Starting phenix.real_space_refine
on Tue Mar  3 11:08:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uur_20900/03_2026/6uur_20900.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uur_20900/03_2026/6uur_20900.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uur_20900/03_2026/6uur_20900.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uur_20900/03_2026/6uur_20900.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uur_20900/03_2026/6uur_20900.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uur_20900/03_2026/6uur_20900.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      40      5.16       5
     C    1740      2.51       5
     N     500      2.21       5
     O     490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2770
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 277
          Classifications: {'peptide': 40}
          Link IDs: {'PTRANS': 1, 'TRANS': 38}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.35, per 1000 atoms: 0.13
  Number of scatterers: 2770
  At special positions: 0
  Unit cell: (86.67, 58.85, 40.66, 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      40     16.00
     O     490      8.00
     N     500      7.00
     C    1740      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 112.2 milliseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  640

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 50.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'H' and resid 107 through 124
      removed outlier: 6.498A  pdb=" N   THR D 107 " --> pdb=" O   ASN H 108 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   LYS H 110 " --> pdb=" O   THR D 107 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   MET D 109 " --> pdb=" O   LYS H 110 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   MET H 112 " --> pdb=" O   MET D 109 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   HIS D 111 " --> pdb=" O   MET H 112 " (cutoff:3.500A)
      removed outlier: 10.439A  pdb=" N   GLY H 114 " --> pdb=" O   HIS D 111 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   ALA D 113 " --> pdb=" O   GLY H 114 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   ALA H 116 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ALA D 115 " --> pdb=" O   ALA H 116 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ALA H 118 " --> pdb=" O   ALA D 115 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ALA D 117 " --> pdb=" O   ALA H 118 " (cutoff:3.500A)
      removed outlier: 8.443A  pdb=" N   ALA H 120 " --> pdb=" O   ALA D 117 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY D 119 " --> pdb=" O   ALA H 120 " (cutoff:3.500A)
      removed outlier: 8.495A  pdb=" N   VAL H 122 " --> pdb=" O   GLY D 119 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL D 121 " --> pdb=" O   VAL H 122 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   GLY H 124 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   GLY D 123 " --> pdb=" O   GLY H 124 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   THR A 107 " --> pdb=" O   ASN D 108 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   LYS D 110 " --> pdb=" O   THR A 107 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   MET A 109 " --> pdb=" O   LYS D 110 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   MET D 112 " --> pdb=" O   MET A 109 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   HIS A 111 " --> pdb=" O   MET D 112 " (cutoff:3.500A)
      removed outlier: 10.404A  pdb=" N   GLY D 114 " --> pdb=" O   HIS A 111 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   ALA A 113 " --> pdb=" O   GLY D 114 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   ALA D 116 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ALA A 115 " --> pdb=" O   ALA D 116 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   ALA D 118 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ALA A 117 " --> pdb=" O   ALA D 118 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ALA D 120 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLY A 119 " --> pdb=" O   ALA D 120 " (cutoff:3.500A)
      removed outlier: 8.508A  pdb=" N   VAL D 122 " --> pdb=" O   GLY A 119 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   VAL A 121 " --> pdb=" O   VAL D 122 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   GLY D 124 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   GLY A 123 " --> pdb=" O   GLY D 124 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   MET A 112 " --> pdb=" O   HIS E 111 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ALA E 113 " --> pdb=" O   MET A 112 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   GLY A 114 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   MET E 112 " --> pdb=" O   HIS I 111 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ALA I 113 " --> pdb=" O   MET E 112 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   GLY E 114 " --> pdb=" O   ALA I 113 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 134 through 135
