Starting phenix.real_space_refine
on Sat Nov 16 12:45:43 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/11_2024/8twz_41673.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/11_2024/8twz_41673.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/11_2024/8twz_41673.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/11_2024/8twz_41673.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/11_2024/8twz_41673.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twz_41673/11_2024/8twz_41673.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.022
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      20      5.16       5
     C    7360      2.51       5
     N    1850      2.21       5
     O    2040      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 11270
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2250
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 13, 'TRANS': 260}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'3CN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 4.51, per 1000 atoms: 0.40
  Number of scatterers: 11270
  At special positions: 0
  Unit cell: (89.723, 89.723, 112.424, 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      20     16.00
     O    2040      8.00
     N    1850      7.00
     C    7360      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: 3.18
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2610

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 20 sheets defined
      31.4% alpha, 47.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 70
      removed outlier: 4.001A  pdb=" N   ARG A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 179
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 221
    Processing helix  chain 'A' and resid 222 through 225
      removed outlier: 3.682A  pdb=" N   LEU A 225 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 222 through 225'
    Processing helix  chain 'A' and resid 228 through 248
      removed outlier: 4.110A  pdb=" N   TYR A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 284
    Processing helix  chain 'B' and resid 61 through 70
      removed outlier: 4.001A  pdb=" N   ARG B  65 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 179
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 221
    Processing helix  chain 'B' and resid 222 through 225
      removed outlier: 3.683A  pdb=" N   LEU B 225 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 222 through 225'
    Processing helix  chain 'B' and resid 228 through 248
      removed outlier: 4.110A  pdb=" N   TYR B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 284
    Processing helix  chain 'C' and resid 61 through 70
      removed outlier: 4.002A  pdb=" N   ARG C  65 " --> pdb=" O   THR C  61 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 179
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 221
    Processing helix  chain 'C' and resid 222 through 225
      removed outlier: 3.682A  pdb=" N   LEU C 225 " --> pdb=" O   VAL C 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 222 through 225'
    Processing helix  chain 'C' and resid 228 through 248
      removed outlier: 4.110A  pdb=" N   TYR C 248 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 284
    Processing helix  chain 'D' and resid 61 through 70
      removed outlier: 4.001A  pdb=" N   ARG D  65 " --> pdb=" O   THR D  61 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 176 through 179
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 221
    Processing helix  chain 'D' and resid 222 through 225
      removed outlier: 3.682A  pdb=" N   LEU D 225 " --> pdb=" O   VAL D 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 222 through 225'
    Processing helix  chain 'D' and resid 228 through 248
      removed outlier: 4.110A  pdb=" N   TYR D 248 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 284
    Processing helix  chain 'E' and resid 61 through 70
      removed outlier: 4.000A  pdb=" N   ARG E  65 " --> pdb=" O   THR E  61 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 176 through 179
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 221
    Processing helix  chain 'E' and resid 222 through 225
      removed outlier: 3.682A  pdb=" N   LEU E 225 " --> pdb=" O   VAL E 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 222 through 225'
    Processing helix  chain 'E' and resid 228 through 248
      removed outlier: 4.110A  pdb=" N   TYR E 248 " --> pdb=" O   ALA E 244 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 284
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59
      removed outlier: 4.117A  pdb=" N   SER A 109 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 59
      removed outlier: 3.607A  pdb=" N   GLY A 108 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   THR A  32 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   GLY A  25 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   LYS A  34 " --> pdb=" O   ILE A  23 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ILE A  23 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ASP A  36 " --> pdb=" O   ASN A  21 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   THR A  44 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASP A  13 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL A  16 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE A  18 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   VAL A 147 " --> pdb=" O   ILE A  18 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE A  20 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.705A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.705A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 59
