Starting phenix.real_space_refine
on Sat Jan 25 15:28:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      92      5.16       5
     C   15111      2.51       5
     N    3933      2.21       5
     O    4853      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 92 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 23989
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1043
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1043
          Classifications: {'peptide': 143}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 136}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V
  Time building chain proxies: 7.05, per 1000 atoms: 0.29
  Number of scatterers: 23989
  At special positions: 0
  Unit cell: (71.688, 71.688, 319.712, 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      92     16.00
     O    4853      8.00
     N    3933      7.00
     C   15111      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 134 " - pdb=" SG  CYS A 147 " distance=2.03

  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: 5.23
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6026

  Finding SS restraints...
    Secondary structure from input PDB file:
      92 helices and 46 sheets defined
      34.3% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 30 through 47
    Processing helix  chain 'A' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR A  52 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 30 through 47
    Processing helix  chain 'B' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR B  52 " --> pdb=" O   PRO B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 64
      No H-bonds generated for 'chain 'B' and resid 62 through 64'
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 30 through 47
    Processing helix  chain 'C' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR C  52 " --> pdb=" O   PRO C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 64
      No H-bonds generated for 'chain 'C' and resid 62 through 64'
    Processing helix  chain 'D' and resid 8 through 23
    Processing helix  chain 'D' and resid 30 through 47
    Processing helix  chain 'D' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR D  52 " --> pdb=" O   PRO D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 64
      No H-bonds generated for 'chain 'D' and resid 62 through 64'
    Processing helix  chain 'E' and resid 8 through 23
    Processing helix  chain 'E' and resid 30 through 47
    Processing helix  chain 'E' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR E  52 " --> pdb=" O   PRO E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 64
      No H-bonds generated for 'chain 'E' and resid 62 through 64'
    Processing helix  chain 'F' and resid 8 through 23
    Processing helix  chain 'F' and resid 30 through 47
    Processing helix  chain 'F' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR F  52 " --> pdb=" O   PRO F  48 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 64
      No H-bonds generated for 'chain 'F' and resid 62 through 64'
    Processing helix  chain 'G' and resid 8 through 23
    Processing helix  chain 'G' and resid 30 through 47
    Processing helix  chain 'G' and resid 48 through 59
      removed outlier: 3.596A  pdb=" N   THR G  52 " --> pdb=" O   PRO G  48 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 64
      No H-bonds generated for 'chain 'G' and resid 62 through 64'
    Processing helix  chain 'H' and resid 8 through 23
    Processing helix  chain 'H' and resid 30 through 47
    Processing helix  chain 'H' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR H  52 " --> pdb=" O   PRO H  48 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 64
      No H-bonds generated for 'chain 'H' and resid 62 through 64'
    Processing helix  chain 'I' and resid 8 through 23
    Processing helix  chain 'I' and resid 30 through 47
    Processing helix  chain 'I' and resid 48 through 59
      removed outlier: 3.594A  pdb=" N   THR I  52 " --> pdb=" O   PRO I  48 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 62 through 64
      No H-bonds generated for 'chain 'I' and resid 62 through 64'
    Processing helix  chain 'J' and resid 8 through 23
    Processing helix  chain 'J' and resid 30 through 47
    Processing helix  chain 'J' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR J  52 " --> pdb=" O   PRO J  48 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 62 through 64
      No H-bonds generated for 'chain 'J' and resid 62 through 64'
    Processing helix  chain 'K' and resid 8 through 23
    Processing helix  chain 'K' and resid 30 through 47
    Processing helix  chain 'K' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR K  52 " --> pdb=" O   PRO K  48 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 62 through 64
      No H-bonds generated for 'chain 'K' and resid 62 through 64'
    Processing helix  chain 'L' and resid 8 through 23
    Processing helix  chain 'L' and resid 30 through 47
    Processing helix  chain 'L' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR L  52 " --> pdb=" O   PRO L  48 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 62 through 64
      No H-bonds generated for 'chain 'L' and resid 62 through 64'
    Processing helix  chain 'M' and resid 8 through 23
    Processing helix  chain 'M' and resid 30 through 47
    Processing helix  chain 'M' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR M  52 " --> pdb=" O   PRO M  48 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 62 through 64
      No H-bonds generated for 'chain 'M' and resid 62 through 64'
    Processing helix  chain 'N' and resid 8 through 23
    Processing helix  chain 'N' and resid 30 through 47
    Processing helix  chain 'N' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR N  52 " --> pdb=" O   PRO N  48 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 64
      No H-bonds generated for 'chain 'N' and resid 62 through 64'
    Processing helix  chain 'O' and resid 8 through 23
    Processing helix  chain 'O' and resid 30 through 47
    Processing helix  chain 'O' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR O  52 " --> pdb=" O   PRO O  48 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 62 through 64
      No H-bonds generated for 'chain 'O' and resid 62 through 64'
    Processing helix  chain 'P' and resid 8 through 23
    Processing helix  chain 'P' and resid 30 through 47
    Processing helix  chain 'P' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR P  52 " --> pdb=" O   PRO P  48 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 62 through 64
      No H-bonds generated for 'chain 'P' and resid 62 through 64'
    Processing helix  chain 'Q' and resid 8 through 23
    Processing helix  chain 'Q' and resid 30 through 47
    Processing helix  chain 'Q' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR Q  52 " --> pdb=" O   PRO Q  48 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 62 through 64
      No H-bonds generated for 'chain 'Q' and resid 62 through 64'
    Processing helix  chain 'R' and resid 8 through 23
    Processing helix  chain 'R' and resid 30 through 47
    Processing helix  chain 'R' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR R  52 " --> pdb=" O   PRO R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 64
      No H-bonds generated for 'chain 'R' and resid 62 through 64'
    Processing helix  chain 'S' and resid 8 through 23
    Processing helix  chain 'S' and resid 30 through 47
    Processing helix  chain 'S' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR S  52 " --> pdb=" O   PRO S  48 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 62 through 64
      No H-bonds generated for 'chain 'S' and resid 62 through 64'
    Processing helix  chain 'T' and resid 8 through 23
    Processing helix  chain 'T' and resid 30 through 47
    Processing helix  chain 'T' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR T  52 " --> pdb=" O   PRO T  48 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 62 through 64
      No H-bonds generated for 'chain 'T' and resid 62 through 64'
    Processing helix  chain 'U' and resid 8 through 23
    Processing helix  chain 'U' and resid 30 through 47
    Processing helix  chain 'U' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR U  52 " --> pdb=" O   PRO U  48 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 62 through 64
      No H-bonds generated for 'chain 'U' and resid 62 through 64'
    Processing helix  chain 'V' and resid 8 through 23
    Processing helix  chain 'V' and resid 30 through 47
    Processing helix  chain 'V' and resid 48 through 59
      removed outlier: 3.595A  pdb=" N   THR V  52 " --> pdb=" O   PRO V  48 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 62 through 64
      No H-bonds generated for 'chain 'V' and resid 62 through 64'
    Processing helix  chain 'W' and resid 8 through 23
    Processing helix  chain 'W' and resid 30 through 47
    Processing helix  chain 'W' and resid 48 through 59
      removed outlier: 3.594A  pdb=" N   THR W  52 " --> pdb=" O   PRO W  48 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 62 through 64
      No H-bonds generated for 'chain 'W' and resid 62 through 64'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 96
    Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 67
    Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 96
    Processing sheet with id=AA5, first strand: chain 'C' and resid 66 through 67
    Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 96
    Processing sheet with id=AA7, first strand: chain 'D' and resid 66 through 67
    Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 96
    Processing sheet with id=AA9, first strand: chain 'E' and resid 66 through 67
    Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 96
    Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 67
    Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 96
    Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 67
    Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 96
    Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 67
    Processing sheet with id=AB7, first strand: chain 'H' and resid 90 through 96
    Processing sheet with id=AB8, first strand: chain 'I' and resid 66 through 67
    Processing sheet with id=AB9, first strand: chain 'I' and resid 90 through 96
    Processing sheet with id=AC1, first strand: chain 'J' and resid 66 through 67
    Processing sheet with id=AC2, first strand: chain 'J' and resid 90 through 96
    Processing sheet with id=AC3, first strand: chain 'K' and resid 66 through 67
    Processing sheet with id=AC4, first strand: chain 'K' and resid 90 through 96
    Processing sheet with id=AC5, first strand: chain 'L' and resid 66 through 67
    Processing sheet with id=AC6, first strand: chain 'L' and resid 90 through 96
    Processing sheet with id=AC7, first strand: chain 'M' and resid 66 through 67
    Processing sheet with id=AC8, first strand: chain 'M' and resid 90 through 96
    Processing sheet with id=AC9, first strand: chain 'N' and resid 66 through 67
    Processing sheet with id=AD1, first strand: chain 'N' and resid 90 through 96
    Processing sheet with id=AD2, first strand: chain 'O' and resid 66 through 67
    Processing sheet with id=AD3, first strand: chain 'O' and resid 90 through 96
    Processing sheet with id=AD4, first strand: chain 'P' and resid 66 through 67
    Processing sheet with id=AD5, first strand: chain 'P' and resid 90 through 96
    Processing sheet with id=AD6, first strand: chain 'Q' and resid 66 through 67
    Processing sheet with id=AD7, first strand: chain 'Q' and resid 90 through 96
    Processing sheet with id=AD8, first strand: chain 'R' and resid 66 through 67
    Processing sheet with id=AD9, first strand: chain 'R' and resid 90 through 96
    Processing sheet with id=AE1, first strand: chain 'S' and resid 66 through 67
    Processing sheet with id=AE2, first strand: chain 'S' and resid 90 through 96
    Processing sheet with id=AE3, first strand: chain 'T' and resid 66 through 67
    Processing sheet with id=AE4, first strand: chain 'T' and resid 90 through 96
    Processing sheet with id=AE5, first strand: chain 'U' and resid 66 through 67
    Processing sheet with id=AE6, first strand: chain 'U' and resid 90 through 96
    Processing sheet with id=AE7, first strand: chain 'V' and resid 66 through 67
    Processing sheet with id=AE8, first strand: chain 'V' and resid 90 through 96
    Processing sheet with id=AE9, first strand: chain 'W' and resid 66 through 67
    Processing sheet with id=AF1, first strand: chain 'W' and resid 90 through 96

    1150 hydrogen bonds defined for protein.