      removed outlier: 6.634A  pdb=" N   MET D 134 " --> pdb=" O   SER H 135 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   MET A 134 " --> pdb=" O   SER D 135 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 138 through 140
      removed outlier: 6.152A  pdb=" N   ILE A 139 " --> pdb=" O   HIS E 140 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   ILE E 139 " --> pdb=" O   HIS I 140 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 107 through 124
      removed outlier: 6.854A  pdb=" N   MET C 112 " --> pdb=" O   HIS G 111 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ALA G 113 " --> pdb=" O   MET C 112 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   GLY C 114 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   MET B 112 " --> pdb=" O   HIS C 111 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ALA C 113 " --> pdb=" O   MET B 112 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   GLY B 114 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   THR B 107 " --> pdb=" O   ASN F 108 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   LYS F 110 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   MET B 109 " --> pdb=" O   LYS F 110 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   MET F 112 " --> pdb=" O   MET B 109 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   HIS B 111 " --> pdb=" O   MET F 112 " (cutoff:3.500A)
      removed outlier: 10.439A  pdb=" N   GLY F 114 " --> pdb=" O   HIS B 111 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   ALA B 113 " --> pdb=" O   GLY F 114 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   ALA F 116 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ALA B 115 " --> pdb=" O   ALA F 116 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ALA F 118 " --> pdb=" O   ALA B 115 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ALA B 117 " --> pdb=" O   ALA F 118 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   ALA F 120 " --> pdb=" O   ALA B 117 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLY B 119 " --> pdb=" O   ALA F 120 " (cutoff:3.500A)
      removed outlier: 8.494A  pdb=" N   VAL F 122 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL B 121 " --> pdb=" O   VAL F 122 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   GLY F 124 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLY B 123 " --> pdb=" O   GLY F 124 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   THR F 107 " --> pdb=" O   ASN J 108 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   LYS J 110 " --> pdb=" O   THR F 107 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   MET F 109 " --> pdb=" O   LYS J 110 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   MET J 112 " --> pdb=" O   MET F 109 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   HIS F 111 " --> pdb=" O   MET J 112 " (cutoff:3.500A)
      removed outlier: 10.439A  pdb=" N   GLY J 114 " --> pdb=" O   HIS F 111 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   ALA F 113 " --> pdb=" O   GLY J 114 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   ALA J 116 " --> pdb=" O   ALA F 113 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ALA F 115 " --> pdb=" O   ALA J 116 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   ALA J 118 " --> pdb=" O   ALA F 115 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ALA F 117 " --> pdb=" O   ALA J 118 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ALA J 120 " --> pdb=" O   ALA F 117 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY F 119 " --> pdb=" O   ALA J 120 " (cutoff:3.500A)
      removed outlier: 8.495A  pdb=" N   VAL J 122 " --> pdb=" O   GLY F 119 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL F 121 " --> pdb=" O   VAL J 122 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   GLY J 124 " --> pdb=" O   VAL F 121 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLY F 123 " --> pdb=" O   GLY J 124 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 134 through 135
      removed outlier: 6.632A  pdb=" N   MET B 134 " --> pdb=" O   SER F 135 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   MET F 134 " --> pdb=" O   SER J 135 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 138 through 140
      removed outlier: 6.176A  pdb=" N   ILE C 139 " --> pdb=" O   HIS G 140 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ILE B 139 " --> pdb=" O   HIS C 140 " (cutoff:3.500A)

    69 hydrogen bonds defined for protein.