      removed outlier: 4.118A  pdb=" N   SER B 109 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 59
      removed outlier: 3.607A  pdb=" N   GLY B 108 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   THR B  32 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LYS B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ILE B  23 " --> pdb=" O   LYS B  34 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ASP B  36 " --> pdb=" O   ASN B  21 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   THR B  44 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASP B  13 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL B  16 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE B  18 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   VAL B 147 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE B  20 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.705A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.705A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 59
      removed outlier: 4.117A  pdb=" N   SER C 109 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 59
      removed outlier: 3.607A  pdb=" N   GLY C 108 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   THR C  32 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   GLY C  25 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   LYS C  34 " --> pdb=" O   ILE C  23 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ILE C  23 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ASP C  36 " --> pdb=" O   ASN C  21 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   THR C  44 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ASP C  13 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL C  16 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE C  18 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   VAL C 147 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE C  20 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.705A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.705A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 59
      removed outlier: 4.117A  pdb=" N   SER D 109 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 59
      removed outlier: 3.606A  pdb=" N   GLY D 108 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   THR D  32 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   GLY D  25 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LYS D  34 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   ILE D  23 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ASP D  36 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   THR D  44 " --> pdb=" O   ASP D  13 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASP D  13 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL D  16 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE D  18 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   VAL D 147 " --> pdb=" O   ILE D  18 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE D  20 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.705A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.705A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 59
      removed outlier: 4.117A  pdb=" N   SER E 109 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 59
      removed outlier: 3.607A  pdb=" N   GLY E 108 " --> pdb=" O   VAL E  35 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   THR E  32 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   GLY E  25 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   LYS E  34 " --> pdb=" O   ILE E  23 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ILE E  23 " --> pdb=" O   LYS E  34 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ASP E  36 " --> pdb=" O   ASN E  21 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   THR E  44 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ASP E  13 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL E  16 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE E  18 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   VAL E 147 " --> pdb=" O   ILE E  18 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE E  20 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.706A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.706A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)

    620 hydrogen bonds defined for protein.
    1800 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: 3.91

  Time building geometry restraints manager: 3.45 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3286
        1.34 -     1.45: 2013
        1.45 -     1.57: 6246
        1.57 -     1.69: 0
        1.69 -     1.80: 40
  Bond restraints: 11585
  Sorted by residual:
  bond pdb=" N   THR D  61 "
