Starting phenix.real_space_refine
on Mon Feb 10 21:37:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uur_20900/02_2025/6uur_20900.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uur_20900/02_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_20900/02_2025/6uur_20900.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uur_20900/02_2025/6uur_20900.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uur_20900/02_2025/6uur_20900.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uur_20900/02_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-5592/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: 2.21, per 1000 atoms: 0.80
  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: 0.66
  Conformation dependent library (CDL) restraints added in 369.3 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: 0.41
  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: 0.65

  Time building geometry restraints manager: 0.77 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:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.620
  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:                     11.600
  Find NCS groups from input model:        0.070
  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:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.550
-------------------------------------------------------------------------------
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  : 0.360 
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: 0.1454
  time to fit residues: 15.4846
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  : 0.305 
-------------------------------------------------------------------------------
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 = 0.145421 restraints weight = 3311.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.148332 restraints weight = 1885.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.150030 restraints weight = 1368.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.4375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
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  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8305 (mttp)
REVERT: A  134 MET cc_start: 0.6355 (tmm) cc_final: 0.6085 (tmm)
REVERT: F  108 ASN cc_start: 0.7683 (t0) cc_final: 0.7308 (t0)
REVERT: G  108 ASN cc_start: 0.8178 (t0) cc_final: 0.7543 (t0)
REVERT: G  110 LYS cc_start: 0.8534 (mttt) cc_final: 0.8324 (mttp)
REVERT: I  134 MET cc_start: 0.6564 (tmm) cc_final: 0.6258 (tmm)
REVERT: J  110 LYS cc_start: 0.8264 (mttt) cc_final: 0.7784 (mtpp)
REVERT: J  112 MET cc_start: 0.8115 (mtm) cc_final: 0.7816 (mtm)
  outliers start: 18
  outliers final: 13
  residues processed: 89
  average time/residue: 0.1342
  time to fit residues: 14.3709
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  : 0.277 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.4610 r_free = 0.4610 target = 0.169333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.145651 restraints weight = 3312.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.148678 restraints weight = 1859.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.150525 restraints weight = 1337.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.4393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   2820  Z= 0.310
  Angle     :  0.794   7.053   3760  Z= 0.398
  Chirality :  0.047   0.134    390
  Planarity :  0.002   0.011    480
  Dihedral  :  4.835  18.244    420
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  7.60 %
    Allowed  : 18.00 %
    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: -4.20 (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   0.004   0.001   HIS B 111 
 PHE   0.009   0.003   PHE G 141 
 TYR   0.006   0.001   TYR H 145 
 ARG   0.000   0.000   ARG C 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
  97 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.7997 (t0) cc_final: 0.7511 (t0)
REVERT: A  110 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8201 (mttm)
REVERT: F  108 ASN cc_start: 0.8022 (t0) cc_final: 0.7722 (t0)
REVERT: I  134 MET cc_start: 0.6595 (tmm) cc_final: 0.6281 (tmm)
REVERT: I  138 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8238 (pt)
REVERT: J  110 LYS cc_start: 0.8229 (mttt) cc_final: 0.7691 (mtpp)
REVERT: J  112 MET cc_start: 0.8125 (mtm) cc_final: 0.7902 (mtm)
  outliers start: 19
  outliers final: 10
  residues processed: 89
  average time/residue: 0.1168
  time to fit residues: 12.8985
Evaluate side-chains
  89 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LYS
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 13 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0770
   chunk 36 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    2.0146

-------------------------------------------------------------------------------
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 = 0.4629 r_free = 0.4629 target = 0.168823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.145089 restraints weight = 3340.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.148038 restraints weight = 1851.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.149481 restraints weight = 1334.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.4397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   2820  Z= 0.324
  Angle     :  0.788   5.485   3760  Z= 0.396
  Chirality :  0.047   0.133    390
  Planarity :  0.002   0.010    480
  Dihedral  :  4.811  18.587    420
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 20.80 %
    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: -4.14 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 140 
 PHE   0.008   0.003   PHE G 141 
 TYR   0.005   0.001   TYR H 145 
 ARG   0.000   0.000   ARG C 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
  93 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.263 
Fit side-chains
REVERT: D  110 LYS cc_start: 0.8333 (mttt) cc_final: 0.7931 (mttm)
REVERT: G  136 ARG cc_start: 0.7162 (ttt180) cc_final: 0.6887 (tpp-160)
REVERT: I  134 MET cc_start: 0.6635 (tmm) cc_final: 0.6317 (tmm)
REVERT: I  138 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8232 (pt)
REVERT: J  110 LYS cc_start: 0.8282 (mttt) cc_final: 0.7717 (mtpp)
REVERT: J  112 MET cc_start: 0.8222 (mtm) cc_final: 0.7986 (mtm)
  outliers start: 16
  outliers final: 11
  residues processed: 88
  average time/residue: 0.1199
  time to fit residues: 12.9631
Evaluate side-chains
  87 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    1.7184