    204 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.39

  Time building geometry restraints manager: 0.29 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: 900
        1.35 -     1.46: 650
        1.46 -     1.58: 1190
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 2820
  Sorted by residual:
  bond pdb=" CB  MET C 112 "
       pdb=" CG  MET C 112 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.30e-01
  bond pdb=" CB  MET F 112 "
       pdb=" CG  MET F 112 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.30e-01
  bond pdb=" CB  MET H 112 "
       pdb=" CG  MET H 112 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.28e-01
  bond pdb=" CB  MET B 112 "
       pdb=" CG  MET B 112 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.28e-01
  bond pdb=" CB  MET D 112 "
       pdb=" CG  MET D 112 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.26e-01
  ... (remaining 2815 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 3455
        1.28 -     2.57: 265
        2.57 -     3.85: 20
        3.85 -     5.13: 10
        5.13 -     6.42: 10
  Bond angle restraints: 3760
  Sorted by residual:
  angle pdb=" CA  LEU J 130 "
        pdb=" CB  LEU J 130 "
        pdb=" CG  LEU J 130 "
      ideal   model   delta    sigma   weight residual
     116.30  122.72   -6.42 3.50e+00 8.16e-02 3.36e+00
  angle pdb=" CA  LEU H 130 "
        pdb=" CB  LEU H 130 "
        pdb=" CG  LEU H 130 "
      ideal   model   delta    sigma   weight residual
     116.30  122.72   -6.42 3.50e+00 8.16e-02 3.36e+00
  angle pdb=" CA  LEU F 130 "
        pdb=" CB  LEU F 130 "
        pdb=" CG  LEU F 130 "
      ideal   model   delta    sigma   weight residual
     116.30  122.71   -6.41 3.50e+00 8.16e-02 3.35e+00
  angle pdb=" CA  LEU C 130 "
        pdb=" CB  LEU C 130 "
        pdb=" CG  LEU C 130 "
      ideal   model   delta    sigma   weight residual
     116.30  122.71   -6.41 3.50e+00 8.16e-02 3.35e+00
  angle pdb=" CA  LEU G 130 "
        pdb=" CB  LEU G 130 "
        pdb=" CG  LEU G 130 "
      ideal   model   delta    sigma   weight residual
     116.30  122.70   -6.40 3.50e+00 8.16e-02 3.35e+00
  ... (remaining 3755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.18: 1130
        8.18 -    16.36: 200
       16.36 -    24.54: 130
       24.54 -    32.72: 110
       32.72 -    40.90: 40
  Dihedral angle restraints: 1610
    sinusoidal: 560
      harmonic: 1050
  Sorted by residual:
  dihedral pdb=" CA  MET F 109 "
           pdb=" C   MET F 109 "
           pdb=" N   LYS F 110 "
           pdb=" CA  LYS F 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.95  -15.05     0      5.00e+00 4.00e-02 9.06e+00
  dihedral pdb=" CA  MET H 109 "
           pdb=" C   MET H 109 "
           pdb=" N   LYS H 110 "
           pdb=" CA  LYS H 110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -165.00  -15.00     0      5.00e+00 4.00e-02 9.00e+00
  dihedral pdb=" CA  MET C 109 "
           pdb=" C   MET C 109 "
           pdb=" N   LYS C 110 "
           pdb=" CA  LYS C 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.00  -15.00     0      5.00e+00 4.00e-02 8.99e+00
  ... (remaining 1607 not shown)

  Histogram of chiral volume deviations from ideal:
       0.004 -    0.030: 206
       0.030 -    0.056: 94
       0.056 -    0.083: 34
       0.083 -    0.109: 29
       0.109 -    0.135: 27
  Chirality restraints: 390
  Sorted by residual:
  chirality pdb=" CA  ILE E 139 "
            pdb=" N   ILE E 139 "
            pdb=" C   ILE E 139 "
            pdb=" CB  ILE E 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  ILE J 139 "
            pdb=" N   ILE J 139 "
            pdb=" C   ILE J 139 "
            pdb=" CB  ILE J 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  ILE B 139 "
            pdb=" N   ILE B 139 "
            pdb=" C   ILE B 139 "
            pdb=" CB  ILE B 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 387 not shown)

  Planarity restraints: 480
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE J 141 "   -0.005 2.00e-02 2.50e+03   3.48e-03 2.12e-01
        pdb=" CG  PHE J 141 "    0.003 2.00e-02 2.50e+03
        pdb=" CD1 PHE J 141 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE J 141 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE J 141 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE J 141 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE J 141 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H 141 "    0.005 2.00e-02 2.50e+03   3.42e-03 2.04e-01
        pdb=" CG  PHE H 141 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD1 PHE H 141 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE H 141 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE H 141 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE H 141 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE H 141 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 141 "   -0.004 2.00e-02 2.50e+03   3.28e-03 1.88e-01