       pdb=" CA  THR D  61 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.026 1.29e-02 6.01e+03 3.98e+00
  bond pdb=" N   THR A  61 "
       pdb=" CA  THR A  61 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.025 1.29e-02 6.01e+03 3.89e+00
  bond pdb=" N   THR B  61 "
       pdb=" CA  THR B  61 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.025 1.29e-02 6.01e+03 3.84e+00
  bond pdb=" N   THR C  61 "
       pdb=" CA  THR C  61 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.025 1.29e-02 6.01e+03 3.83e+00
  bond pdb=" N   THR E  61 "
       pdb=" CA  THR E  61 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.024 1.29e-02 6.01e+03 3.58e+00
  ... (remaining 11580 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 15085
        1.49 -     2.99: 567
        2.99 -     4.48: 83
        4.48 -     5.97: 29
        5.97 -     7.47: 26
  Bond angle restraints: 15790
  Sorted by residual:
  angle pdb=" C   VAL A  58 "
        pdb=" N   GLU A  59 "
        pdb=" CA  GLU A  59 "
      ideal   model   delta    sigma   weight residual
     122.64  116.77    5.87 1.77e+00 3.19e-01 1.10e+01
  angle pdb=" C   VAL C  58 "
        pdb=" N   GLU C  59 "
        pdb=" CA  GLU C  59 "
      ideal   model   delta    sigma   weight residual
     122.64  116.77    5.87 1.77e+00 3.19e-01 1.10e+01
  angle pdb=" C   VAL E  58 "
        pdb=" N   GLU E  59 "
        pdb=" CA  GLU E  59 "
      ideal   model   delta    sigma   weight residual
     122.64  116.80    5.84 1.77e+00 3.19e-01 1.09e+01
  angle pdb=" C   VAL B  58 "
        pdb=" N   GLU B  59 "
        pdb=" CA  GLU B  59 "
      ideal   model   delta    sigma   weight residual
     122.64  116.82    5.82 1.77e+00 3.19e-01 1.08e+01
  angle pdb=" C   VAL D  58 "
        pdb=" N   GLU D  59 "
        pdb=" CA  GLU D  59 "
      ideal   model   delta    sigma   weight residual
     122.64  116.82    5.82 1.77e+00 3.19e-01 1.08e+01
  ... (remaining 15785 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.96: 6041
       15.96 -    31.92: 544
       31.92 -    47.87: 115
       47.87 -    63.83: 40
       63.83 -    79.79: 15
  Dihedral angle restraints: 6755
    sinusoidal: 2715
      harmonic: 4040
  Sorted by residual:
  dihedral pdb=" CG  ARG B 255 "
           pdb=" CD  ARG B 255 "
           pdb=" NE  ARG B 255 "
           pdb=" CZ  ARG B 255 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.53   48.47     2      1.50e+01 4.44e-03 1.20e+01
  dihedral pdb=" CG  ARG E 255 "
           pdb=" CD  ARG E 255 "
           pdb=" NE  ARG E 255 "
           pdb=" CZ  ARG E 255 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.54   48.46     2      1.50e+01 4.44e-03 1.20e+01
  dihedral pdb=" CG  ARG D 255 "
           pdb=" CD  ARG D 255 "
           pdb=" NE  ARG D 255 "
           pdb=" CZ  ARG D 255 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.58   48.42     2      1.50e+01 4.44e-03 1.19e+01
  ... (remaining 6752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1131
       0.041 -    0.082: 399
       0.082 -    0.124: 165
       0.124 -    0.165: 34
       0.165 -    0.206: 11
  Chirality restraints: 1740
  Sorted by residual:
  chirality pdb=" CB  THR D 149 "
            pdb=" CA  THR D 149 "
            pdb=" OG1 THR D 149 "
            pdb=" CG2 THR D 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  THR C 149 "
            pdb=" CA  THR C 149 "
            pdb=" OG1 THR C 149 "
            pdb=" CG2 THR C 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  THR A 149 "
            pdb=" CA  THR A 149 "
            pdb=" OG1 THR A 149 "
            pdb=" CG2 THR A 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1737 not shown)

  Planarity restraints: 2005
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 255 "   -0.184 9.50e-02 1.11e+02   8.32e-02 5.53e+00
        pdb=" NE  ARG B 255 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 255 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 255 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 255 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 255 "   -0.185 9.50e-02 1.11e+02   8.35e-02 5.52e+00
        pdb=" NE  ARG E 255 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 255 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 255 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 255 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 255 "   -0.184 9.50e-02 1.11e+02   8.32e-02 5.52e+00
        pdb=" NE  ARG A 255 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 255 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 255 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 255 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 2002 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3369
        2.83 -     3.35: 9583
        3.35 -     3.86: 18756
        3.86 -     4.38: 21893
        4.38 -     4.90: 39594
  Nonbonded interactions: 93195
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 245 "
            pdb=" OH  TYR E 270 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   SER B 221 "
            pdb=" OG  SER B 221 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   SER A 221 "
            pdb=" OG  SER A 221 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   SER C 221 "
