Starting phenix.real_space_refine
on Wed Mar  5 16:36:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uur_20900/03_2025/6uur_20900.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uur_20900/03_2025/6uur_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_2025/6uur_20900.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uur_20900/03_2025/6uur_20900.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uur_20900/03_2025/6uur_20900.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uur_20900/03_2025/6uur_20900.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 2.30, per 1000 atoms: 0.83
  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: 0.71
  Conformation dependent library (CDL) restraints added in 353.1 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: 0.39
  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: 0.61

  Time building geometry restraints manager: 0.75 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain '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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.770
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.180
-------------------------------------------------------------------------------
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= 0.252
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.46 (0.30), 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
 HIS   0.003   0.002   HIS E 140 
 PHE   0.006   0.003   PHE J 141 
 TYR   0.005   0.001   TYR C 128 
 ARG   0.000   0.000   ARG C 136 

*********************** 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  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.7521 (t0) cc_final: 0.7187 (t0)
REVERT: C  108 ASN cc_start: 0.7606 (t0) cc_final: 0.7250 (t0)
REVERT: E  108 ASN cc_start: 0.7362 (t0) cc_final: 0.6505 (t0)
REVERT: F  108 ASN cc_start: 0.7517 (t0) cc_final: 0.7177 (t0)
REVERT: H  108 ASN cc_start: 0.7936 (t0) cc_final: 0.6878 (t0)
REVERT: I  108 ASN cc_start: 0.7743 (t0) cc_final: 0.7099 (t0)
REVERT: J  110 LYS cc_start: 0.7840 (mttt) cc_final: 0.7560 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1677
  time to fit residues: 17.7577
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  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 31 optimal weight:    0.1980
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
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 = 0.4596 r_free = 0.4596 target = 0.169376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.145420 restraints weight = 3311.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.148219 restraints weight = 1885.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.150229 restraints weight = 1376.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.4382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   2820  Z= 0.374
  Angle     :  0.832   5.473   3760  Z= 0.414
  Chirality :  0.048   0.130    390
  Planarity :  0.003   0.010    480
  Dihedral  :  5.088  18.714    420
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.33 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J 111 
 PHE   0.013   0.004   PHE G 141 
 TYR   0.007   0.001   TYR C 145 
 ARG   0.000   0.000   ARG D 136 

*********************** 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
  97 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8301 (mttp)
REVERT: A  134 MET cc_start: 0.6352 (tmm) cc_final: 0.6085 (tmm)
REVERT: F  108 ASN cc_start: 0.7683 (t0) cc_final: 0.7306 (t0)
REVERT: G  108 ASN cc_start: 0.8174 (t0) cc_final: 0.7541 (t0)
REVERT: G  110 LYS cc_start: 0.8527 (mttt) cc_final: 0.8321 (mttp)
REVERT: I  134 MET cc_start: 0.6566 (tmm) cc_final: 0.6262 (tmm)
REVERT: J  110 LYS cc_start: 0.8261 (mttt) cc_final: 0.7780 (mtpp)
REVERT: J  112 MET cc_start: 0.8114 (mtm) cc_final: 0.7818 (mtm)
  outliers start: 18
  outliers final: 13
  residues processed: 89
  average time/residue: 0.1333
  time to fit residues: 14.2669
Evaluate side-chains
  89 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LYS
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 37 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0470
   chunk 2 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.3284

-------------------------------------------------------------------------------
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**
G 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 = 0.4665 r_free = 0.4665 target = 0.172587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.149973 restraints weight = 3236.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.152691 restraints weight = 1866.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.154502 restraints weight = 1371.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2820  Z= 0.248
  Angle     :  0.751   7.080   3760  Z= 0.375
  Chirality :  0.047   0.133    390
  Planarity :  0.002   0.009    480
  Dihedral  :  4.667  19.064    420
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 18.40 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.23 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.22 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I 111 
 PHE   0.007   0.002   PHE G 141 
 TYR   0.003   0.001   TYR C 145 
 ARG   0.000   0.000   ARG I 136 