        pdb=" CG  PHE C 141 "    0.003 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 141 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 141 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 141 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 141 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 141 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 477 not shown)

  Histogram of nonbonded interaction distances:
        2.64 -     3.09: 1589
        3.09 -     3.55: 2685
        3.55 -     4.00: 4124
        4.00 -     4.45: 5058
        4.45 -     4.90: 9474
  Nonbonded interactions: 22930
  Sorted by model distance:
  nonbonded pdb=" N   GLY J 126 "
            pdb=" O   GLY J 126 "
     model   vdw
     2.644 2.496
  nonbonded pdb=" N   GLY I 126 "
            pdb=" O   GLY I 126 "
     model   vdw
     2.644 2.496
  nonbonded pdb=" N   GLY B 126 "
            pdb=" O   GLY B 126 "
     model   vdw
     2.644 2.496
  nonbonded pdb=" N   GLY F 126 "
            pdb=" O   GLY F 126 "
     model   vdw
     2.644 2.496
  nonbonded pdb=" N   GLY E 126 "
            pdb=" O   GLY E 126 "
     model   vdw
     2.644 2.496
  ... (remaining 22925 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.290
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
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      :  0.004   0.024   2820  Z= 0.181
  Angle     :  0.760   6.416   3760  Z= 0.384
  Chirality :  0.051   0.135    390
  Planarity :  0.002   0.010    480
  Dihedral  : 15.648  40.900    970
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.20 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.46 (0.30), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C 136 
 TYR   0.005   0.001   TYR C 128 
 PHE   0.006   0.003   PHE J 141 
 HIS   0.003   0.002   HIS E 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 2820)
  covalent geometry    : angle       0.75992 ( 3760)
  hydrogen bonds       : bond        0.17837 (   69)
  hydrogen bonds       : angle      10.33401 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.7521 (t0) cc_final: 0.7183 (t0)
REVERT: C  108 ASN cc_start: 0.7605 (t0) cc_final: 0.7264 (t0)
REVERT: E  108 ASN cc_start: 0.7363 (t0) cc_final: 0.6497 (t0)
REVERT: F  108 ASN cc_start: 0.7518 (t0) cc_final: 0.7184 (t0)
REVERT: H  108 ASN cc_start: 0.7936 (t0) cc_final: 0.6873 (t0)
REVERT: I  108 ASN cc_start: 0.7743 (t0) cc_final: 0.7101 (t0)
REVERT: J  110 LYS cc_start: 0.7840 (mttt) cc_final: 0.7585 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0533
  time to fit residues: 5.7626
Evaluate side-chains
  79 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 108 ASN
** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.167112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.143621 restraints weight = 3390.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.146376 restraints weight = 2019.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.147931 restraints weight = 1492.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.149111 restraints weight = 1264.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 13)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.149272 restraints weight = 1128.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.4363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   2820  Z= 0.286
  Angle     :  0.884   6.037   3760  Z= 0.439
  Chirality :  0.048   0.132    390
  Planarity :  0.003   0.010    480
  Dihedral  :  5.274  19.445    420
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 16.80 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.32 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG H 136 
 TYR   0.008   0.001   TYR C 145 
 PHE   0.013   0.005   PHE G 141 
 HIS   0.005   0.002   HIS J 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00661 ( 2820)
  covalent geometry    : angle       0.88386 ( 3760)
  hydrogen bonds       : bond        0.03835 (   69)
  hydrogen bonds       : angle       7.87615 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  108 ASN cc_start: 0.8119 (t0) cc_final: 0.7658 (t0)
REVERT: C  110 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8410 (mttp)
REVERT: D  108 ASN cc_start: 0.7812 (t0) cc_final: 0.7611 (t0)
REVERT: G  108 ASN cc_start: 0.8105 (t0) cc_final: 0.7508 (t0)
REVERT: G  110 LYS cc_start: 0.8584 (mttt) cc_final: 0.8367 (mttp)
REVERT: I  108 ASN cc_start: 0.8059 (t0) cc_final: 0.7640 (t0)
REVERT: I  134 MET cc_start: 0.6628 (tmm) cc_final: 0.6367 (tmm)
REVERT: J  110 LYS cc_start: 0.8306 (mttt) cc_final: 0.7805 (mtpp)
REVERT: J  112 MET cc_start: 0.8055 (mtm) cc_final: 0.7753 (mtm)
  outliers start: 18
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0476
  time to fit residues: 5.2544
Evaluate side-chains
  89 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain C residue  138 ILE
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain G residue  130 LEU
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain J residue  108 ASN