            pdb=" OG  SER C 221 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   SER E 221 "
            pdb=" OG  SER E 221 "
     model   vdw
     2.330 3.040
  ... (remaining 93190 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.260
  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:             0.020
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     26.260
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.030
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
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   0.033  11585  Z= 0.277
  Angle     :  0.715   7.466  15790  Z= 0.371
  Chirality :  0.052   0.206   1740
  Planarity :  0.006   0.084   2005
  Dihedral  : 14.021  79.790   4145
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  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: -0.87 (0.22), residues: 1360
  helix: -0.43 (0.23), residues: 425
  sheet:  0.71 (0.25), residues: 465
  loop : -2.01 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 206 
 HIS   0.004   0.001   HIS D 177 
 PHE   0.009   0.002   PHE E 116 
 TYR   0.013   0.001   TYR B 248 
 ARG   0.020   0.002   ARG B 255 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.515 
Fit side-chains
REVERT: B  129 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7289 (mt-10)
REVERT: C  114 MET cc_start: 0.8537 (ttm) cc_final: 0.8286 (ttm)
REVERT: C  263 ASP cc_start: 0.7575 (m-30) cc_final: 0.7285 (m-30)
REVERT: D  172 ASP cc_start: 0.8108 (m-30) cc_final: 0.7905 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.2662
  time to fit residues: 70.4138
Evaluate side-chains
  170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 102 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 69 optimal weight:    0.0980
   chunk 54 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 122 optimal weight:    0.0980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
A  89 ASN
B  60 ASN
B  89 ASN
B 169 HIS
B 233 GLN
C  60 ASN
C  89 ASN
D  60 ASN
D  89 ASN
D 233 GLN
E  60 ASN
E  89 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  11585  Z= 0.156
  Angle     :  0.511   5.937  15790  Z= 0.258
  Chirality :  0.046   0.133   1740
  Planarity :  0.003   0.020   2005
  Dihedral  :  4.134  14.964   1510
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  7.74 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.23), residues: 1360
  helix:  1.04 (0.24), residues: 395
  sheet:  0.79 (0.27), residues: 445
  loop : -1.73 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 206 
 HIS   0.001   0.001   HIS C 177 
 PHE   0.015   0.001   PHE B 236 
 TYR   0.010   0.001   TYR B 245 
 ARG   0.003   0.001   ARG C  91 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 172
  time to evaluate  : 1.296 
Fit side-chains
REVERT: A  270 TYR cc_start: 0.7771 (m-10) cc_final: 0.7554 (m-80)
REVERT: B  129 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7171 (mt-10)
REVERT: B  236 PHE cc_start: 0.7356 (m-80) cc_final: 0.7108 (m-80)
REVERT: C  114 MET cc_start: 0.8499 (ttm) cc_final: 0.8251 (ttm)
REVERT: C  174 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7650 (ttm-80)
REVERT: D   97 ASP cc_start: 0.7792 (p0) cc_final: 0.7541 (p0)
REVERT: D  150 GLU cc_start: 0.6168 (pt0) cc_final: 0.5880 (mt-10)
REVERT: D  172 ASP cc_start: 0.8025 (m-30) cc_final: 0.7653 (m-30)
REVERT: D  255 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7704 (mtt90)
  outliers start: 10
  outliers final: 8
  residues processed: 182
  average time/residue: 0.2411
  time to fit residues: 62.6854
Evaluate side-chains
  152 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   60 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 102 optimal weight:    9.9990
   chunk 83 optimal weight:    4.9990
   chunk 33 optimal weight:    0.1980
   chunk 122 optimal weight:   20.0000
   chunk 132 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9980
   chunk 121 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0570
   overall best weight:    0.5900

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
A 169 HIS
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  60 ASN
C  60 ASN
C 169 HIS
D  60 ASN
** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  27 ASN
E  60 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11585  Z= 0.147
  Angle     :  0.502   7.383  15790  Z= 0.251
  Chirality :  0.046   0.147   1740
  Planarity :  0.003   0.023   2005
  Dihedral  :  3.839  11.929   1510
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.84 %
    Favored  : 88.95 %
  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:  0.29 (0.23), residues: 1360
  helix:  1.40 (0.25), residues: 395
  sheet:  1.37 (0.27), residues: 415
  loop : -1.75 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 206 
 HIS   0.001   0.000   HIS B 169 
 PHE   0.016   0.001   PHE E 236 
 TYR   0.013   0.001   TYR C 245 
 ARG   0.003   0.000   ARG E 163 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 1.360 
Fit side-chains
REVERT: B  129 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7170 (mt-10)
REVERT: C  114 MET cc_start: 0.8489 (ttm) cc_final: 0.8225 (ttm)
REVERT: C  174 ARG cc_start: 0.7987 (ttm110) cc_final: 0.7585 (tpp-160)
REVERT: C  245 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.7266 (t80)