*********************** 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
  98 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.7815 (t0) cc_final: 0.7506 (t0)
REVERT: A  110 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8310 (mttm)
REVERT: A  134 MET cc_start: 0.6292 (tmm) cc_final: 0.6026 (tmm)
REVERT: D  109 MET cc_start: 0.7213 (ttt) cc_final: 0.6866 (ttt)
REVERT: F  108 ASN cc_start: 0.7791 (t0) cc_final: 0.7453 (t0)
REVERT: H  108 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8360 (t0)
REVERT: I  138 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8176 (pt)
REVERT: J  110 LYS cc_start: 0.8183 (mttt) cc_final: 0.7811 (mtpt)
  outliers start: 18
  outliers final: 11
  residues processed: 88
  average time/residue: 0.1199
  time to fit residues: 13.0286
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  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LYS
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  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 34 optimal weight:    9.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 = 0.4583 r_free = 0.4583 target = 0.165438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.141479 restraints weight = 3421.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.144386 restraints weight = 1890.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.146152 restraints weight = 1366.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.4346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   2820  Z= 0.462
  Angle     :  0.884   5.901   3760  Z= 0.445
  Chirality :  0.048   0.135    390
  Planarity :  0.003   0.011    480
  Dihedral  :  5.150  18.280    420
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.16 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS I 140 
 PHE   0.012   0.004   PHE H 141 
 TYR   0.007   0.001   TYR J 145 
 ARG   0.001   0.000   ARG D 136 

*********************** 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
  97 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.7893 (t0) cc_final: 0.7639 (m110)
REVERT: A  112 MET cc_start: 0.8339 (mtm) cc_final: 0.7949 (mtm)
REVERT: B  136 ARG cc_start: 0.7160 (ttt180) cc_final: 0.6914 (ttm110)
REVERT: E  108 ASN cc_start: 0.8004 (t0) cc_final: 0.7757 (t0)
REVERT: G  136 ARG cc_start: 0.7175 (ttt180) cc_final: 0.6881 (tpp-160)
REVERT: I  108 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8193 (t0)
REVERT: I  136 ARG cc_start: 0.7074 (ttt180) cc_final: 0.6871 (tpp-160)
REVERT: I  138 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8258 (pt)
REVERT: J  110 LYS cc_start: 0.8384 (mttt) cc_final: 0.7807 (mtpp)
REVERT: J  136 ARG cc_start: 0.7069 (ttt180) cc_final: 0.6808 (ttm110)
  outliers start: 17
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1538
  time to fit residues: 16.6325
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  : 0.259 
-------------------------------------------------------------------------------
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  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  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 3 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4712 r_free = 0.4712 target = 0.172761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.148833 restraints weight = 3307.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.151608 restraints weight = 1948.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.153550 restraints weight = 1450.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.4479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   2820  Z= 0.245
  Angle     :  0.738   6.473   3760  Z= 0.372
  Chirality :  0.047   0.132    390
  Planarity :  0.002   0.012    480
  Dihedral  :  4.726  20.405    420
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 21.20 %
    Favored  : 72.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 111 
 PHE   0.005   0.001   PHE G 141 
 TYR   0.003   0.001   TYR H 128 
 ARG   0.002   0.000   ARG D 136 

*********************** 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
  98 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.277 
Fit side-chains
REVERT: D  110 LYS cc_start: 0.8336 (mttt) cc_final: 0.8076 (mttm)
REVERT: E  108 ASN cc_start: 0.7778 (t0) cc_final: 0.6349 (t0)
REVERT: E  110 LYS cc_start: 0.8486 (mttt) cc_final: 0.8150 (mttp)
REVERT: F  108 ASN cc_start: 0.7699 (m-40) cc_final: 0.7295 (t0)
REVERT: I  112 MET cc_start: 0.7446 (mtm) cc_final: 0.6850 (mmt)
REVERT: I  138 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8175 (pt)
  outliers start: 15
  outliers final: 9
  residues processed: 89
  average time/residue: 0.1122
  time to fit residues: 12.4320
Evaluate side-chains
  90 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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  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:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0040
   chunk 16 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   chunk 34 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   overall best weight:    2.8998