Chi-restraints excluded: chain J residue  138 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 30 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.168188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.144327 restraints weight = 3394.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.147230 restraints weight = 1862.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.149293 restraints weight = 1335.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.150360 restraints weight = 1093.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.150956 restraints weight = 977.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   2820  Z= 0.237
  Angle     :  0.791   7.127   3760  Z= 0.398
  Chirality :  0.047   0.135    390
  Planarity :  0.002   0.008    480
  Dihedral  :  4.981  17.498    420
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  6.80 %
    Allowed  : 18.00 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.17 (0.33), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C 136 
 TYR   0.006   0.001   TYR H 145 
 PHE   0.010   0.003   PHE G 141 
 HIS   0.005   0.002   HIS I 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 2820)
  covalent geometry    : angle       0.79077 ( 3760)
  hydrogen bonds       : bond        0.03505 (   69)
  hydrogen bonds       : angle       7.37496 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.8088 (t0) cc_final: 0.7715 (t0)
REVERT: A  110 LYS cc_start: 0.8503 (mttt) cc_final: 0.8193 (mttp)
REVERT: D  108 ASN cc_start: 0.8106 (t0) cc_final: 0.7827 (t0)
REVERT: D  109 MET cc_start: 0.7101 (ttt) cc_final: 0.6871 (ttt)
REVERT: I  138 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8218 (pt)
REVERT: J  110 LYS cc_start: 0.8296 (mttt) cc_final: 0.7732 (mtpp)
  outliers start: 17
  outliers final: 10
  residues processed: 90
  average time/residue: 0.0481
  time to fit residues: 5.4378
Evaluate side-chains
  89 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain C residue  138 ILE
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain I residue  138 ILE
Chi-restraints excluded: chain J residue  108 ASN
Chi-restraints excluded: chain J residue  138 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
F 108 ASN
** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.172639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.148215 restraints weight = 3286.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.151157 restraints weight = 1845.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.153131 restraints weight = 1335.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.154005 restraints weight = 1110.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.154005 restraints weight = 1011.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2820  Z= 0.172
  Angle     :  0.719   4.796   3760  Z= 0.361
  Chirality :  0.047   0.131    390
  Planarity :  0.002   0.009    480
  Dihedral  :  4.691  19.066    420
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  6.80 %
    Allowed  : 20.00 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.08 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 136 
 TYR   0.004   0.001   TYR H 128 
 PHE   0.006   0.002   PHE I 141 
 HIS   0.004   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 2820)
  covalent geometry    : angle       0.71877 ( 3760)
  hydrogen bonds       : bond        0.03030 (   69)
  hydrogen bonds       : angle       6.80619 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.7925 (t0) cc_final: 0.7713 (t0)
REVERT: A  110 LYS cc_start: 0.8399 (mttt) cc_final: 0.8101 (mttt)
REVERT: A  112 MET cc_start: 0.8206 (mtm) cc_final: 0.7778 (mtt)
REVERT: C  108 ASN cc_start: 0.8157 (t0) cc_final: 0.7546 (t0)
REVERT: D  109 MET cc_start: 0.7260 (ttt) cc_final: 0.6949 (ttt)
REVERT: E  108 ASN cc_start: 0.7901 (t0) cc_final: 0.7633 (t0)
REVERT: I  108 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8022 (t0)
REVERT: I  138 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8194 (pt)
  outliers start: 17
  outliers final: 11
  residues processed: 92
  average time/residue: 0.0437
  time to fit residues: 5.0181
Evaluate side-chains
  92 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain C residue  138 ILE
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain F residue  108 ASN
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain I residue  108 ASN
Chi-restraints excluded: chain I residue  138 ILE
Chi-restraints excluded: chain J residue  108 ASN
Chi-restraints excluded: chain J residue  138 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 31 optimal weight:    0.5980
   chunk 13 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.163568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.139727 restraints weight = 3438.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.142169 restraints weight = 2031.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.143510 restraints weight = 1541.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.144676 restraints weight = 1330.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.144676 restraints weight = 1208.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.055   2820  Z= 0.333