REVERT: D   97 ASP cc_start: 0.7907 (p0) cc_final: 0.7399 (p0)
REVERT: D  150 GLU cc_start: 0.6190 (pt0) cc_final: 0.5872 (mt-10)
REVERT: D  172 ASP cc_start: 0.7996 (m-30) cc_final: 0.7659 (m-30)
REVERT: D  236 PHE cc_start: 0.7148 (m-80) cc_final: 0.6778 (m-80)
REVERT: E   30 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6693 (mt-10)
  outliers start: 15
  outliers final: 8
  residues processed: 185
  average time/residue: 0.2328
  time to fit residues: 61.4395
Evaluate side-chains
  160 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain E residue   30 GLU
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   60 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 121 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   chunk 123 optimal weight:    8.9990
   chunk 130 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  21 ASN
D  27 ASN
D  60 ASN
** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  27 ASN
E  60 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11585  Z= 0.343
  Angle     :  0.573   7.584  15790  Z= 0.291
  Chirality :  0.050   0.161   1740
  Planarity :  0.003   0.022   2005
  Dihedral  :  4.192  14.350   1510
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.02 %
    Favored  : 86.05 %
  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:  0.27 (0.23), residues: 1360
  helix:  1.46 (0.25), residues: 395
  sheet:  1.27 (0.27), residues: 415
  loop : -1.75 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 206 
 HIS   0.003   0.001   HIS C 177 
 PHE   0.008   0.002   PHE E 236 
 TYR   0.015   0.002   TYR B 245 
 ARG   0.004   0.000   ARG C  91 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 1.246 
Fit side-chains
REVERT: B  114 MET cc_start: 0.8529 (ttm) cc_final: 0.8100 (ttm)
REVERT: B  245 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7253 (t80)
REVERT: C   34 LYS cc_start: 0.8453 (mttp) cc_final: 0.8143 (mttt)
REVERT: C  245 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7195 (t80)
REVERT: D  172 ASP cc_start: 0.8039 (m-30) cc_final: 0.7732 (m-30)
REVERT: E   30 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6821 (mt-10)
REVERT: E  236 PHE cc_start: 0.7342 (m-80) cc_final: 0.7091 (m-80)
  outliers start: 24
  outliers final: 11
  residues processed: 185
  average time/residue: 0.3018
  time to fit residues: 76.7347
Evaluate side-chains
  159 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 1.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   30 GLU
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue  167 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 111 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 117 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  60 ASN
C  60 ASN
D  27 ASN
** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  11585  Z= 0.240
  Angle     :  0.531   7.024  15790  Z= 0.267
  Chirality :  0.048   0.138   1740
  Planarity :  0.003   0.021   2005
  Dihedral  :  4.101  14.386   1510
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.87 %
    Favored  : 84.27 %
  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:  0.21 (0.24), residues: 1360
  helix:  1.55 (0.25), residues: 390
  sheet:  1.20 (0.27), residues: 415
  loop : -1.85 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 206 
 HIS   0.003   0.001   HIS B 177 
 PHE   0.011   0.001   PHE A 121 
 TYR   0.020   0.001   TYR A 245 
 ARG   0.005   0.000   ARG C 123 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 1.400 
Fit side-chains
REVERT: B  114 MET cc_start: 0.8519 (ttm) cc_final: 0.8062 (ttm)
REVERT: B  245 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7179 (t80)
REVERT: C   34 LYS cc_start: 0.8435 (mttp) cc_final: 0.8132 (mttt)
REVERT: C  245 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7112 (t80)
REVERT: D   97 ASP cc_start: 0.8036 (p0) cc_final: 0.7648 (p0)
REVERT: D  172 ASP cc_start: 0.8037 (m-30) cc_final: 0.7717 (m-30)
REVERT: D  255 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.8024 (mtt90)
REVERT: E   30 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6887 (mt-10)
  outliers start: 23
  outliers final: 14
  residues processed: 181
  average time/residue: 0.2848
  time to fit residues: 72.0381
Evaluate side-chains
  173 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   30 GLU
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  240 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 117 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 125 optimal weight:    0.8980
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11585  Z= 0.320
  Angle     :  0.582   9.569  15790  Z= 0.296
  Chirality :  0.049   0.137   1740
  Planarity :  0.003   0.038   2005
  Dihedral  :  4.299  15.509   1510
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.60 %
    Favored  : 83.23 %
  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:  0.04 (0.24), residues: 1360
  helix:  1.41 (0.25), residues: 390
  sheet:  1.07 (0.27), residues: 415
  loop : -1.91 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 206 
 HIS   0.003   0.001   HIS B 177 
 PHE   0.009   0.001   PHE A 121 
 TYR   0.018   0.002   TYR A 245 
 ARG   0.007   0.000   ARG E 123 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 160