-------------------------------------------------------------------------------
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**
** 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 = 0.4604 r_free = 0.4604 target = 0.164339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.140658 restraints weight = 3439.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.143175 restraints weight = 2033.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.145015 restraints weight = 1525.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   2820  Z= 0.435
  Angle     :  0.873   6.749   3760  Z= 0.438
  Chirality :  0.048   0.134    390
  Planarity :  0.003   0.022    480
  Dihedral  :  5.142  18.508    420
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.16 %
    Favored  : 86.84 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 21.20 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.26 (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
 HIS   0.006   0.002   HIS G 140 
 PHE   0.010   0.004   PHE G 141 
 TYR   0.006   0.001   TYR H 145 
 ARG   0.001   0.000   ARG D 136 

*********************** 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
  88 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: G  136 ARG cc_start: 0.7164 (ttt180) cc_final: 0.6952 (tpp-160)
REVERT: I  136 ARG cc_start: 0.7073 (ttt180) cc_final: 0.6854 (tpp-160)
REVERT: I  138 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8249 (pt)
REVERT: J  108 ASN cc_start: 0.8445 (m-40) cc_final: 0.8136 (m110)
REVERT: J  110 LYS cc_start: 0.8784 (mttt) cc_final: 0.8536 (mttt)
REVERT: J  136 ARG cc_start: 0.7053 (ttt180) cc_final: 0.6834 (ttm110)
  outliers start: 11
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1395
  time to fit residues: 14.5464
Evaluate side-chains
  84 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
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  138 ILE
Chi-restraints excluded: chain I residue  138 ILE
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 32 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0040
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.8000

-------------------------------------------------------------------------------
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**
** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 108 ASN
** 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 = 0.4662 r_free = 0.4662 target = 0.167809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.143057 restraints weight = 3512.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.146080 restraints weight = 1962.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.147879 restraints weight = 1423.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.4420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   2820  Z= 0.306
  Angle     :  0.790   6.184   3760  Z= 0.397
  Chirality :  0.048   0.133    390
  Planarity :  0.002   0.016    480
  Dihedral  :  4.970  19.806    420
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.40 %
    Favored  : 72.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.30 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS I 111 
 PHE   0.007   0.002   PHE G 141 
 TYR   0.004   0.001   TYR H 145 
 ARG   0.002   0.000   ARG B 136 

*********************** 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
  86 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8187 (mtm) cc_final: 0.7874 (mtt)
REVERT: E  108 ASN cc_start: 0.7962 (t0) cc_final: 0.7639 (t0)
REVERT: G  136 ARG cc_start: 0.7188 (ttt180) cc_final: 0.6946 (tpp-160)
REVERT: I  112 MET cc_start: 0.7378 (mtt) cc_final: 0.6970 (mmt)
REVERT: I  138 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8248 (pt)
REVERT: J  108 ASN cc_start: 0.8328 (m110) cc_final: 0.8117 (m-40)
REVERT: J  112 MET cc_start: 0.8021 (mtm) cc_final: 0.7729 (mtm)
  outliers start: 12
  outliers final: 9
  residues processed: 84
  average time/residue: 0.1219
  time to fit residues: 12.6164
Evaluate side-chains
  84 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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  107 THR
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  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 28 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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**
** 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 = 0.4745 r_free = 0.4745 target = 0.172309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.148807 restraints weight = 3312.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.151618 restraints weight = 1938.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.153497 restraints weight = 1446.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2820  Z= 0.226
  Angle     :  0.734   5.179   3760  Z= 0.368
  Chirality :  0.047   0.131    390
  Planarity :  0.002   0.019    480
  Dihedral  :  4.760  19.629    420
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 20.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.35 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.24), residues: 380