    3381 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 7.68

  Time building geometry restraints manager: 6.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 7843
        1.35 -     1.46: 4991
        1.46 -     1.58: 11339
        1.58 -     1.69: 0
        1.69 -     1.81: 138
  Bond restraints: 24311
  Sorted by residual:
  bond pdb=" CG  GLN K 109 "
       pdb=" CD  GLN K 109 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 2.50e-02 1.60e+03 5.54e-01
  bond pdb=" CG  GLN F 109 "
       pdb=" CD  GLN F 109 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 2.50e-02 1.60e+03 5.47e-01
  bond pdb=" CG  GLN J 109 "
       pdb=" CD  GLN J 109 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 2.50e-02 1.60e+03 5.36e-01
  bond pdb=" CG  GLN O 109 "
       pdb=" CD  GLN O 109 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 2.50e-02 1.60e+03 5.35e-01
  bond pdb=" CG  GLN P 109 "
       pdb=" CD  GLN P 109 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 2.50e-02 1.60e+03 5.30e-01
  ... (remaining 24306 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 32130
        0.91 -     1.81: 682
        1.81 -     2.72: 216
        2.72 -     3.63: 92
        3.63 -     4.54: 23
  Bond angle restraints: 33143
  Sorted by residual:
  angle pdb=" CB  GLN E 109 "
        pdb=" CG  GLN E 109 "
        pdb=" CD  GLN E 109 "
      ideal   model   delta    sigma   weight residual
     112.60  115.48   -2.88 1.70e+00 3.46e-01 2.87e+00
  angle pdb=" CB  GLN R 109 "
        pdb=" CG  GLN R 109 "
        pdb=" CD  GLN R 109 "
      ideal   model   delta    sigma   weight residual
     112.60  115.47   -2.87 1.70e+00 3.46e-01 2.86e+00
  angle pdb=" CB  GLN H 109 "
        pdb=" CG  GLN H 109 "
        pdb=" CD  GLN H 109 "
      ideal   model   delta    sigma   weight residual
     112.60  115.46   -2.86 1.70e+00 3.46e-01 2.84e+00
  angle pdb=" CB  GLN P 109 "
        pdb=" CG  GLN P 109 "
        pdb=" CD  GLN P 109 "
      ideal   model   delta    sigma   weight residual
     112.60  115.46   -2.86 1.70e+00 3.46e-01 2.83e+00
  angle pdb=" CB  GLN N 109 "
        pdb=" CG  GLN N 109 "
        pdb=" CD  GLN N 109 "
      ideal   model   delta    sigma   weight residual
     112.60  115.45   -2.85 1.70e+00 3.46e-01 2.81e+00
  ... (remaining 33138 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 12721
       16.52 -    33.04: 1426
       33.04 -    49.56: 369
       49.56 -    66.07: 46
       66.07 -    82.59: 115
  Dihedral angle restraints: 14677
    sinusoidal: 5316
      harmonic: 9361
  Sorted by residual:
  dihedral pdb=" CA  GLU B  77 "
           pdb=" CB  GLU B  77 "
           pdb=" CG  GLU B  77 "
           pdb=" CD  GLU B  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  115.07  -55.07     3      1.50e+01 4.44e-03 9.32e+00
  dihedral pdb=" CA  GLU R  77 "
           pdb=" CB  GLU R  77 "
           pdb=" CG  GLU R  77 "
           pdb=" CD  GLU R  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  115.07  -55.07     3      1.50e+01 4.44e-03 9.32e+00
  dihedral pdb=" CA  GLU L  77 "
           pdb=" CB  GLU L  77 "
           pdb=" CG  GLU L  77 "
           pdb=" CD  GLU L  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  115.07  -55.07     3      1.50e+01 4.44e-03 9.32e+00
  ... (remaining 14674 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 2396
       0.026 -    0.052: 967
       0.052 -    0.078: 412
       0.078 -    0.104: 238
       0.104 -    0.131: 173
  Chirality restraints: 4186
  Sorted by residual:
  chirality pdb=" CA  ILE B 104 "
            pdb=" N   ILE B 104 "
            pdb=" C   ILE B 104 "
            pdb=" CB  ILE B 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE F 104 "
            pdb=" N   ILE F 104 "
            pdb=" C   ILE F 104 "
            pdb=" CB  ILE F 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  ILE V 104 "
            pdb=" N   ILE V 104 "
            pdb=" C   ILE V 104 "
            pdb=" CB  ILE V 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 4183 not shown)

  Planarity restraints: 4209
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE S  10 "    0.004 2.00e-02 2.50e+03   7.66e-03 5.87e-01
        pdb=" C   ILE S  10 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   ILE S  10 "    0.005 2.00e-02 2.50e+03
        pdb=" N   GLU S  11 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE P  10 "    0.004 2.00e-02 2.50e+03   7.46e-03 5.56e-01
        pdb=" C   ILE P  10 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   ILE P  10 "    0.005 2.00e-02 2.50e+03
        pdb=" N   GLU P  11 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE W  10 "    0.004 2.00e-02 2.50e+03   7.42e-03 5.50e-01
        pdb=" C   ILE W  10 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   ILE W  10 "    0.005 2.00e-02 2.50e+03
        pdb=" N   GLU W  11 "    0.004 2.00e-02 2.50e+03
  ... (remaining 4206 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 137
        2.60 -     3.18: 21554
        3.18 -     3.75: 36500
        3.75 -     4.33: 53745
        4.33 -     4.90: 90824
  Nonbonded interactions: 202760
  Sorted by model distance:
  nonbonded pdb=" SG  CYS P 134 "
            pdb=" SG  CYS P 147 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS W 134 "
            pdb=" SG  CYS W 147 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS D 134 "
            pdb=" SG  CYS D 147 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS O 134 "
            pdb=" SG  CYS O 147 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS M 134 "
            pdb=" SG  CYS M 147 "
     model   vdw
     2.032 3.760
  ... (remaining 202755 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: 0.25
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'R'
  selection = chain 'U'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'V'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.180
  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:          0.960
  Check model and map are aligned:         0.190
  Set scattering table:                    0.230
  Process input model:                     44.020
  Find NCS groups from input model:        0.760
  Set up NCS constraints:                  0.100
  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:             0.010
  Load rotamer database and sin/cos tables:2.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
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      :  0.002   0.019  24311  Z= 0.136
  Angle     :  0.416   4.536  33143  Z= 0.226
  Chirality :  0.044   0.131   4186
  Planarity :  0.003   0.017   4209
  Dihedral  : 17.574  82.593   8648
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 26.36 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.15), residues: 3243
  helix:  2.22 (0.17), residues: 1081
  sheet:  0.79 (0.20), residues: 713
  loop :  2.47 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP T 132 
 PHE   0.004   0.001   PHE Q 142 
 TYR   0.006   0.001   TYR D  33 
 ARG   0.001   0.000   ARG L  59 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  639 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 616
  time to evaluate  : 2.972 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 VAL cc_start: 0.8742 (m) cc_final: 0.8461 (m)
REVERT: A  136 SER cc_start: 0.8544 (t) cc_final: 0.8274 (p)
REVERT: B   65 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7720 (mttt)
REVERT: B   77 GLU cc_start: 0.8336 (mp0) cc_final: 0.7999 (mp0)
REVERT: C  124 LEU cc_start: 0.9135 (mt) cc_final: 0.8883 (mp)
REVERT: D   65 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8327 (mmtp)
REVERT: E  103 ASP cc_start: 0.8694 (p0) cc_final: 0.8433 (p0)
REVERT: I   70 THR cc_start: 0.8556 (p) cc_final: 0.8238 (m)
REVERT: I   97 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7731 (mm-30)
REVERT: I  116 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7784 (mmtt)
REVERT: K   29 GLN cc_start: 0.7969 (tt0) cc_final: 0.7512 (tt0)
REVERT: L  103 ASP cc_start: 0.8283 (p0) cc_final: 0.7895 (p0)
REVERT: M   29 GLN cc_start: 0.7881 (tt0) cc_final: 0.7350 (mt0)
REVERT: M   70 THR cc_start: 0.8636 (p) cc_final: 0.8315 (m)
REVERT: N  129 ASP cc_start: 0.7671 (m-30) cc_final: 0.7330 (m-30)
REVERT: O   29 GLN cc_start: 0.7816 (tt0) cc_final: 0.7514 (mt0)
REVERT: O   43 LEU cc_start: 0.9028 (tp) cc_final: 0.8805 (tp)
REVERT: O   61 ILE cc_start: 0.8400 (mt) cc_final: 0.8197 (mt)
REVERT: P   29 GLN cc_start: 0.7492 (tt0) cc_final: 0.7146 (mt0)
REVERT: P   85 ASP cc_start: 0.7915 (p0) cc_final: 0.7667 (p0)
REVERT: Q  116 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8377 (mmtp)
REVERT: Q  125 ASN cc_start: 0.8845 (t0) cc_final: 0.8610 (t0)
REVERT: Q  135 LYS cc_start: 0.7812 (tptt) cc_final: 0.7470 (tttm)
  outliers start: 23
  outliers final: 3
  residues processed: 638
  average time/residue: 0.3704
  time to fit residues: 364.9291
Evaluate side-chains
  454 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 451
  time to evaluate  : 2.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   52 THR
Chi-restraints excluded: chain O residue   52 THR
Chi-restraints excluded: chain U residue   52 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 271 optimal weight:    9.9990
   chunk 244 optimal weight:   10.0000
   chunk 135 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   chunk 164 optimal weight:    6.9990
   chunk 130 optimal weight:    0.9990
   chunk 252 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 153 optimal weight:    0.0970
   chunk 187 optimal weight:    0.5980
   chunk 292 optimal weight:    7.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
B  29 GLN
B  47 ASN
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 ASN
** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
C 149 ASN
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
D 149 ASN
E  31 GLN
E 149 ASN
F  29 GLN
** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 149 ASN
G 109 GLN
G 149 ASN
H 149 ASN
** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 149 ASN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 149 ASN
K  29 GLN
K 149 ASN
L  29 GLN
L  87 ASN
L 149 ASN
M  29 GLN
M 109 GLN
M 149 ASN
N 149 ASN
O  87 ASN
O 149 ASN
P 149 ASN
** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 149 ASN
S  29 GLN
** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 149 ASN
T 149 ASN
U 149 ASN
V 149 ASN
W 149 ASN

Total number of N/Q/H flips: 36

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.099798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.091237 restraints weight = 33056.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 1.17
r_work: 0.2874 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  24311  Z= 0.142
  Angle     :  0.442   4.543  33143  Z= 0.238
  Chirality :  0.046   0.146   4186
  Planarity :  0.003   0.020   4209
  Dihedral  :  3.497  14.534   3430
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.16 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.18 (0.15), residues: 3243
  helix:  2.50 (0.17), residues: 1081
  sheet:  1.33 (0.20), residues: 713
  loop :  2.51 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Q 132 
 PHE   0.006   0.001   PHE R 108 
 TYR   0.008   0.001   TYR G  33 
 ARG   0.002   0.000   ARG R 126 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  575 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 487
  time to evaluate  : 2.719 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 VAL cc_start: 0.8591 (m) cc_final: 0.8303 (m)
REVERT: B   43 LEU cc_start: 0.9084 (tp) cc_final: 0.8871 (tp)
REVERT: B   65 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7305 (mttt)
REVERT: C  135 LYS cc_start: 0.8138 (tptt) cc_final: 0.7885 (mttp)
REVERT: D   65 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8108 (mmtp)