  time to evaluate  : 1.323 
Fit side-chains
REVERT: A  245 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7365 (t80)
REVERT: B  114 MET cc_start: 0.8526 (ttm) cc_final: 0.8082 (ttm)
REVERT: B  245 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.6846 (t80)
REVERT: C   34 LYS cc_start: 0.8450 (mttp) cc_final: 0.8126 (mttt)
REVERT: C  245 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.6854 (t80)
REVERT: D  172 ASP cc_start: 0.8031 (m-30) cc_final: 0.7735 (m-30)
REVERT: D  255 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.8050 (mtt90)
REVERT: E   30 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6981 (mt-10)
  outliers start: 27
  outliers final: 17
  residues processed: 181
  average time/residue: 0.2695
  time to fit residues: 67.4425
Evaluate side-chains
  170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   30 GLU
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  240 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 233 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11585  Z= 0.224
  Angle     :  0.545   8.420  15790  Z= 0.275
  Chirality :  0.047   0.136   1740
  Planarity :  0.003   0.032   2005
  Dihedral  :  4.104  15.167   1510
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.40 %
    Favored  : 82.74 %
  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:  0.04 (0.23), residues: 1360
  helix:  1.43 (0.25), residues: 390
  sheet:  1.06 (0.27), residues: 415
  loop : -1.92 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E 206 
 HIS   0.003   0.001   HIS B 177 
 PHE   0.018   0.001   PHE B 236 
 TYR   0.017   0.001   TYR E 245 
 ARG   0.007   0.000   ARG C 123 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 1.386 
Fit side-chains
REVERT: A  245 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7270 (t80)
REVERT: B  239 MET cc_start: 0.7339 (tpp) cc_final: 0.7019 (ttp)
REVERT: B  245 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.6831 (t80)
REVERT: C   34 LYS cc_start: 0.8453 (mttp) cc_final: 0.8162 (mttt)
REVERT: C  245 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.6861 (t80)
REVERT: D  172 ASP cc_start: 0.8012 (m-30) cc_final: 0.7740 (m-30)
REVERT: D  255 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.8014 (mtt90)
REVERT: E   30 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6899 (mt-10)
REVERT: E  245 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.6784 (t80)
  outliers start: 23
  outliers final: 16
  residues processed: 166
  average time/residue: 0.2689
  time to fit residues: 62.1868
Evaluate side-chains
  166 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain E residue   30 GLU
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  240 LEU
Chi-restraints excluded: chain E residue  245 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 51 optimal weight:    0.2980
   chunk 77 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0870
   chunk 64 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 118 optimal weight:    0.4980
   chunk 124 optimal weight:    6.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
B 169 HIS
D  21 ASN
E 169 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11585  Z= 0.138
  Angle     :  0.510   7.710  15790  Z= 0.255
  Chirality :  0.046   0.136   1740
  Planarity :  0.003   0.035   2005
  Dihedral  :  3.829  13.609   1510
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.13 %
    Favored  : 82.34 %
  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:  0.20 (0.24), residues: 1360
  helix:  1.58 (0.25), residues: 390
  sheet:  1.16 (0.27), residues: 415
  loop : -1.84 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E 206 
 HIS   0.002   0.000   HIS D 177 
 PHE   0.013   0.001   PHE A 121 
 TYR   0.014   0.001   TYR E 245 
 ARG   0.008   0.000   ARG E 123 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  245 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7325 (t80)
REVERT: B   61 THR cc_start: 0.7892 (t) cc_final: 0.7522 (p)
REVERT: B  239 MET cc_start: 0.7117 (tpp) cc_final: 0.6841 (ttp)
REVERT: B  245 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7061 (t80)
REVERT: C   34 LYS cc_start: 0.8405 (mttp) cc_final: 0.8123 (mttt)
REVERT: C  245 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.6942 (t80)
REVERT: D  172 ASP cc_start: 0.8006 (m-30) cc_final: 0.7753 (m-30)
REVERT: D  255 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.7995 (mtt90)
REVERT: E  245 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.6606 (t80)
  outliers start: 19
  outliers final: 11
  residues processed: 168
  average time/residue: 0.2783
  time to fit residues: 64.4035
Evaluate side-chains
  156 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue  240 LEU
Chi-restraints excluded: chain E residue  245 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 124 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 95 optimal weight:    8.9990
   chunk 37 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9980
   chunk 114 optimal weight:    0.5980
   chunk 120 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  21 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11585  Z= 0.161
  Angle     :  0.519   8.004  15790  Z= 0.258
  Chirality :  0.046   0.135   1740
  Planarity :  0.003   0.041   2005