-------------------------------------------------------------------------------
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
** 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 = 0.169967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.146275 restraints weight = 3304.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.148981 restraints weight = 1970.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.150892 restraints weight = 1456.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.4429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2614

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= 0.299
  Angle     :  0.778   6.236   3760  Z= 0.391
  Chirality :  0.047   0.134    390
  Planarity :  0.002   0.010    480
  Dihedral  :  4.818  19.670    420
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 22.00 %
    Favored  : 72.00 %
  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: -4.19 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 111 
 PHE   0.007   0.002   PHE G 141 
 TYR   0.004   0.001   TYR H 145 
 ARG   0.000   0.000   ARG C 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
  95 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  108 ASN cc_start: 0.7851 (m-40) cc_final: 0.7497 (t0)
REVERT: G  108 ASN cc_start: 0.8254 (t0) cc_final: 0.8008 (t0)
REVERT: G  110 LYS cc_start: 0.8554 (mttp) cc_final: 0.8313 (mttt)
REVERT: I  112 MET cc_start: 0.7372 (mtt) cc_final: 0.7099 (mmt)
REVERT: I  134 MET cc_start: 0.6612 (tmm) cc_final: 0.6304 (tmm)
REVERT: I  138 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8199 (pt)
REVERT: J  112 MET cc_start: 0.8112 (mtm) cc_final: 0.7874 (mtm)
  outliers start: 15
  outliers final: 10
  residues processed: 90
  average time/residue: 0.1161
  time to fit residues: 12.9364
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  : 0.279 
-------------------------------------------------------------------------------
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  108 ASN
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:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 30 optimal weight:    0.0170
   chunk 25 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0050
   chunk 34 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    3.2038

-------------------------------------------------------------------------------
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**
** D 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 = 0.4578 r_free = 0.4578 target = 0.163691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.139875 restraints weight = 3451.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.142388 restraints weight = 2058.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.144076 restraints weight = 1545.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   2820  Z= 0.466
  Angle     :  0.878   5.390   3760  Z= 0.445
  Chirality :  0.049   0.135    390
  Planarity :  0.003   0.011    480
  Dihedral  :  5.163  19.433    420
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.32 %
    Favored  : 88.68 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 23.20 %
    Favored  : 72.00 %
  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: -4.30 (0.32), 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   0.007   0.002   HIS G 140 
 PHE   0.012   0.004   PHE H 141 
 TYR   0.007   0.001   TYR H 145 
 ARG   0.001   0.000   ARG C 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
  93 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8250 (mtm) cc_final: 0.7858 (mtt)
REVERT: D  136 ARG cc_start: 0.7431 (ttt180) cc_final: 0.7222 (ttm110)
REVERT: G  136 ARG cc_start: 0.7172 (ttt180) cc_final: 0.6961 (tpp-160)
REVERT: I  136 ARG cc_start: 0.7101 (ttt180) cc_final: 0.6884 (tpp-160)
REVERT: I  138 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8264 (pt)
REVERT: J  108 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8339 (m-40)
REVERT: J  136 ARG cc_start: 0.7057 (ttt180) cc_final: 0.6758 (ttm110)
  outliers start: 12
  outliers final: 9
  residues processed: 91
  average time/residue: 0.1462
  time to fit residues: 15.6885
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  : 0.303 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   chunk 18 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0670
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.0722

-------------------------------------------------------------------------------
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 = 0.4710 r_free = 0.4710 target = 0.171170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.146496 restraints weight = 3446.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.149581 restraints weight = 1912.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.151392 restraints weight = 1376.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.4484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2971

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= 0.234
  Angle     :  0.736   5.799   3760  Z= 0.375
  Chirality :  0.048   0.133    390
  Planarity :  0.002   0.016    480
  Dihedral  :  4.843  20.834    420
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 22.80 %
    Favored  : 70.80 %
  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: -4.33 (0.31), 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   0.007   0.002   HIS J 111 
 PHE   0.005   0.001   PHE G 141 
 TYR   0.003   0.001   TYR H 128 
 ARG   0.003   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
  92 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8203 (mtm) cc_final: 0.7852 (mtt)
REVERT: F  108 ASN cc_start: 0.7692 (m-40) cc_final: 0.7231 (t0)
REVERT: I  112 MET cc_start: 0.7273 (mtm) cc_final: 0.6837 (mmt)
REVERT: I  138 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8144 (pt)
  outliers start: 16
  outliers final: 8
  residues processed: 83
  average time/residue: 0.1146
  time to fit residues: 11.8336
Evaluate side-chains
  84 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.4694 r_free = 0.4694 target = 0.170117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.146396 restraints weight = 3386.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.149177 restraints weight = 1982.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.150685 restraints weight = 1473.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.4459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3044