REVERT: I   70 THR cc_start: 0.8682 (p) cc_final: 0.8438 (m)
REVERT: I   91 VAL cc_start: 0.9193 (m) cc_final: 0.8924 (t)
REVERT: I   97 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7686 (mm-30)
REVERT: I  116 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7876 (mmtt)
REVERT: I  148 ASP cc_start: 0.7929 (m-30) cc_final: 0.7505 (t0)
REVERT: K   91 VAL cc_start: 0.9006 (m) cc_final: 0.8724 (t)
REVERT: L  135 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7856 (mtpt)
REVERT: M   29 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7526 (mt0)
REVERT: N  129 ASP cc_start: 0.7683 (m-30) cc_final: 0.7394 (m-30)
REVERT: O   43 LEU cc_start: 0.8999 (tp) cc_final: 0.8732 (tp)
REVERT: P  135 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7805 (mptt)
REVERT: Q  135 LYS cc_start: 0.7997 (tptt) cc_final: 0.7704 (tttm)
REVERT: R  135 LYS cc_start: 0.8262 (tptt) cc_final: 0.7793 (ttpp)
REVERT: R  141 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8256 (ptm)
REVERT: W    8 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6350 (m)
REVERT: W  135 LYS cc_start: 0.8404 (tptt) cc_final: 0.8118 (mtpp)
  outliers start: 88
  outliers final: 58
  residues processed: 544
  average time/residue: 0.3480
  time to fit residues: 300.2088
Evaluate side-chains
  497 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 436
  time to evaluate  : 2.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain E residue   73 SER
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain F residue  112 THR
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   19 ILE
Chi-restraints excluded: chain I residue   85 ASP
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain J residue   73 SER
Chi-restraints excluded: chain J residue   92 ILE
Chi-restraints excluded: chain J residue  103 ASP
Chi-restraints excluded: chain J residue  141 MET
Chi-restraints excluded: chain K residue    8 THR
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  112 THR
Chi-restraints excluded: chain L residue   29 GLN
Chi-restraints excluded: chain L residue   85 ASP
Chi-restraints excluded: chain M residue   29 GLN
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain M residue  147 CYS
Chi-restraints excluded: chain N residue   73 SER
Chi-restraints excluded: chain O residue   73 SER
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue  112 THR
Chi-restraints excluded: chain O residue  141 MET
Chi-restraints excluded: chain P residue    8 THR
Chi-restraints excluded: chain P residue  116 LYS
Chi-restraints excluded: chain Q residue    8 THR
Chi-restraints excluded: chain Q residue   41 SER
Chi-restraints excluded: chain Q residue   78 THR
Chi-restraints excluded: chain Q residue   85 ASP
Chi-restraints excluded: chain Q residue  112 THR
Chi-restraints excluded: chain R residue    8 THR
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  141 MET
Chi-restraints excluded: chain T residue    8 THR
Chi-restraints excluded: chain T residue   11 GLU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue  112 THR
Chi-restraints excluded: chain U residue    8 THR
Chi-restraints excluded: chain U residue   73 SER
Chi-restraints excluded: chain U residue   98 ASP
Chi-restraints excluded: chain U residue  110 THR
Chi-restraints excluded: chain U residue  141 MET
Chi-restraints excluded: chain V residue   97 GLU
Chi-restraints excluded: chain V residue  136 SER
Chi-restraints excluded: chain W residue    8 THR
Chi-restraints excluded: chain W residue   64 SER
Chi-restraints excluded: chain W residue   73 SER
Chi-restraints excluded: chain W residue   82 VAL
Chi-restraints excluded: chain W residue  112 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 193 optimal weight:    4.9990
   chunk 129 optimal weight:    0.9980
   chunk 180 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 159 optimal weight:    9.9990
   chunk 318 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 136 optimal weight:    0.8980
   chunk 305 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    3.7786

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B 138 GLN
B 149 ASN
** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
D  31 GLN
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
F 149 ASN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 149 ASN
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 149 ASN
I 109 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 109 GLN
O  29 GLN
O 149 ASN
P 149 ASN
R 109 GLN
R 125 ASN
S 109 GLN
T 109 GLN
U 109 GLN
U 138 GLN
U 149 ASN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.091841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.083192 restraints weight = 33524.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 1.17
r_work: 0.2742 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2635 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  24311  Z= 0.385
  Angle     :  0.563   4.840  33143  Z= 0.307
  Chirality :  0.051   0.209   4186
  Planarity :  0.004   0.038   4209
  Dihedral  :  4.532  25.038   3427
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 19.85 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.15), residues: 3243
  helix:  2.04 (0.17), residues: 1081
  sheet:  1.28 (0.19), residues: 713
  loop :  2.07 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F 132 
 PHE   0.013   0.002   PHE E 142 
 TYR   0.012   0.002   TYR I  30 
 ARG   0.004   0.001   ARG Q  59 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  571 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 131
    poor density    : 440
  time to evaluate  : 2.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8610 (mp)
REVERT: B   31 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8203 (pt0)
REVERT: B   65 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7379 (mttt)
REVERT: C   22 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8124 (mp)
REVERT: C  135 LYS cc_start: 0.8305 (tptt) cc_final: 0.8025 (mptt)
REVERT: C  148 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7145 (m-30)
REVERT: D   65 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8093 (mmtp)
REVERT: E  141 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8137 (ptt)
REVERT: F   22 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8084 (mp)
REVERT: I   91 VAL cc_start: 0.9284 (m) cc_final: 0.9066 (t)
REVERT: I   97 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7732 (mm-30)
REVERT: I  148 ASP cc_start: 0.8002 (m-30) cc_final: 0.7661 (m-30)
REVERT: J   22 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8076 (mp)
REVERT: K   31 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7845 (pt0)
REVERT: L   22 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8285 (mp)
REVERT: L  135 LYS cc_start: 0.8154 (tmtt) cc_final: 0.7819 (mtpt)
REVERT: M    7 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7009 (t80)
REVERT: M   22 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8122 (mp)
REVERT: M  135 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8496 (tttp)
REVERT: N   87 ASN cc_start: 0.9076 (t0) cc_final: 0.8755 (t0)
REVERT: N  129 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7402 (m-30)
REVERT: O    7 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7537 (t80)
REVERT: O  129 ASP cc_start: 0.8330 (t70) cc_final: 0.7800 (t0)
REVERT: P   22 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8394 (mp)
REVERT: P  135 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8182 (tttp)
REVERT: Q   22 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8320 (mp)
REVERT: Q   87 ASN cc_start: 0.8670 (t0) cc_final: 0.8433 (t0)
REVERT: Q  135 LYS cc_start: 0.8033 (tptt) cc_final: 0.7672 (tttm)
REVERT: R  135 LYS cc_start: 0.8405 (tptt) cc_final: 0.7747 (ttpp)
REVERT: S   22 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: T  135 LYS cc_start: 0.8479 (tptt) cc_final: 0.8130 (mmtm)
  outliers start: 131
  outliers final: 85
  residues processed: 536
  average time/residue: 0.3483
  time to fit residues: 297.5247
Evaluate side-chains
  517 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 416
  time to evaluate  : 2.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  148 ASP
Chi-restraints excluded: chain D residue    7 PHE
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   73 SER
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  141 MET
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   31 GLN
Chi-restraints excluded: chain F residue  112 THR
Chi-restraints excluded: chain G residue   31 GLN
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   85 ASP
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain J residue   22 LEU
Chi-restraints excluded: chain J residue   73 SER
Chi-restraints excluded: chain K residue    8 THR
Chi-restraints excluded: chain K residue   31 GLN
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  112 THR
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   22 LEU
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain M residue    7 PHE
Chi-restraints excluded: chain M residue    8 THR
Chi-restraints excluded: chain M residue   21 ILE
Chi-restraints excluded: chain M residue   22 LEU
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain N residue    8 THR
Chi-restraints excluded: chain N residue   73 SER
Chi-restraints excluded: chain N residue  103 ASP
Chi-restraints excluded: chain N residue  129 ASP
Chi-restraints excluded: chain N residue  147 CYS
Chi-restraints excluded: chain O residue    7 PHE
Chi-restraints excluded: chain O residue   73 SER
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue  112 THR
Chi-restraints excluded: chain O residue  141 MET
Chi-restraints excluded: chain P residue    8 THR
Chi-restraints excluded: chain P residue   22 LEU
Chi-restraints excluded: chain P residue  116 LYS
Chi-restraints excluded: chain Q residue    8 THR
Chi-restraints excluded: chain Q residue   22 LEU
Chi-restraints excluded: chain Q residue   41 SER
Chi-restraints excluded: chain Q residue   74 THR
Chi-restraints excluded: chain Q residue   78 THR
Chi-restraints excluded: chain Q residue   82 VAL
Chi-restraints excluded: chain Q residue   85 ASP
Chi-restraints excluded: chain Q residue  112 THR
Chi-restraints excluded: chain R residue    8 THR
Chi-restraints excluded: chain R residue   73 SER
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain S residue   22 LEU
Chi-restraints excluded: chain S residue   73 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   91 VAL
Chi-restraints excluded: chain S residue  112 THR
Chi-restraints excluded: chain T residue    8 THR
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   85 ASP
Chi-restraints excluded: chain T residue  103 ASP
Chi-restraints excluded: chain T residue  112 THR
Chi-restraints excluded: chain T residue  125 ASN
Chi-restraints excluded: chain T residue  141 MET
Chi-restraints excluded: chain U residue    8 THR
Chi-restraints excluded: chain U residue   73 SER
Chi-restraints excluded: chain U residue   98 ASP
Chi-restraints excluded: chain U residue  110 THR
Chi-restraints excluded: chain U residue  125 ASN
Chi-restraints excluded: chain U residue  141 MET
Chi-restraints excluded: chain U residue  147 CYS
Chi-restraints excluded: chain V residue  139 ASP
Chi-restraints excluded: chain W residue   64 SER
Chi-restraints excluded: chain W residue   73 SER
Chi-restraints excluded: chain W residue   80 VAL
Chi-restraints excluded: chain W residue   82 VAL
Chi-restraints excluded: chain W residue  112 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 201 optimal weight:    5.9990
   chunk 232 optimal weight:    3.9990
   chunk 196 optimal weight:    4.9990
   chunk 282 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0670
   chunk 236 optimal weight:    9.9990
   chunk 225 optimal weight:    0.9990
   chunk 319 optimal weight:    9.9990