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

*********************** 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
  91 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: D  110 LYS cc_start: 0.8174 (mttt) cc_final: 0.7920 (mttt)
REVERT: I  138 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8165 (pt)
REVERT: J  110 LYS cc_start: 0.8626 (mttt) cc_final: 0.8317 (mttt)
REVERT: J  112 MET cc_start: 0.7988 (mtm) cc_final: 0.7440 (mtm)
  outliers start: 12
  outliers final: 9
  residues processed: 86
  average time/residue: 0.1164
  time to fit residues: 12.3781
Evaluate side-chains
  87 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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  138 ILE
Chi-restraints excluded: chain I residue  138 ILE
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 22 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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**
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 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 = 0.4495 r_free = 0.4495 target = 0.151387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.125689 restraints weight = 3559.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.128343 restraints weight = 1927.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.130077 restraints weight = 1397.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   2820  Z= 0.391
  Angle     :  0.868   7.380   3760  Z= 0.433
  Chirality :  0.048   0.134    390
  Planarity :  0.003   0.018    480
  Dihedral  :  5.136  18.326    420
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.79 %
    Favored  : 89.21 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 20.80 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.47 (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
 HIS   0.006   0.002   HIS G 140 
 PHE   0.008   0.003   PHE G 141 
 TYR   0.006   0.001   TYR H 145 
 ARG   0.001   0.000   ARG B 136 

*********************** 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
  86 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8386 (mtm) cc_final: 0.8060 (mtm)
REVERT: F  108 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7834 (m110)
REVERT: G  136 ARG cc_start: 0.7243 (ttt180) cc_final: 0.6909 (tpp-160)
REVERT: I  109 MET cc_start: 0.7461 (ttt) cc_final: 0.6885 (ttt)
REVERT: I  138 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8257 (pt)
  outliers start: 13
  outliers final: 9
  residues processed: 84
  average time/residue: 0.1071
  time to fit residues: 11.3098
Evaluate side-chains
  84 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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  143 SER
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  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:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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**
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 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 = 0.4554 r_free = 0.4554 target = 0.155961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.130408 restraints weight = 3512.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.133210 restraints weight = 1883.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.134787 restraints weight = 1352.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2820  Z= 0.292
  Angle     :  0.799   7.974   3760  Z= 0.398
  Chirality :  0.048   0.133    390
  Planarity :  0.002   0.019    480
  Dihedral  :  4.973  18.936    420
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 21.20 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.49 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS F 111 
 PHE   0.006   0.002   PHE G 141 
 TYR   0.004   0.001   TYR D 128 
 ARG   0.001   0.000   ARG D 136 

********************** 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
  83 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8353 (mtm) cc_final: 0.8034 (mtm)
REVERT: D  110 LYS cc_start: 0.8178 (mttt) cc_final: 0.7874 (mttt)
REVERT: I  109 MET cc_start: 0.7558 (ttt) cc_final: 0.7306 (ttt)
REVERT: I  138 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8245 (pt)
  outliers start: 12
  outliers final: 10
  residues processed: 81
  average time/residue: 0.1017
  time to fit residues: 10.4887
Evaluate side-chains
  82 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  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  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 23 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 4 optimal weight:    0.6980
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0570
   chunk 35 optimal weight:    0.0010
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    2.5508

-------------------------------------------------------------------------------
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**
** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 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 = 0.4502 r_free = 0.4502 target = 0.152841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.127393 restraints weight = 3532.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.129948 restraints weight = 1854.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.131766 restraints weight = 1338.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3257

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= 0.381
  Angle     :  0.846   6.822   3760  Z= 0.425
  Chirality :  0.049   0.134    390
  Planarity :  0.003   0.018    480
  Dihedral  :  5.173  18.834    420
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.32 %
    Favored  : 88.68 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 20.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.54 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.46 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS G 140 
 PHE   0.009   0.003   PHE G 141 
 TYR   0.005   0.001   TYR H 145 
 ARG   0.001   0.000   ARG B 136 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1322.68 seconds
wall clock time: 23 minutes 47.65 seconds (1427.65 seconds total)