
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain P residue  305 SER
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain Q residue  334 TRP
Chi-restraints excluded: chain Q residue  339 MET
Chi-restraints excluded: chain R residue  305 SER
Chi-restraints excluded: chain R residue  334 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 346 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 = 0.4892 r_free = 0.4892 target = 0.327664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 194)---------------|
| r_work = 0.4974 r_free = 0.4974 target = 0.235803 restraints weight = 8866.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.5078 r_free = 0.5078 target = 0.235333 restraints weight = 10627.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.5077 r_free = 0.5077 target = 0.235260 restraints weight = 11068.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.5077 r_free = 0.5077 target = 0.235260 restraints weight = 11234.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5077 r_free = 0.5077 target = 0.235260 restraints weight = 11245.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.4736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.6959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5616  Z= 0.134
  Angle     :  0.682   8.156   7470  Z= 0.315
  Chirality :  0.038   0.115    720
  Planarity :  0.002   0.015   1026
  Dihedral  :  4.851  21.298    792
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 33.91 %
    Favored  : 61.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.43 (0.17), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.13), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHE D 313 
 TRP   0.014   0.003   TRP E 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5616)
  covalent geometry    : angle       0.68182 ( 7470)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: B  322 MET cc_start: 0.4477 (ptp) cc_final: 0.4053 (pmm)
REVERT: C  322 MET cc_start: 0.4581 (ptp) cc_final: 0.3986 (pmm)
REVERT: F  323 MET cc_start: 0.7065 (ttt) cc_final: 0.6780 (ttt)
REVERT: G  322 MET cc_start: 0.6097 (mmm) cc_final: 0.4940 (ptt)
REVERT: G  327 GLN cc_start: 0.8354 (tp40) cc_final: 0.8000 (tp40)
REVERT: G  336 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7870 (ttp)
REVERT: G  337 MET cc_start: 0.7501 (mmt) cc_final: 0.7085 (mmt)
REVERT: H  327 GLN cc_start: 0.8319 (tp40) cc_final: 0.7810 (tp40)
REVERT: H  346 GLN cc_start: 0.7697 (mt0) cc_final: 0.7134 (mt0)
REVERT: I  322 MET cc_start: 0.6534 (mmt) cc_final: 0.5445 (ptp)
REVERT: I  327 GLN cc_start: 0.8180 (tp40) cc_final: 0.7768 (tp40)
REVERT: J  322 MET cc_start: 0.6410 (mmt) cc_final: 0.6140 (mmt)
REVERT: J  336 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7861 (ttt)
REVERT: K  327 GLN cc_start: 0.8356 (tp40) cc_final: 0.8125 (tp40)
REVERT: L  322 MET cc_start: 0.6843 (mmt) cc_final: 0.6617 (mmt)
REVERT: P  322 MET cc_start: 0.5336 (mtt) cc_final: 0.5115 (mtt)
REVERT: Q  307 MET cc_start: 0.8327 (ttt) cc_final: 0.8018 (ttp)
REVERT: Q  339 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7644 (mmp)
REVERT: R  322 MET cc_start: 0.5756 (mtt) cc_final: 0.5309 (mtt)
  outliers start: 24
  outliers final: 17
  residues processed: 216
  average time/residue: 0.0558
  time to fit residues: 16.8816
Evaluate side-chains
  226 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  336 MET
Chi-restraints excluded: chain E residue  322 MET
Chi-restraints excluded: chain E residue  336 MET
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  336 MET
Chi-restraints excluded: chain H residue  344 GLN
Chi-restraints excluded: chain I residue  305 SER
Chi-restraints excluded: chain J residue  305 SER
Chi-restraints excluded: chain J residue  336 MET
Chi-restraints excluded: chain L residue  305 SER
Chi-restraints excluded: chain L residue  336 MET
Chi-restraints excluded: chain M residue  305 SER
Chi-restraints excluded: chain N residue  305 SER
Chi-restraints excluded: chain O residue  305 SER
Chi-restraints excluded: chain P residue  305 SER
Chi-restraints excluded: chain Q residue  305 SER
Chi-restraints excluded: chain Q residue  334 TRP
Chi-restraints excluded: chain Q residue  339 MET
Chi-restraints excluded: chain R residue  305 SER
Chi-restraints excluded: chain R residue  334 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    0.3980
   chunk 40 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 36 optimal weight:   10.0000
   overall best weight:    0.8182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.329924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 163)---------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.239513 restraints weight = 8795.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.238440 restraints weight = 13507.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.4904 r_free = 0.4904 target = 0.237899 restraints weight = 16282.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4906 r_free = 0.4906 target = 0.237416 restraints weight = 15456.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4908 r_free = 0.4908 target = 0.237448 restraints weight = 15083.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.4691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.7135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5616  Z= 0.129
  Angle     :  0.687   7.964   7470  Z= 0.322
  Chirality :  0.038   0.116    720
  Planarity :  0.002   0.015   1026
  Dihedral  :  4.754  21.508    792
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 33.14 %
    Favored  : 62.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.46 (0.17), residues: 774
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.13), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHE D 313 
 TRP   0.015   0.003   TRP E 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5616)
  covalent geometry    : angle       0.68744 ( 7470)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1132.03 seconds
wall clock time: 20 minutes 7.26 seconds (1207.26 seconds total)