   chunk 173 optimal weight:    5.9990
   chunk 318 optimal weight:    5.9990
   chunk 180 optimal weight:    2.9990
   overall best weight:    1.7924

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B 138 GLN
D 109 GLN
D 125 ASN
G 109 GLN
H 109 GLN
J 109 GLN
M 109 GLN
P 149 ASN
U  29 GLN
U 138 GLN
V  31 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.094318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.085748 restraints weight = 33587.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 1.16
r_work: 0.2783 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  24311  Z= 0.207
  Angle     :  0.465   5.203  33143  Z= 0.251
  Chirality :  0.047   0.156   4186
  Planarity :  0.003   0.028   4209
  Dihedral  :  4.096  25.002   3427
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 20.85 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.15), residues: 3243
  helix:  2.30 (0.17), residues: 1081
  sheet:  1.19 (0.19), residues: 713
  loop :  2.09 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP O 132 
 PHE   0.007   0.001   PHE W 108 
 TYR   0.007   0.001   TYR B  33 
 ARG   0.002   0.000   ARG E  59 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  543 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 111
    poor density    : 432
  time to evaluate  : 3.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASP cc_start: 0.8082 (p0) cc_final: 0.7776 (p0)
REVERT: B   31 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8104 (pt0)
REVERT: B   65 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7403 (mttt)
REVERT: B   77 GLU cc_start: 0.8174 (mp0) cc_final: 0.7782 (mp0)
REVERT: C   77 GLU cc_start: 0.8254 (mp0) cc_final: 0.7910 (mp0)
REVERT: C  135 LYS cc_start: 0.8358 (tptt) cc_final: 0.8022 (mptt)
REVERT: D   65 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8101 (mmtp)
REVERT: E  141 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8174 (ptt)
REVERT: I   97 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7760 (mm-30)
REVERT: I  148 ASP cc_start: 0.8038 (m-30) cc_final: 0.7688 (m-30)
REVERT: J   13 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8321 (mmm)
REVERT: K   22 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: K   31 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7718 (pt0)
REVERT: K   91 VAL cc_start: 0.9002 (m) cc_final: 0.8729 (t)
REVERT: L  103 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7535 (p0)
REVERT: L  129 ASP cc_start: 0.7617 (t0) cc_final: 0.7377 (t0)
REVERT: L  135 LYS cc_start: 0.8169 (tmtt) cc_final: 0.7837 (mtpt)
REVERT: M    7 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6985 (t80)
REVERT: M   29 GLN cc_start: 0.8144 (tt0) cc_final: 0.7571 (mt0)
REVERT: M  135 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8506 (tttp)
REVERT: N   22 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: N  129 ASP cc_start: 0.7647 (m-30) cc_final: 0.7345 (m-30)
REVERT: O    7 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7576 (t80)
REVERT: O  129 ASP cc_start: 0.8321 (t70) cc_final: 0.7754 (t0)
REVERT: P  135 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8185 (tttp)
REVERT: Q   77 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: Q   87 ASN cc_start: 0.8624 (t0) cc_final: 0.8420 (t0)
REVERT: Q  135 LYS cc_start: 0.8081 (tptt) cc_final: 0.7677 (tttm)
REVERT: R  135 LYS cc_start: 0.8387 (tptt) cc_final: 0.7778 (ttpp)
REVERT: S    7 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7257 (t80)
REVERT: S   91 VAL cc_start: 0.9221 (m) cc_final: 0.8985 (t)
REVERT: T  135 LYS cc_start: 0.8497 (tptt) cc_final: 0.8136 (mmtm)
REVERT: W   10 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8179 (mm)
  outliers start: 111
  outliers final: 80
  residues processed: 511
  average time/residue: 0.3584
  time to fit residues: 292.9084
Evaluate side-chains
  502 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 411
  time to evaluate  : 2.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain D residue    7 PHE
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   73 SER
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  141 MET
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue  112 THR
Chi-restraints excluded: chain G residue   31 GLN
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   85 ASP
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain J residue   13 MET
Chi-restraints excluded: chain J residue   73 SER
Chi-restraints excluded: chain J residue  103 ASP
Chi-restraints excluded: chain K residue   22 LEU
Chi-restraints excluded: chain K residue   29 GLN
Chi-restraints excluded: chain K residue   31 GLN
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  112 THR
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue  103 ASP
Chi-restraints excluded: chain L residue  112 THR
Chi-restraints excluded: chain L residue  141 MET
Chi-restraints excluded: chain M residue    7 PHE
Chi-restraints excluded: chain M residue    8 THR
Chi-restraints excluded: chain M residue   92 ILE
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain N residue   22 LEU
Chi-restraints excluded: chain N residue   73 SER
Chi-restraints excluded: chain N residue   92 ILE
Chi-restraints excluded: chain O residue    7 PHE
Chi-restraints excluded: chain O residue    8 THR
Chi-restraints excluded: chain O residue   22 LEU
Chi-restraints excluded: chain O residue   73 SER
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue  112 THR
Chi-restraints excluded: chain O residue  141 MET
Chi-restraints excluded: chain Q residue    8 THR
Chi-restraints excluded: chain Q residue   41 SER
Chi-restraints excluded: chain Q residue   78 THR
Chi-restraints excluded: chain Q residue   85 ASP
Chi-restraints excluded: chain R residue    8 THR
Chi-restraints excluded: chain R residue   73 SER
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  129 ASP
Chi-restraints excluded: chain S residue    7 PHE
Chi-restraints excluded: chain S residue   73 SER
Chi-restraints excluded: chain S residue  112 THR
Chi-restraints excluded: chain T residue    8 THR
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   85 ASP
Chi-restraints excluded: chain T residue   91 VAL
Chi-restraints excluded: chain T residue  112 THR
Chi-restraints excluded: chain T residue  141 MET
Chi-restraints excluded: chain U residue    8 THR
Chi-restraints excluded: chain U residue   73 SER
Chi-restraints excluded: chain U residue  110 THR
Chi-restraints excluded: chain U residue  125 ASN
Chi-restraints excluded: chain U residue  141 MET
Chi-restraints excluded: chain V residue   31 GLN
Chi-restraints excluded: chain V residue   85 ASP
Chi-restraints excluded: chain V residue  103 ASP
Chi-restraints excluded: chain W residue   10 ILE
Chi-restraints excluded: chain W residue   64 SER
Chi-restraints excluded: chain W residue   73 SER
Chi-restraints excluded: chain W residue   82 VAL
Chi-restraints excluded: chain W residue  112 THR
Chi-restraints excluded: chain W residue  135 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 175 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 233 optimal weight:    0.0060
   chunk 313 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 252 optimal weight:    0.0980
   chunk 35 optimal weight:   10.0000
   chunk 193 optimal weight:    6.9990
   chunk 267 optimal weight:    8.9990
   chunk 234 optimal weight:    7.9990
   chunk 265 optimal weight:    4.9990
   overall best weight:    3.0202

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B 138 GLN
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
E 149 ASN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 GLN
I 109 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 149 ASN
** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  29 GLN
P 149 ASN
R 109 GLN
T  87 ASN
T 149 ASN
V  31 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.092010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.083124 restraints weight = 33831.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.25
r_work: 0.2737 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  24311  Z= 0.319
  Angle     :  0.519   7.368  33143  Z= 0.281
  Chirality :  0.049   0.174   4186
  Planarity :  0.004   0.034   4209
  Dihedral  :  4.429  31.196   3427
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 19.35 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.15), residues: 3243
  helix:  2.10 (0.17), residues: 1081
  sheet:  0.96 (0.19), residues: 713
  loop :  1.94 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 132 
 PHE   0.010   0.001   PHE E 142 
 TYR   0.014   0.001   TYR G  33 
 ARG   0.003   0.001   ARG S  59 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  557 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 141
    poor density    : 416
  time to evaluate  : 2.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8154 (pt0)
REVERT: B   65 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7367 (mttt)
REVERT: B   77 GLU cc_start: 0.8201 (mp0) cc_final: 0.7860 (mp0)
REVERT: C   22 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8146 (mp)
REVERT: C  135 LYS cc_start: 0.8248 (tptt) cc_final: 0.7936 (mptt)
REVERT: D   65 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8059 (mmtp)
REVERT: E  141 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8218 (ptt)
REVERT: F   22 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8090 (mp)
REVERT: H   31 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7416 (pt0)
REVERT: I   97 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7675 (mm-30)
REVERT: I  129 ASP cc_start: 0.8099 (t70) cc_final: 0.7877 (t70)
REVERT: J   22 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8035 (mp)
REVERT: J  129 ASP cc_start: 0.7564 (m-30) cc_final: 0.6816 (t70)
REVERT: K   22 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8016 (mp)
REVERT: K   31 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7770 (pt0)
REVERT: L   22 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8239 (mp)
REVERT: L  103 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7554 (p0)
REVERT: L  135 LYS cc_start: 0.8164 (tmtt) cc_final: 0.7800 (mtpt)
REVERT: M    7 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7003 (t80)
REVERT: M   22 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8091 (mp)
REVERT: M  135 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8535 (tttp)
REVERT: N   22 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8540 (mp)
REVERT: N  129 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7349 (m-30)
REVERT: O    7 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7770 (t80)
REVERT: O   11 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7937 (tt0)
REVERT: O  129 ASP cc_start: 0.8302 (t70) cc_final: 0.7720 (t0)
REVERT: P   22 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8338 (mp)
REVERT: P  135 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8197 (tttp)
REVERT: Q   31 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8016 (pt0)
REVERT: Q   77 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8113 (mt-10)
REVERT: Q   87 ASN cc_start: 0.8685 (t0) cc_final: 0.8448 (t0)
REVERT: Q  135 LYS cc_start: 0.8196 (tptt) cc_final: 0.7718 (tttm)
REVERT: R  135 LYS cc_start: 0.8450 (tptt) cc_final: 0.7828 (ttpp)
REVERT: R  141 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8288 (ptm)
REVERT: S    7 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7324 (t80)
REVERT: S   22 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8359 (mp)
REVERT: S   91 VAL cc_start: 0.9173 (m) cc_final: 0.8928 (t)
REVERT: T  135 LYS cc_start: 0.8517 (tptt) cc_final: 0.8199 (mmtm)
REVERT: V  135 LYS cc_start: 0.8533 (mptt) cc_final: 0.8123 (mttt)
REVERT: W   10 ILE cc_start: 0.8522 (mt) cc_final: 0.8296 (mm)
REVERT: W   31 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7831 (pt0)