  Dihedral  :  3.796  14.704   1510
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.61 %
    Favored  : 81.85 %
  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:  0.23 (0.23), residues: 1360
  helix:  1.59 (0.25), residues: 390
  sheet:  1.18 (0.27), residues: 415
  loop : -1.81 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 206 
 HIS   0.002   0.001   HIS B 177 
 PHE   0.013   0.001   PHE A 121 
 TYR   0.014   0.001   TYR B 245 
 ARG   0.009   0.000   ARG E 123 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
REVERT: A  236 PHE cc_start: 0.7158 (m-80) cc_final: 0.6951 (m-80)
REVERT: A  245 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7339 (t80)
REVERT: B   61 THR cc_start: 0.7888 (t) cc_final: 0.7459 (p)
REVERT: B  239 MET cc_start: 0.7105 (tpp) cc_final: 0.6837 (ttp)
REVERT: B  245 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7102 (t80)
REVERT: C   34 LYS cc_start: 0.8394 (mttp) cc_final: 0.8103 (mttt)
REVERT: C  123 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6857 (mtp-110)
REVERT: C  245 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.6941 (t80)
REVERT: D  172 ASP cc_start: 0.8008 (m-30) cc_final: 0.7751 (m-30)
REVERT: D  236 PHE cc_start: 0.7229 (m-80) cc_final: 0.7016 (m-80)
REVERT: D  255 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7977 (mtt90)
REVERT: E  245 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6574 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 157
  average time/residue: 0.2745
  time to fit residues: 59.3094
Evaluate side-chains
  150 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  240 LEU
Chi-restraints excluded: chain E residue  245 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 128 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9980
   chunk 123 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11585  Z= 0.183
  Angle     :  0.528   8.045  15790  Z= 0.262
  Chirality :  0.047   0.135   1740
  Planarity :  0.003   0.043   2005
  Dihedral  :  3.848  15.230   1510
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.77 %
    Favored  : 81.53 %
  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:  0.21 (0.24), residues: 1360
  helix:  1.58 (0.25), residues: 390
  sheet:  1.16 (0.27), residues: 415
  loop : -1.81 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 206 
 HIS   0.002   0.001   HIS A 177 
 PHE   0.012   0.001   PHE A 121 
 TYR   0.014   0.001   TYR E 245 
 ARG   0.008   0.000   ARG E 123 

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

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

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2720 Ramachandran restraints generated.
    1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  236 PHE cc_start: 0.7166 (m-80) cc_final: 0.6923 (m-80)
REVERT: A  245 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7305 (t80)
REVERT: B   61 THR cc_start: 0.7836 (t) cc_final: 0.7393 (p)
REVERT: B  239 MET cc_start: 0.7118 (tpp) cc_final: 0.6856 (ttp)
REVERT: B  245 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6984 (t80)
REVERT: C   34 LYS cc_start: 0.8410 (mttp) cc_final: 0.8137 (mttt)
REVERT: C  123 ARG cc_start: 0.7127 (mtp85) cc_final: 0.6898 (mtp-110)
REVERT: C  245 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.6973 (t80)
REVERT: D  172 ASP cc_start: 0.8005 (m-30) cc_final: 0.7741 (m-30)
REVERT: D  236 PHE cc_start: 0.7214 (m-80) cc_final: 0.6954 (m-80)
REVERT: D  255 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.7984 (mtt90)
REVERT: E  245 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6575 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 150
  average time/residue: 0.2851
  time to fit residues: 58.2938
Evaluate side-chains
  154 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  245 TYR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  245 TYR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  245 TYR
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  240 LEU
Chi-restraints excluded: chain E residue  245 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 114 optimal weight:    0.0570
   chunk 32 optimal weight:    3.9990
   chunk 98 optimal weight:    0.2980
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.8300

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.147551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.114161 restraints weight = 12406.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.89
r_work: 0.3166 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11585  Z= 0.155
  Angle     :  0.517   8.273  15790  Z= 0.255
  Chirality :  0.046   0.134   1740
  Planarity :  0.003   0.041   2005
  Dihedral  :  3.769  14.668   1510
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.69 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.23), residues: 1360
  helix:  1.59 (0.25), residues: 390
  sheet:  1.18 (0.27), residues: 415
  loop : -1.78 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 206 
 HIS   0.002   0.001   HIS B 177 
 PHE   0.014   0.001   PHE A 121 
 TYR   0.014   0.001   TYR E 245 
 ARG   0.008   0.000   ARG E 123 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2479.21 seconds
wall clock time: 45 minutes 56.32 seconds (2756.32 seconds total)