  Angle     :  0.920   6.777   3760  Z= 0.464
  Chirality :  0.049   0.134    390
  Planarity :  0.003   0.013    480
  Dihedral  :  5.367  19.634    420
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.63 %
    Favored  : 87.37 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 22.00 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.19 (0.33), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 136 
 TYR   0.008   0.001   TYR H 145 
 PHE   0.013   0.004   PHE I 141 
 HIS   0.008   0.002   HIS G 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00777 ( 2820)
  covalent geometry    : angle       0.91965 ( 3760)
  hydrogen bonds       : bond        0.03729 (   69)
  hydrogen bonds       : angle       7.11830 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.8693 (mttt) cc_final: 0.8436 (mttp)
REVERT: A  112 MET cc_start: 0.8227 (mtm) cc_final: 0.7809 (mtt)
REVERT: C  108 ASN cc_start: 0.8178 (t0) cc_final: 0.7868 (t0)
REVERT: C  110 LYS cc_start: 0.8543 (mttt) cc_final: 0.8234 (mttp)
REVERT: E  108 ASN cc_start: 0.7983 (t0) cc_final: 0.7761 (t0)
REVERT: G  136 ARG cc_start: 0.7164 (ttt180) cc_final: 0.6962 (tpp-160)
REVERT: I  136 ARG cc_start: 0.7088 (ttt180) cc_final: 0.6876 (tpp-160)
REVERT: I  138 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8246 (pt)
REVERT: J  112 MET cc_start: 0.7938 (mtm) cc_final: 0.7667 (mtm)
REVERT: J  136 ARG cc_start: 0.7051 (ttt180) cc_final: 0.6775 (ttm110)
  outliers start: 14
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0731
  time to fit residues: 8.1254
Evaluate side-chains
  90 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain C residue  138 ILE
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain H residue  108 ASN
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain I residue  138 ILE
Chi-restraints excluded: chain J residue  138 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0870
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.174286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.149829 restraints weight = 3314.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.152898 restraints weight = 1850.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.154655 restraints weight = 1335.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.156014 restraints weight = 1117.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.156526 restraints weight = 993.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.4550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2820  Z= 0.128
  Angle     :  0.705   5.317   3760  Z= 0.354
  Chirality :  0.048   0.132    390
  Planarity :  0.002   0.016    480
  Dihedral  :  4.714  21.188    420
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 24.00 %
    Favored  : 71.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.26 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 136 
 TYR   0.003   0.000   TYR H 128 
 PHE   0.003   0.001   PHE F 141 
 HIS   0.008   0.002   HIS J 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2820)
  covalent geometry    : angle       0.70458 ( 3760)
  hydrogen bonds       : bond        0.02509 (   69)
  hydrogen bonds       : angle       6.34596 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8214 (mtm) cc_final: 0.7737 (mtt)
REVERT: E  108 ASN cc_start: 0.7985 (t0) cc_final: 0.7734 (t0)
REVERT: H  108 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8411 (t0)
REVERT: I  112 MET cc_start: 0.7242 (mtt) cc_final: 0.6728 (mmt)
REVERT: I  138 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8357 (pt)
REVERT: J  108 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8098 (m110)
  outliers start: 12
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0504
  time to fit residues: 5.7172
Evaluate side-chains
  94 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain H residue  108 ASN
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain I residue  138 ILE
Chi-restraints excluded: chain J residue  108 ASN
Chi-restraints excluded: chain J residue  138 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 34 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.165223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.141211 restraints weight = 3408.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.143821 restraints weight = 2015.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.145516 restraints weight = 1511.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.146598 restraints weight = 1280.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.146796 restraints weight = 1163.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   2820  Z= 0.269
  Angle     :  0.849   5.526   3760  Z= 0.431
  Chirality :  0.048   0.134    390
  Planarity :  0.003   0.020    480
  Dihedral  :  5.095  18.572    420
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.63 %
    Favored  : 87.37 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 21.60 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.34 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 136 