  outliers start: 141
  outliers final: 103
  residues processed: 518
  average time/residue: 0.3408
  time to fit residues: 282.6507
Evaluate side-chains
  531 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 125
    poor density    : 406
  time to evaluate  : 2.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain D residue    7 PHE
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   73 SER
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  141 MET
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   31 GLN
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  112 THR
Chi-restraints excluded: chain G residue   31 GLN
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain H residue   31 GLN
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   85 ASP
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain J residue   22 LEU
Chi-restraints excluded: chain J residue   73 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  103 ASP
Chi-restraints excluded: chain K residue    8 THR
Chi-restraints excluded: chain K residue   22 LEU
Chi-restraints excluded: chain K residue   29 GLN
Chi-restraints excluded: chain K residue   31 GLN
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  112 THR
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   22 LEU
Chi-restraints excluded: chain L residue   85 ASP
Chi-restraints excluded: chain L residue  103 ASP
Chi-restraints excluded: chain L residue  112 THR
Chi-restraints excluded: chain L residue  141 MET
Chi-restraints excluded: chain M residue    7 PHE
Chi-restraints excluded: chain M residue    8 THR
Chi-restraints excluded: chain M residue   22 LEU
Chi-restraints excluded: chain M residue   92 ILE
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain N residue   22 LEU
Chi-restraints excluded: chain N residue   73 SER
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   92 ILE
Chi-restraints excluded: chain N residue  103 ASP
Chi-restraints excluded: chain N residue  129 ASP
Chi-restraints excluded: chain O residue    7 PHE
Chi-restraints excluded: chain O residue    8 THR
Chi-restraints excluded: chain O residue   11 GLU
Chi-restraints excluded: chain O residue   22 LEU
Chi-restraints excluded: chain O residue   73 SER
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue   92 ILE
Chi-restraints excluded: chain O residue  112 THR
Chi-restraints excluded: chain O residue  141 MET
Chi-restraints excluded: chain P residue    8 THR
Chi-restraints excluded: chain P residue   22 LEU
Chi-restraints excluded: chain P residue   77 GLU
Chi-restraints excluded: chain Q residue    8 THR
Chi-restraints excluded: chain Q residue   31 GLN
Chi-restraints excluded: chain Q residue   41 SER
Chi-restraints excluded: chain Q residue   78 THR
Chi-restraints excluded: chain Q residue   82 VAL
Chi-restraints excluded: chain Q residue   85 ASP
Chi-restraints excluded: chain R residue    7 PHE
Chi-restraints excluded: chain R residue    8 THR
Chi-restraints excluded: chain R residue   73 SER
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  141 MET
Chi-restraints excluded: chain R residue  148 ASP
Chi-restraints excluded: chain S residue    7 PHE
Chi-restraints excluded: chain S residue   22 LEU
Chi-restraints excluded: chain S residue   73 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  112 THR
Chi-restraints excluded: chain T residue    8 THR
Chi-restraints excluded: chain T residue   22 LEU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   85 ASP
Chi-restraints excluded: chain T residue   87 ASN
Chi-restraints excluded: chain T residue   91 VAL
Chi-restraints excluded: chain T residue  112 THR
Chi-restraints excluded: chain T residue  125 ASN
Chi-restraints excluded: chain T residue  141 MET
Chi-restraints excluded: chain U residue    8 THR
Chi-restraints excluded: chain U residue   73 SER
Chi-restraints excluded: chain U residue   78 THR
Chi-restraints excluded: chain U residue  110 THR
Chi-restraints excluded: chain U residue  125 ASN
Chi-restraints excluded: chain U residue  141 MET
Chi-restraints excluded: chain V residue   85 ASP
Chi-restraints excluded: chain V residue  103 ASP
Chi-restraints excluded: chain V residue  112 THR
Chi-restraints excluded: chain V residue  139 ASP
Chi-restraints excluded: chain W residue   31 GLN
Chi-restraints excluded: chain W residue   64 SER
Chi-restraints excluded: chain W residue   73 SER
Chi-restraints excluded: chain W residue   80 VAL
Chi-restraints excluded: chain W residue   82 VAL
Chi-restraints excluded: chain W residue  112 THR
Chi-restraints excluded: chain W residue  135 LYS
Chi-restraints excluded: chain W residue  148 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 139 optimal weight:    8.9990
   chunk 298 optimal weight:    0.9980
   chunk 137 optimal weight:    9.9990
   chunk 282 optimal weight:    3.9990
   chunk 131 optimal weight:    5.9990
   chunk 159 optimal weight:    7.9990
   chunk 156 optimal weight:    0.9990
   chunk 190 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 297 optimal weight:    5.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
B  29 GLN
B  47 ASN
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 109 GLN
T  87 ASN
V  31 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.091610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.083106 restraints weight = 33717.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 1.16
r_work: 0.2745 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2639 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8696
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  24311  Z= 0.315
  Angle     :  0.520   7.277  33143  Z= 0.282
  Chirality :  0.049   0.168   4186
  Planarity :  0.004   0.033   4209
  Dihedral  :  4.493  32.943   3427
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 19.43 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.15), residues: 3243
  helix:  2.06 (0.17), residues: 1081
  sheet:  0.79 (0.18), residues: 713
  loop :  1.86 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 132 
 PHE   0.009   0.001   PHE E 142 
 TYR   0.013   0.001   TYR G  33 
 ARG   0.004   0.001   ARG P  59 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  556 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 143
    poor density    : 413
  time to evaluate  : 2.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8173 (pt0)
REVERT: B   65 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7416 (mttt)
REVERT: B   77 GLU cc_start: 0.8165 (mp0) cc_final: 0.7669 (mp0)
REVERT: C   22 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8174 (mp)
REVERT: C  135 LYS cc_start: 0.8229 (tptt) cc_final: 0.7880 (mttp)
REVERT: D   65 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8106 (mmtp)
REVERT: E  141 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8210 (ptt)
REVERT: F   22 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8148 (mp)
REVERT: H   31 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7464 (pt0)
REVERT: I   97 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7708 (mm-30)
REVERT: I  129 ASP cc_start: 0.8077 (t70) cc_final: 0.7823 (t70)
REVERT: J   22 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8058 (mp)
REVERT: J  129 ASP cc_start: 0.7549 (m-30) cc_final: 0.6904 (t70)
REVERT: K   22 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8032 (mp)
REVERT: K   31 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7764 (pt0)
REVERT: L   22 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8274 (mp)
REVERT: L  103 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7465 (p0)
REVERT: L  135 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7749 (mtpt)
REVERT: M    7 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7000 (t80)
REVERT: M   22 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: M  135 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8526 (tttp)
REVERT: N   22 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8531 (mp)
REVERT: N  129 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7376 (m-30)
REVERT: O   11 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7913 (tt0)
REVERT: O  129 ASP cc_start: 0.8323 (t70) cc_final: 0.7747 (t0)
REVERT: P   22 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8331 (mp)
REVERT: P  135 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8193 (tttp)
REVERT: Q   31 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8020 (pt0)
REVERT: Q   77 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8087 (mt-10)
REVERT: Q   87 ASN cc_start: 0.8679 (t0) cc_final: 0.8442 (t0)
REVERT: Q  135 LYS cc_start: 0.8269 (tptt) cc_final: 0.7832 (tttm)
REVERT: R  135 LYS cc_start: 0.8438 (tptt) cc_final: 0.7844 (ttpp)
REVERT: R  141 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8285 (ptm)
REVERT: S   22 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8352 (mp)
REVERT: S   91 VAL cc_start: 0.9213 (m) cc_final: 0.8948 (t)
REVERT: T  135 LYS cc_start: 0.8479 (tptt) cc_final: 0.8177 (mmtm)
REVERT: V  135 LYS cc_start: 0.8522 (mptt) cc_final: 0.8179 (mttt)
REVERT: W   31 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7832 (pt0)
  outliers start: 143
  outliers final: 109
  residues processed: 519
  average time/residue: 0.3469
  time to fit residues: 287.9852
Evaluate side-chains
  534 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 129
    poor density    : 405
  time to evaluate  : 2.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain D residue    7 PHE
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   73 SER
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  141 MET
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   31 GLN
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  112 THR
Chi-restraints excluded: chain G residue   31 GLN
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain H residue   31 GLN
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   85 ASP
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain J residue   22 LEU
Chi-restraints excluded: chain J residue   73 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  103 ASP
Chi-restraints excluded: chain K residue    8 THR
Chi-restraints excluded: chain K residue   22 LEU
Chi-restraints excluded: chain K residue   29 GLN
Chi-restraints excluded: chain K residue   31 GLN
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  112 THR
Chi-restraints excluded: chain K residue  149 ASN
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   22 LEU
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue  103 ASP
Chi-restraints excluded: chain L residue  112 THR
Chi-restraints excluded: chain L residue  141 MET
Chi-restraints excluded: chain L residue  148 ASP
Chi-restraints excluded: chain M residue    7 PHE
Chi-restraints excluded: chain M residue    8 THR
Chi-restraints excluded: chain M residue   11 GLU
Chi-restraints excluded: chain M residue   22 LEU
Chi-restraints excluded: chain M residue   92 ILE
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain N residue   22 LEU
Chi-restraints excluded: chain N residue   73 SER
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   92 ILE
Chi-restraints excluded: chain N residue  103 ASP
Chi-restraints excluded: chain N residue  129 ASP
Chi-restraints excluded: chain O residue    8 THR
Chi-restraints excluded: chain O residue   11 GLU
Chi-restraints excluded: chain O residue   22 LEU
Chi-restraints excluded: chain O residue   73 SER
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue   92 ILE
Chi-restraints excluded: chain O residue  112 THR
Chi-restraints excluded: chain O residue  141 MET
Chi-restraints excluded: chain P residue    8 THR
Chi-restraints excluded: chain P residue   22 LEU
Chi-restraints excluded: chain P residue   77 GLU
Chi-restraints excluded: chain Q residue    8 THR