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= 0.276
  Angle     :  0.776   5.691   3760  Z= 0.389
  Chirality :  0.047   0.134    390
  Planarity :  0.002   0.020    480
  Dihedral  :  4.876  19.380    420
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  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: -4.40 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D 111 
 PHE   0.005   0.002   PHE G 141 
 TYR   0.004   0.001   TYR A 128 
 ARG   0.001   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
  84 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8262 (mtm) cc_final: 0.7841 (mtt)
REVERT: C  108 ASN cc_start: 0.8220 (t0) cc_final: 0.7968 (t0)
REVERT: G  112 MET cc_start: 0.7749 (mtm) cc_final: 0.6746 (mmt)
REVERT: I  112 MET cc_start: 0.7199 (mtm) cc_final: 0.6861 (mmt)
REVERT: I  138 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8181 (pt)
REVERT: J  112 MET cc_start: 0.8129 (mtm) cc_final: 0.7831 (mtm)
  outliers start: 12
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1041
  time to fit residues: 10.8063
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  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain B residue  109 MET
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  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:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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**
** 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 = 0.4667 r_free = 0.4667 target = 0.168108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.144268 restraints weight = 3401.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.146954 restraints weight = 2005.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.148719 restraints weight = 1497.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.4436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   2820  Z= 0.312
  Angle     :  0.819   7.081   3760  Z= 0.408
  Chirality :  0.048   0.133    390
  Planarity :  0.002   0.019    480
  Dihedral  :  4.933  18.508    420
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.80 %
    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 (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 : -3.41 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS G 140 
 PHE   0.006   0.002   PHE G 141 
 TYR   0.004   0.001   TYR H 128 
 ARG   0.000   0.000   ARG A 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
  84 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8277 (mtm) cc_final: 0.7888 (mtt)
REVERT: G  112 MET cc_start: 0.7720 (mtm) cc_final: 0.6710 (mmt)
REVERT: I  112 MET cc_start: 0.7144 (mtm) cc_final: 0.6814 (mmt)
REVERT: I  138 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8252 (pt)
REVERT: J  112 MET cc_start: 0.8147 (mtm) cc_final: 0.7884 (mtm)
  outliers start: 12
  outliers final: 10
  residues processed: 83
  average time/residue: 0.1090
  time to fit residues: 11.4857
Evaluate side-chains
  83 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain B residue  109 MET
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  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:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0980
   chunk 21 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**
** D 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 = 0.4634 r_free = 0.4634 target = 0.165858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.142100 restraints weight = 3460.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.144670 restraints weight = 2040.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.146317 restraints weight = 1527.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.4391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3185

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= 0.369
  Angle     :  0.842   6.977   3760  Z= 0.426
  Chirality :  0.049   0.135    390
  Planarity :  0.002   0.019    480
  Dihedral  :  5.086  18.203    420
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 22.00 %
    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: -4.52 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS G 140 
 PHE   0.008   0.003   PHE G 141 
 TYR   0.005   0.001   TYR H 145 
 ARG   0.001   0.000   ARG B 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
  86 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.8295 (mtm) cc_final: 0.7905 (mtt)
REVERT: B  134 MET cc_start: 0.6623 (tmm) cc_final: 0.6318 (tmm)
REVERT: D  108 ASN cc_start: 0.7491 (m-40) cc_final: 0.7281 (t0)
REVERT: D  136 ARG cc_start: 0.7377 (ttt180) cc_final: 0.7151 (ttm110)
REVERT: G  112 MET cc_start: 0.7819 (mtm) cc_final: 0.6696 (mmt)
REVERT: G  136 ARG cc_start: 0.7201 (ttt180) cc_final: 0.6987 (tpp-160)
REVERT: I  112 MET cc_start: 0.7250 (mtm) cc_final: 0.6725 (mmt)
REVERT: I  138 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8259 (pt)
REVERT: J  112 MET cc_start: 0.8179 (mtm) cc_final: 0.7894 (mtm)
  outliers start: 13
  outliers final: 10
  residues processed: 84
  average time/residue: 0.1157
  time to fit residues: 11.9907
Evaluate side-chains
  83 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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  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:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   overall best weight:    3.2986

-------------------------------------------------------------------------------
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**
** D 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 = 0.4571 r_free = 0.4571 target = 0.162369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.139020 restraints weight = 3411.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.141464 restraints weight = 2034.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.143085 restraints weight = 1538.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.4337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3249

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= 0.474
  Angle     :  0.935   6.964   3760  Z= 0.471
  Chirality :  0.050   0.134    390
  Planarity :  0.003   0.018    480
  Dihedral  :  5.364  17.784    420
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  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: -4.59 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS G 140 
 PHE   0.012   0.004   PHE G 141 
 TYR   0.006   0.001   TYR H 145 
 ARG   0.002   0.000   ARG B 136 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1310.60 seconds
wall clock time: 24 minutes 24.33 seconds (1464.33 seconds total)