 TYR   0.006   0.001   TYR H 145 
 PHE   0.009   0.003   PHE G 141 
 HIS   0.007   0.002   HIS G 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00627 ( 2820)
  covalent geometry    : angle       0.84868 ( 3760)
  hydrogen bonds       : bond        0.03290 (   69)
  hydrogen bonds       : angle       6.57240 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  112 MET cc_start: 0.8289 (mtm) cc_final: 0.7785 (mtt)
REVERT: D  110 LYS cc_start: 0.8512 (mttt) cc_final: 0.8059 (mttt)
REVERT: E  108 ASN cc_start: 0.8108 (t0) cc_final: 0.7767 (t0)
REVERT: H  108 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8136 (m110)
REVERT: I  112 MET cc_start: 0.7500 (mtt) cc_final: 0.6941 (mmt)
REVERT: I  138 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8255 (pt)
  outliers start: 13
  outliers final: 10
  residues processed: 84
  average time/residue: 0.0433
  time to fit residues: 4.6456
Evaluate side-chains
  83 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain G residue  121 VAL
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain H residue  108 ASN
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain I residue  138 ILE
Chi-restraints excluded: chain J residue  138 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    0.0870
   chunk 5 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.6164

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

Flipped N/Q/H residues before XYZ refinement:
** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.168153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.143484 restraints weight = 3450.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.146500 restraints weight = 1953.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.148031 restraints weight = 1419.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.149351 restraints weight = 1203.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.149686 restraints weight = 1077.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2820  Z= 0.184
  Angle     :  0.768   5.570   3760  Z= 0.388
  Chirality :  0.048   0.133    390
  Planarity :  0.002   0.018    480
  Dihedral  :  4.928  18.658    420
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  6.80 %
    Allowed  : 19.60 %
    Favored  : 73.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.38 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 136 
 TYR   0.003   0.001   TYR H 145 
 PHE   0.006   0.002   PHE G 141 
 HIS   0.006   0.002   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 2820)
  covalent geometry    : angle       0.76756 ( 3760)
  hydrogen bonds       : bond        0.02862 (   69)
  hydrogen bonds       : angle       6.32458 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8295 (mtm) cc_final: 0.7770 (mtt)
REVERT: E  108 ASN cc_start: 0.8114 (t0) cc_final: 0.7777 (t0)
REVERT: H  108 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8138 (m-40)
REVERT: I  112 MET cc_start: 0.7307 (mtt) cc_final: 0.6798 (mmt)
REVERT: I  138 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8251 (pt)
REVERT: J  112 MET cc_start: 0.7881 (mtm) cc_final: 0.7559 (mtm)
  outliers start: 17
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0468
  time to fit residues: 5.0627
Evaluate side-chains
  86 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  143 SER
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain H residue  108 ASN
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain I residue  138 ILE
Chi-restraints excluded: chain J residue  121 VAL
Chi-restraints excluded: chain J residue  138 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0980
   chunk 20 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.171644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.147250 restraints weight = 3454.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.150178 restraints weight = 2025.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.152023 restraints weight = 1495.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.152971 restraints weight = 1257.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.153503 restraints weight = 1142.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.4523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2820  Z= 0.162
  Angle     :  0.741   5.937   3760  Z= 0.375
  Chirality :  0.048   0.133    390
  Planarity :  0.002   0.018    480
  Dihedral  :  4.865  19.502    420
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  6.80 %
    Allowed  : 20.80 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.42 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 136 
 TYR   0.003   0.001   TYR H 145 
 PHE   0.004   0.001   PHE I 141 
 HIS   0.007   0.002   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 2820)
  covalent geometry    : angle       0.74086 ( 3760)
  hydrogen bonds       : bond        0.02690 (   69)
  hydrogen bonds       : angle       6.10499 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8235 (mtm) cc_final: 0.7716 (mtt)