Chi-restraints excluded: chain Q residue   31 GLN
Chi-restraints excluded: chain Q residue   41 SER
Chi-restraints excluded: chain Q residue   78 THR
Chi-restraints excluded: chain Q residue   82 VAL
Chi-restraints excluded: chain Q residue   85 ASP
Chi-restraints excluded: chain R residue    7 PHE
Chi-restraints excluded: chain R residue    8 THR
Chi-restraints excluded: chain R residue   73 SER
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  141 MET
Chi-restraints excluded: chain R residue  148 ASP
Chi-restraints excluded: chain S residue   22 LEU
Chi-restraints excluded: chain S residue   73 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  112 THR
Chi-restraints excluded: chain T residue    8 THR
Chi-restraints excluded: chain T residue   22 LEU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   85 ASP
Chi-restraints excluded: chain T residue   87 ASN
Chi-restraints excluded: chain T residue   91 VAL
Chi-restraints excluded: chain T residue  112 THR
Chi-restraints excluded: chain T residue  125 ASN
Chi-restraints excluded: chain T residue  141 MET
Chi-restraints excluded: chain U residue    8 THR
Chi-restraints excluded: chain U residue   73 SER
Chi-restraints excluded: chain U residue   78 THR
Chi-restraints excluded: chain U residue  110 THR
Chi-restraints excluded: chain U residue  125 ASN
Chi-restraints excluded: chain U residue  141 MET
Chi-restraints excluded: chain U residue  149 ASN
Chi-restraints excluded: chain V residue   85 ASP
Chi-restraints excluded: chain V residue  103 ASP
Chi-restraints excluded: chain V residue  112 THR
Chi-restraints excluded: chain V residue  139 ASP
Chi-restraints excluded: chain W residue   31 GLN
Chi-restraints excluded: chain W residue   64 SER
Chi-restraints excluded: chain W residue   73 SER
Chi-restraints excluded: chain W residue   80 VAL
Chi-restraints excluded: chain W residue   82 VAL
Chi-restraints excluded: chain W residue  112 THR
Chi-restraints excluded: chain W residue  135 LYS
Chi-restraints excluded: chain W residue  148 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 208 optimal weight:    6.9990
   chunk 229 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 254 optimal weight:    8.9990
   chunk 147 optimal weight:    3.9990
   chunk 320 optimal weight:    7.9990
   chunk 317 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 209 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B 109 GLN
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
G  29 GLN
G 109 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 109 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.094048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.085529 restraints weight = 33475.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 1.16
r_work: 0.2784 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  24311  Z= 0.192
  Angle     :  0.461   6.319  33143  Z= 0.248
  Chirality :  0.047   0.149   4186
  Planarity :  0.004   0.031   4209
  Dihedral  :  4.119  29.752   3427
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 20.39 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.15), residues: 3243
  helix:  2.32 (0.17), residues: 1081
  sheet:  0.81 (0.18), residues: 713
  loop :  1.97 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP O 132 
 PHE   0.006   0.001   PHE W 108 
 TYR   0.009   0.001   TYR G  33 
 ARG   0.003   0.000   ARG S 126 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  546 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 122
    poor density    : 424
  time to evaluate  : 2.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 ASN cc_start: 0.8262 (t0) cc_final: 0.7898 (t0)
REVERT: B   31 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8094 (pt0)
REVERT: B   65 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7436 (mttt)
REVERT: B   77 GLU cc_start: 0.8169 (mp0) cc_final: 0.7729 (mp0)
REVERT: C   22 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8184 (mp)
REVERT: C   77 GLU cc_start: 0.8207 (mp0) cc_final: 0.7918 (mp0)
REVERT: C  135 LYS cc_start: 0.8226 (tptt) cc_final: 0.7991 (mtmm)
REVERT: D   65 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8100 (mmtp)
REVERT: E  141 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8199 (ptt)
REVERT: H   31 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7349 (pt0)
REVERT: I   97 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7708 (mm-30)
REVERT: I  129 ASP cc_start: 0.8034 (t70) cc_final: 0.7813 (t70)
REVERT: J   22 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: J  129 ASP cc_start: 0.7503 (m-30) cc_final: 0.6856 (t70)
REVERT: K   22 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8031 (mp)
REVERT: K   31 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7709 (pt0)
REVERT: L   22 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: L  103 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7383 (p0)
REVERT: L  135 LYS cc_start: 0.8130 (tmtt) cc_final: 0.7755 (mtpt)
REVERT: M    7 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7031 (t80)
REVERT: M   22 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8043 (mp)
REVERT: M   29 GLN cc_start: 0.8134 (tt0) cc_final: 0.7577 (mt0)
REVERT: M   67 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8192 (mtmt)
REVERT: M  135 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8490 (tttp)
REVERT: N   22 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8511 (mp)
REVERT: N  129 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7282 (m-30)
REVERT: O  129 ASP cc_start: 0.8326 (t70) cc_final: 0.7767 (t0)
REVERT: Q   77 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8132 (mt-10)
REVERT: Q  135 LYS cc_start: 0.8262 (tptt) cc_final: 0.7820 (tttm)
REVERT: R  135 LYS cc_start: 0.8428 (tptt) cc_final: 0.7846 (ttpp)
REVERT: R  141 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8244 (ptm)
REVERT: S   22 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8419 (mp)
REVERT: S   91 VAL cc_start: 0.9195 (m) cc_final: 0.8973 (t)
REVERT: T  135 LYS cc_start: 0.8466 (tptt) cc_final: 0.8157 (mmtm)
REVERT: V  135 LYS cc_start: 0.8520 (mptt) cc_final: 0.8157 (mttt)
REVERT: W   31 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7787 (pt0)
  outliers start: 122
  outliers final: 89
  residues processed: 514
  average time/residue: 0.3363
  time to fit residues: 276.4402
Evaluate side-chains
  518 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 105
    poor density    : 413
  time to evaluate  : 2.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 PHE
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain D residue    7 PHE
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   73 SER
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  141 MET
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  112 THR
Chi-restraints excluded: chain G residue   31 GLN
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain H residue   31 GLN
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   85 ASP
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain J residue   22 LEU
Chi-restraints excluded: chain J residue   73 SER
Chi-restraints excluded: chain J residue  103 ASP
Chi-restraints excluded: chain K residue   22 LEU
Chi-restraints excluded: chain K residue   29 GLN
Chi-restraints excluded: chain K residue   31 GLN
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  112 THR
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   22 LEU
Chi-restraints excluded: chain L residue  103 ASP
Chi-restraints excluded: chain L residue  112 THR
Chi-restraints excluded: chain L residue  141 MET
Chi-restraints excluded: chain M residue    7 PHE
Chi-restraints excluded: chain M residue    8 THR
Chi-restraints excluded: chain M residue   11 GLU
Chi-restraints excluded: chain M residue   22 LEU
Chi-restraints excluded: chain M residue   92 ILE
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain N residue   22 LEU
Chi-restraints excluded: chain N residue   73 SER
Chi-restraints excluded: chain N residue   92 ILE
Chi-restraints excluded: chain N residue  103 ASP
Chi-restraints excluded: chain N residue  129 ASP
Chi-restraints excluded: chain O residue    8 THR
Chi-restraints excluded: chain O residue   22 LEU
Chi-restraints excluded: chain O residue   73 SER
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue   92 ILE
Chi-restraints excluded: chain O residue  112 THR
Chi-restraints excluded: chain O residue  141 MET
Chi-restraints excluded: chain P residue    8 THR
Chi-restraints excluded: chain P residue   74 THR
Chi-restraints excluded: chain P residue   77 GLU
Chi-restraints excluded: chain Q residue    8 THR
Chi-restraints excluded: chain Q residue   41 SER
Chi-restraints excluded: chain Q residue   78 THR
Chi-restraints excluded: chain R residue    8 THR
Chi-restraints excluded: chain R residue   73 SER
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  141 MET
Chi-restraints excluded: chain R residue  148 ASP
Chi-restraints excluded: chain S residue   22 LEU
Chi-restraints excluded: chain S residue   73 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  112 THR
Chi-restraints excluded: chain T residue    8 THR
Chi-restraints excluded: chain T residue   22 LEU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue  112 THR
Chi-restraints excluded: chain T residue  141 MET
Chi-restraints excluded: chain U residue    8 THR
Chi-restraints excluded: chain U residue   73 SER
Chi-restraints excluded: chain U residue   78 THR
Chi-restraints excluded: chain U residue  110 THR
Chi-restraints excluded: chain V residue    7 PHE
Chi-restraints excluded: chain V residue   13 MET
Chi-restraints excluded: chain V residue  103 ASP
Chi-restraints excluded: chain V residue  112 THR
Chi-restraints excluded: chain W residue   31 GLN
Chi-restraints excluded: chain W residue   64 SER
Chi-restraints excluded: chain W residue   73 SER
Chi-restraints excluded: chain W residue   82 VAL
Chi-restraints excluded: chain W residue  112 THR
Chi-restraints excluded: chain W residue  135 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 216 optimal weight:    8.9990
   chunk 224 optimal weight:    4.9990
   chunk 215 optimal weight:    4.9990
   chunk 303 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   chunk 207 optimal weight:    5.9990
   chunk 120 optimal weight:    7.9990
   chunk 168 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 300 optimal weight:    7.9990
   chunk 124 optimal weight:    5.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B 109 GLN
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
D 149 ASN
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  31 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 149 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.091302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.082826 restraints weight = 33743.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 1.16
r_work: 0.2741 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2635 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  24311  Z= 0.345
  Angle     :  0.536   8.316  33143  Z= 0.290
  Chirality :  0.050   0.173   4186
  Planarity :  0.004   0.033   4209
  Dihedral  :  4.587  33.116   3427
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 19.85 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.15), residues: 3243
  helix:  2.03 (0.17), residues: 1081
  sheet:  0.66 (0.18), residues: 713
  loop :  1.81 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 132 
 PHE   0.010   0.001   PHE E 142 
 TYR   0.014   0.001   TYR G  33 
 ARG   0.004   0.001   ARG P  59 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  546 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 138
    poor density    : 408
  time to evaluate  : 2.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 ASN cc_start: 0.8282 (t0) cc_final: 0.7871 (t0)
REVERT: B   31 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8208 (pt0)
REVERT: B   65 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7442 (mttt)
REVERT: B   77 GLU cc_start: 0.8177 (mp0) cc_final: 0.7754 (mp0)
REVERT: C   22 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8120 (mp)
REVERT: C  135 LYS cc_start: 0.8256 (tptt) cc_final: 0.7990 (mtmm)
REVERT: D   65 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8108 (mmtp)
REVERT: E  141 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8234 (ptt)
REVERT: H   31 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7496 (pt0)
REVERT: I   97 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7717 (mm-30)
REVERT: J   22 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8066 (mp)
REVERT: J  129 ASP cc_start: 0.7541 (m-30) cc_final: 0.6959 (t70)
REVERT: K   22 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8035 (mp)
REVERT: K   31 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7808 (pt0)
REVERT: L   22 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8255 (mp)
REVERT: L  103 ASP cc_start: 0.7919 (p0) cc_final: 0.7460 (p0)
REVERT: L  129 ASP cc_start: 0.7891 (t0) cc_final: 0.7616 (t0)
REVERT: L  135 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7771 (mtpt)
REVERT: M    7 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.7009 (t80)
REVERT: M   22 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8121 (mp)
REVERT: M   67 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8261 (mtmt)
REVERT: M  135 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8547 (tttp)
REVERT: N  129 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7313 (m-30)
REVERT: O  129 ASP cc_start: 0.8314 (t70) cc_final: 0.7729 (t0)
REVERT: P    7 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7889 (t80)
REVERT: P   22 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8335 (mp)
REVERT: Q   31 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8027 (pt0)
REVERT: Q   77 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8116 (mt-10)
REVERT: Q  135 LYS cc_start: 0.8207 (tptt) cc_final: 0.7776 (tttm)
REVERT: R  135 LYS cc_start: 0.8433 (tptt) cc_final: 0.7870 (ttpp)
REVERT: R  141 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8283 (ptm)
REVERT: S   22 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8402 (mp)
REVERT: S   91 VAL cc_start: 0.9194 (m) cc_final: 0.8928 (t)
REVERT: T  135 LYS cc_start: 0.8451 (tptt) cc_final: 0.8163 (mmtm)
REVERT: V   22 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8430 (mp)
REVERT: V   97 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7620 (mp0)
REVERT: V  135 LYS cc_start: 0.8520 (mptt) cc_final: 0.8151 (mttt)
REVERT: W   31 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7891 (pt0)
  outliers start: 138
  outliers final: 109
  residues processed: 512
  average time/residue: 0.3441
  time to fit residues: 280.3024
Evaluate side-chains
  529 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 128
    poor density    : 401
  time to evaluate  : 2.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue   31 GLN
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  109 GLN
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain D residue    7 PHE
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   76 THR
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   73 SER
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  141 MET
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   76 THR
Chi-restraints excluded: chain F residue  112 THR
Chi-restraints excluded: chain F residue  141 MET
Chi-restraints excluded: chain G residue   31 GLN
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain G residue  148 ASP
Chi-restraints excluded: chain H residue   31 GLN
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   85 ASP
Chi-restraints excluded: chain I residue  112 THR
Chi-restraints excluded: chain J residue   22 LEU
Chi-restraints excluded: chain J residue   73 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  103 ASP
Chi-restraints excluded: chain K residue   22 LEU
Chi-restraints excluded: chain K residue   29 GLN
Chi-restraints excluded: chain K residue   31 GLN
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  112 THR
Chi-restraints excluded: chain K residue  149 ASN
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue   22 LEU
Chi-restraints excluded: chain L residue  112 THR
Chi-restraints excluded: chain L residue  141 MET
Chi-restraints excluded: chain L residue  148 ASP
Chi-restraints excluded: chain M residue    7 PHE
Chi-restraints excluded: chain M residue    8 THR
Chi-restraints excluded: chain M residue   11 GLU
Chi-restraints excluded: chain M residue   22 LEU
Chi-restraints excluded: chain M residue   92 ILE
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain N residue   22 LEU
Chi-restraints excluded: chain N residue   73 SER
Chi-restraints excluded: chain N residue   92 ILE
Chi-restraints excluded: chain N residue  103 ASP
Chi-restraints excluded: chain N residue  129 ASP
Chi-restraints excluded: chain O residue    8 THR
Chi-restraints excluded: chain O residue   22 LEU
Chi-restraints excluded: chain O residue   73 SER
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue   92 ILE
Chi-restraints excluded: chain O residue  112 THR
Chi-restraints excluded: chain O residue  141 MET
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain P residue    8 THR
Chi-restraints excluded: chain P residue   22 LEU
Chi-restraints excluded: chain P residue   74 THR
Chi-restraints excluded: chain P residue   77 GLU
Chi-restraints excluded: chain P residue  116 LYS
Chi-restraints excluded: chain Q residue    8 THR
Chi-restraints excluded: chain Q residue   31 GLN
Chi-restraints excluded: chain Q residue   41 SER
Chi-restraints excluded: chain Q residue   78 THR
Chi-restraints excluded: chain Q residue   82 VAL
Chi-restraints excluded: chain R residue    8 THR
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue   73 SER
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue   82 VAL
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  141 MET
Chi-restraints excluded: chain R residue  148 ASP
Chi-restraints excluded: chain S residue   22 LEU
Chi-restraints excluded: chain S residue   73 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  112 THR
Chi-restraints excluded: chain T residue    8 THR
Chi-restraints excluded: chain T residue   22 LEU
Chi-restraints excluded: chain T residue   52 THR
Chi-restraints excluded: chain T residue   85 ASP
Chi-restraints excluded: chain T residue  112 THR
Chi-restraints excluded: chain T residue  125 ASN
Chi-restraints excluded: chain T residue  141 MET
Chi-restraints excluded: chain U residue    8 THR
Chi-restraints excluded: chain U residue   73 SER
Chi-restraints excluded: chain U residue   78 THR
Chi-restraints excluded: chain U residue  110 THR
Chi-restraints excluded: chain U residue  125 ASN
Chi-restraints excluded: chain U residue  141 MET
Chi-restraints excluded: chain U residue  149 ASN
Chi-restraints excluded: chain V residue   22 LEU
Chi-restraints excluded: chain V residue   97 GLU
Chi-restraints excluded: chain V residue  103 ASP
Chi-restraints excluded: chain V residue  112 THR
Chi-restraints excluded: chain V residue  139 ASP
Chi-restraints excluded: chain W residue   31 GLN
Chi-restraints excluded: chain W residue   64 SER
Chi-restraints excluded: chain W residue   73 SER
Chi-restraints excluded: chain W residue   80 VAL
Chi-restraints excluded: chain W residue   82 VAL
Chi-restraints excluded: chain W residue  112 THR
Chi-restraints excluded: chain W residue  135 LYS
Chi-restraints excluded: chain W residue  148 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 161 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 121 optimal weight:    0.0270
   chunk 76 optimal weight:    5.9990
   chunk 108 optimal weight:    0.0970
   chunk 199 optimal weight:    0.8980
   chunk 237 optimal weight:    0.9980
   chunk 292 optimal weight:    1.9990
   chunk 207 optimal weight:    0.8980
   chunk 189 optimal weight:    6.9990
   chunk 303 optimal weight:    6.9990
   overall best weight:    0.5836

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
G  29 GLN
G 109 GLN
I  31 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  87 ASN
Q  87 ASN
Q 149 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.097196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.088732 restraints weight = 33266.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 1.16
r_work: 0.2831 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  24311  Z= 0.125
  Angle     :  0.434   7.877  33143  Z= 0.232
  Chirality :  0.046   0.146   4186
  Planarity :  0.003   0.029   4209
  Dihedral  :  3.848  25.569   3427
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.97 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.15), residues: 3243
  helix:  2.47 (0.17), residues: 1081
  sheet:  0.84 (0.19), residues: 713
  loop :  2.02 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 132 
 PHE   0.005   0.001   PHE B 108 
 TYR   0.008   0.001   TYR I  33 
 ARG   0.004   0.000   ARG P  59 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  527 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 442
  time to evaluate  : 2.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASP cc_start: 0.8026 (p0) cc_final: 0.7680 (p0)
REVERT: A  125 ASN cc_start: 0.8170 (t0) cc_final: 0.7811 (t0)
REVERT: B   65 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7418 (mttt)
REVERT: B   77 GLU cc_start: 0.8131 (mp0) cc_final: 0.7775 (mp0)
REVERT: C   22 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8174 (mp)
REVERT: C   77 GLU cc_start: 0.8214 (mp0) cc_final: 0.7855 (mp0)
REVERT: C  135 LYS cc_start: 0.8239 (tptt) cc_final: 0.7978 (mtmm)
REVERT: D   65 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8059 (mmtp)
REVERT: E  141 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8181 (ptt)
REVERT: G   85 ASP cc_start: 0.8267 (p0) cc_final: 0.7971 (p0)
REVERT: G  141 MET cc_start: 0.8466 (ptp) cc_final: 0.8177 (ptm)
REVERT: H   31 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7229 (pt0)
REVERT: I   97 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7738 (mm-30)
REVERT: J   67 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8486 (mmtt)
REVERT: J  129 ASP cc_start: 0.7496 (m-30) cc_final: 0.6859 (t70)
REVERT: K   31 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7651 (pt0)
REVERT: K   65 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8336 (mmtp)
REVERT: K   91 VAL cc_start: 0.8950 (m) cc_final: 0.8697 (t)
REVERT: L  135 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7768 (mtpt)
REVERT: M    7 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6948 (t80)
REVERT: M   22 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8014 (mp)
REVERT: M   29 GLN cc_start: 0.8021 (tt0) cc_final: 0.7479 (mt0)
REVERT: M   67 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8200 (mtmt)
REVERT: M  135 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8519 (tttp)
REVERT: N   22 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8495 (mp)
REVERT: N   87 ASN cc_start: 0.9135 (t0) cc_final: 0.8897 (t0)
REVERT: O   43 LEU cc_start: 0.9016 (tp) cc_final: 0.8740 (tp)
REVERT: O  129 ASP cc_start: 0.8405 (t70) cc_final: 0.7932 (t0)
REVERT: P    7 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7849 (t80)
REVERT: Q   77 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8128 (mt-10)
REVERT: Q  135 LYS cc_start: 0.8213 (tptt) cc_final: 0.7813 (tttm)
REVERT: R  135 LYS cc_start: 0.8346 (tptt) cc_final: 0.7759 (ttpp)
REVERT: S   91 VAL cc_start: 0.9225 (m) cc_final: 0.9015 (t)
REVERT: T  135 LYS cc_start: 0.8436 (tptt) cc_final: 0.8110 (mmtm)