REVERT: B  109 MET cc_start: 0.6340 (ttt) cc_final: 0.5997 (ttt)
REVERT: C  108 ASN cc_start: 0.8103 (t0) cc_final: 0.7866 (t0)
REVERT: D  109 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6575 (ttt)
REVERT: E  108 ASN cc_start: 0.8036 (t0) cc_final: 0.7708 (t0)
REVERT: F  108 ASN cc_start: 0.7669 (t0) cc_final: 0.7444 (t0)
REVERT: I  138 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8175 (pt)
REVERT: J  112 MET cc_start: 0.7761 (mtm) cc_final: 0.7393 (mtm)
  outliers start: 17
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0493
  time to fit residues: 5.4975
Evaluate side-chains
  92 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  138 ILE
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain F residue  110 LYS
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  143 SER
Chi-restraints excluded: chain G residue  121 VAL
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain I residue  138 ILE
Chi-restraints excluded: chain J residue  138 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 4 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 37 optimal weight:   10.0000
   chunk 3 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 27 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.162558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.136282 restraints weight = 3399.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.139209 restraints weight = 1848.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.141067 restraints weight = 1330.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.141997 restraints weight = 1114.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.142703 restraints weight = 1016.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.4428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2820  Z= 0.124
  Angle     :  0.677   5.300   3760  Z= 0.341
  Chirality :  0.047   0.132    390
  Planarity :  0.002   0.017    480
  Dihedral  :  4.644  18.871    420
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 21.20 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.46 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 136 
 TYR   0.003   0.000   TYR H 128 
 PHE   0.003   0.001   PHE G 141 
 HIS   0.007   0.002   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2820)
  covalent geometry    : angle       0.67712 ( 3760)
  hydrogen bonds       : bond        0.02324 (   69)
  hydrogen bonds       : angle       5.86418 (  204)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8353 (mtm) cc_final: 0.7833 (mtt)
REVERT: C  108 ASN cc_start: 0.8155 (t0) cc_final: 0.7911 (t0)
REVERT: E  108 ASN cc_start: 0.8082 (t0) cc_final: 0.7744 (t0)
REVERT: F  108 ASN cc_start: 0.7932 (t0) cc_final: 0.7656 (t0)
REVERT: F  134 MET cc_start: 0.6061 (tmm) cc_final: 0.5830 (tmm)
REVERT: G  112 MET cc_start: 0.7348 (mtm) cc_final: 0.6320 (mmt)
REVERT: I  138 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8177 (pt)
  outliers start: 14
  outliers final: 12
  residues processed: 84
  average time/residue: 0.0487
  time to fit residues: 5.1418
Evaluate side-chains
  91 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  138 ILE
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain F residue  110 LYS
Chi-restraints excluded: chain F residue  138 ILE
Chi-restraints excluded: chain F residue  143 SER
Chi-restraints excluded: chain G residue  138 ILE
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain I residue  138 ILE
Chi-restraints excluded: chain J residue  138 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 29 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    9.9990
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.162725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.136491 restraints weight = 3379.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.139368 restraints weight = 1847.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.141281 restraints weight = 1337.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.142117 restraints weight = 1119.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.142117 restraints weight = 1028.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.4428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2820  Z= 0.122
  Angle     :  0.669   5.311   3760  Z= 0.337
  Chirality :  0.047   0.130    390
  Planarity :  0.002   0.016    480
  Dihedral  :  4.587  18.011    420
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 19.60 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.47 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 136 
 TYR   0.003   0.001   TYR G 128 
 PHE   0.003   0.001   PHE E 141 
 HIS   0.006   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 2820)
  covalent geometry    : angle       0.66943 ( 3760)
  hydrogen bonds       : bond        0.02268 (   69)
  hydrogen bonds       : angle       5.71262 (  204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 735.97 seconds
wall clock time: 13 minutes 20.31 seconds (800.31 seconds total)