REVERT: V   22 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8482 (mp)
REVERT: V   97 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7414 (mp0)
REVERT: V  103 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7858 (p0)
REVERT: V  135 LYS cc_start: 0.8492 (mptt) cc_final: 0.8156 (mttt)
REVERT: W   77 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7688 (mt-10)
  outliers start: 85
  outliers final: 56
  residues processed: 502
  average time/residue: 0.3436
  time to fit residues: 274.7982
Evaluate side-chains
  489 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 422
  time to evaluate  : 2.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 PHE
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain E residue   73 SER
Chi-restraints excluded: chain E residue  141 MET
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain H residue   31 GLN
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   85 ASP
Chi-restraints excluded: chain J residue   73 SER
Chi-restraints excluded: chain J residue  103 ASP
Chi-restraints excluded: chain K residue    8 THR
Chi-restraints excluded: chain K residue   29 GLN
Chi-restraints excluded: chain K residue   31 GLN
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue  141 MET
Chi-restraints excluded: chain L residue  148 ASP
Chi-restraints excluded: chain M residue    7 PHE
Chi-restraints excluded: chain M residue    8 THR
Chi-restraints excluded: chain M residue   11 GLU
Chi-restraints excluded: chain M residue   22 LEU
Chi-restraints excluded: chain M residue   92 ILE
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain N residue   22 LEU
Chi-restraints excluded: chain N residue   73 SER
Chi-restraints excluded: chain N residue   92 ILE
Chi-restraints excluded: chain N residue  129 ASP
Chi-restraints excluded: chain O residue    8 THR
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue  141 MET
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain P residue    8 THR
Chi-restraints excluded: chain P residue   74 THR
Chi-restraints excluded: chain Q residue   29 GLN
Chi-restraints excluded: chain Q residue   41 SER
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain R residue  141 MET
Chi-restraints excluded: chain S residue   73 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  112 THR
Chi-restraints excluded: chain T residue    8 THR
Chi-restraints excluded: chain T residue   78 THR
Chi-restraints excluded: chain U residue    8 THR
Chi-restraints excluded: chain U residue   73 SER
Chi-restraints excluded: chain U residue   78 THR
Chi-restraints excluded: chain U residue  141 MET
Chi-restraints excluded: chain V residue    7 PHE
Chi-restraints excluded: chain V residue   22 LEU
Chi-restraints excluded: chain V residue   97 GLU
Chi-restraints excluded: chain V residue  103 ASP
Chi-restraints excluded: chain V residue  112 THR
Chi-restraints excluded: chain W residue   73 SER
Chi-restraints excluded: chain W residue   82 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 248 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 167 optimal weight:    1.9990
   chunk 223 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 253 optimal weight:    8.9990
   chunk 246 optimal weight:    2.9990
   chunk 318 optimal weight:    0.1980
   chunk 268 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B 109 GLN
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
G  29 GLN
G 109 GLN
H  29 GLN
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 109 GLN
T 149 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.095563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.087077 restraints weight = 33406.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 1.16
r_work: 0.2815 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  24311  Z= 0.164
  Angle     :  0.450   7.593  33143  Z= 0.240
  Chirality :  0.046   0.147   4186
  Planarity :  0.003   0.030   4209
  Dihedral  :  3.890  23.596   3427
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.82 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.74 (0.15), residues: 3243
  helix:  2.50 (0.17), residues: 1081
  sheet:  0.86 (0.19), residues: 713
  loop :  2.05 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 132 
 PHE   0.006   0.001   PHE W   7 
 TYR   0.009   0.001   TYR I  33 
 ARG   0.003   0.000   ARG P  59 

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

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

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6486 Ramachandran restraints generated.
    3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  499 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 426
  time to evaluate  : 2.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASP cc_start: 0.8002 (p0) cc_final: 0.7651 (p0)
REVERT: A  125 ASN cc_start: 0.8204 (t0) cc_final: 0.7836 (t0)
REVERT: B   65 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7420 (mttt)
REVERT: B   77 GLU cc_start: 0.8131 (mp0) cc_final: 0.7749 (mp0)
REVERT: C   22 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8126 (mp)
REVERT: C   77 GLU cc_start: 0.8190 (mp0) cc_final: 0.7923 (mp0)
REVERT: C  135 LYS cc_start: 0.8265 (tptt) cc_final: 0.8013 (mtmm)
REVERT: D   65 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8073 (mmtp)
REVERT: E  141 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8214 (ptt)
REVERT: G  141 MET cc_start: 0.8458 (ptp) cc_final: 0.8161 (ptm)
REVERT: H   31 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7271 (pt0)
REVERT: I   97 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7766 (mm-30)
REVERT: J   67 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8495 (mmtt)
REVERT: J  129 ASP cc_start: 0.7523 (m-30) cc_final: 0.6900 (t70)
REVERT: K   31 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7702 (pt0)
REVERT: K   65 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8329 (mmtp)
REVERT: L  135 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7795 (mtpt)
REVERT: M    7 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6938 (t80)
REVERT: M   22 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8002 (mp)
REVERT: M   29 GLN cc_start: 0.8120 (tt0) cc_final: 0.7564 (mt0)
REVERT: M   67 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8211 (mtmt)
REVERT: M  135 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8516 (tttp)
REVERT: N   87 ASN cc_start: 0.9136 (t0) cc_final: 0.8873 (t0)
REVERT: O  129 ASP cc_start: 0.8358 (t70) cc_final: 0.7845 (t0)
REVERT: P    7 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7895 (t80)
REVERT: Q   77 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8136 (mt-10)
REVERT: Q  135 LYS cc_start: 0.8183 (tptt) cc_final: 0.7617 (tttm)
REVERT: R  135 LYS cc_start: 0.8382 (tptt) cc_final: 0.7753 (ttpp)
REVERT: S   91 VAL cc_start: 0.9221 (m) cc_final: 0.8987 (t)
REVERT: T  135 LYS cc_start: 0.8403 (tptt) cc_final: 0.8101 (mmtm)
REVERT: V   22 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8487 (mp)
REVERT: V   97 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7446 (mp0)
REVERT: V  103 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7863 (p0)
REVERT: V  135 LYS cc_start: 0.8495 (mptt) cc_final: 0.8153 (mttt)
REVERT: W   77 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7690 (mt-10)
  outliers start: 73
  outliers final: 59
  residues processed: 479
  average time/residue: 0.3426
  time to fit residues: 260.5507
Evaluate side-chains
  488 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 419
  time to evaluate  : 2.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 PHE
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   11 GLU
Chi-restraints excluded: chain B residue  109 GLN
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain E residue   73 SER
Chi-restraints excluded: chain E residue  141 MET
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue  112 THR
Chi-restraints excluded: chain G residue  112 THR
Chi-restraints excluded: chain H residue   31 GLN
Chi-restraints excluded: chain H residue   82 VAL
Chi-restraints excluded: chain I residue    8 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue   85 ASP
Chi-restraints excluded: chain J residue   73 SER
Chi-restraints excluded: chain J residue   78 THR
Chi-restraints excluded: chain J residue  103 ASP
Chi-restraints excluded: chain K residue   29 GLN
Chi-restraints excluded: chain K residue   31 GLN
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   73 SER
Chi-restraints excluded: chain K residue  149 ASN
Chi-restraints excluded: chain L residue    8 THR
Chi-restraints excluded: chain L residue  141 MET
Chi-restraints excluded: chain L residue  148 ASP
Chi-restraints excluded: chain M residue    7 PHE
Chi-restraints excluded: chain M residue   11 GLU
Chi-restraints excluded: chain M residue   22 LEU
Chi-restraints excluded: chain M residue   92 ILE
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain N residue   22 LEU
Chi-restraints excluded: chain N residue   73 SER
Chi-restraints excluded: chain N residue   92 ILE
Chi-restraints excluded: chain N residue  129 ASP
Chi-restraints excluded: chain O residue    8 THR
Chi-restraints excluded: chain O residue   82 VAL
Chi-restraints excluded: chain O residue  141 MET
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain P residue    8 THR
Chi-restraints excluded: chain P residue   74 THR
Chi-restraints excluded: chain Q residue   41 SER
Chi-restraints excluded: chain R residue   78 THR
Chi-restraints excluded: chain S residue   73 SER
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  112 THR
Chi-restraints excluded: chain T residue    8 THR
Chi-restraints excluded: chain T residue   78 THR
Chi-restraints excluded: chain T residue  149 ASN
Chi-restraints excluded: chain U residue    8 THR
Chi-restraints excluded: chain U residue   73 SER
Chi-restraints excluded: chain U residue   78 THR
Chi-restraints excluded: chain U residue  141 MET
Chi-restraints excluded: chain V residue    7 PHE
Chi-restraints excluded: chain V residue   22 LEU
Chi-restraints excluded: chain V residue   97 GLU
Chi-restraints excluded: chain V residue  103 ASP
Chi-restraints excluded: chain V residue  112 THR
Chi-restraints excluded: chain W residue   64 SER
Chi-restraints excluded: chain W residue   73 SER
Chi-restraints excluded: chain W residue   82 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 322
   random chunks:
   chunk 250 optimal weight:    7.9990
   chunk 241 optimal weight:    0.7980
   chunk 155 optimal weight:    7.9990
   chunk 106 optimal weight:   10.0000
   chunk 156 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 174 optimal weight:    8.9990
   chunk 319 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
B 109 GLN
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
F  31 GLN
G  29 GLN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  87 ASN
Q 149 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.092483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.084000 restraints weight = 33612.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 1.16
r_work: 0.2760 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  24311  Z= 0.276
  Angle     :  0.509   7.841  33143  Z= 0.274
  Chirality :  0.049   0.161   4186
  Planarity :  0.004   0.031   4209
  Dihedral  :  4.312  26.743   3427
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 22.66 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.15), residues: 3243
  helix:  2.27 (0.17), residues: 1081
  sheet:  0.71 (0.19), residues: 713
  loop :  1.96 (0.16), residues: 1449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 132 
 PHE   0.008   0.001   PHE E 142 
 TYR   0.013   0.001   TYR H  33 
 ARG   0.007   0.001   ARG P  59 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10461.38 seconds
wall clock time: 189 minutes 54.69 seconds (11394.69 seconds total)