Starting phenix.real_space_refine
on Wed Mar  5 16:37:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oln_16959/03_2025/8oln_16959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oln_16959/03_2025/8oln_16959.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oln_16959/03_2025/8oln_16959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oln_16959/03_2025/8oln_16959.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oln_16959/03_2025/8oln_16959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oln_16959/03_2025/8oln_16959.cif"
  }
  resolution = 3.3
  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=   1.001
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      10      5.16       5
     C    1800      2.51       5
     N     510      2.21       5
     O     510      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2830
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 283
          Classifications: {'peptide': 36}
          Link IDs: {'TRANS': 35}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 2.30, per 1000 atoms: 0.81
  Number of scatterers: 2830
  At special positions: 0
  Unit cell: (91.304, 89.688, 42.016, 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      10     16.00
     O     510      8.00
     N     510      7.00
     C    1800      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: 0.60
  Conformation dependent library (CDL) restraints added in 328.1 milliseconds
  

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 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 10 sheets defined
      0.0% alpha, 49.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4
      removed outlier: 6.510A  pdb=" N   ALA A   2 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ARG C   5 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   PHE A   4 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   ASP C   7 " --> pdb=" O   PHE A   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 4
      removed outlier: 6.510A  pdb=" N   ALA A   2 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ARG C   5 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   PHE A   4 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   ASP C   7 " --> pdb=" O   PHE A   4 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ALA C   2 " --> pdb=" O   GLU E   3 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ARG E   5 " --> pdb=" O   ALA C   2 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   PHE C   4 " --> pdb=" O   ARG E   5 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ASP E   7 " --> pdb=" O   PHE C   4 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   HIS C   6 " --> pdb=" O   ASP E   7 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   GLY E   9 " --> pdb=" O   HIS C   6 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   SER C   8 " --> pdb=" O   GLY E   9 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   GLU E  11 " --> pdb=" O   SER C   8 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   TYR C  10 " --> pdb=" O   GLU E  11 " (cutoff:3.500A)
      removed outlier: 8.536A  pdb=" N   HIS E  13 " --> pdb=" O   TYR C  10 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   VAL C  12 " --> pdb=" O   HIS E  13 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ALA E   2 " --> pdb=" O   GLU G   3 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   ARG G   5 " --> pdb=" O   ALA E   2 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   PHE E   4 " --> pdb=" O   ARG G   5 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   ASP G   7 " --> pdb=" O   PHE E   4 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   HIS E   6 " --> pdb=" O   ASP G   7 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   GLY G   9 " --> pdb=" O   HIS E   6 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   SER E   8 " --> pdb=" O   GLY G   9 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   GLU G  11 " --> pdb=" O   SER E   8 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   TYR E  10 " --> pdb=" O   GLU G  11 " (cutoff:3.500A)
      removed outlier: 8.446A  pdb=" N   HIS G  13 " --> pdb=" O   TYR E  10 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   VAL E  12 " --> pdb=" O   HIS G  13 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLU I   3 " --> pdb=" O   ALA G   2 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   HIS G   6 " --> pdb=" O   ARG I   5 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 24
      removed outlier: 6.783A  pdb=" N   ALA A  21 " --> pdb=" O   GLN C  22 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   VAL C  24 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ASN A  23 " --> pdb=" O   VAL C  24 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   ALA C  21 " --> pdb=" O   GLN E  22 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   VAL E  24 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   ASN C  23 " --> pdb=" O   VAL E  24 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ALA E  21 " --> pdb=" O   GLN G  22 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   VAL G  24 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ASN E  23 " --> pdb=" O   VAL G  24 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ALA G  21 " --> pdb=" O   GLN I  22 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   VAL I  24 " --> pdb=" O   ALA G  21 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   ASN G  23 " --> pdb=" O   VAL I  24 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32
    Processing sheet with id=AA5, first strand: chain 'J' and resid 2 through 13
      removed outlier: 6.711A  pdb=" N   GLU J   3 " --> pdb=" O   PHE H   4 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   HIS H   6 " --> pdb=" O   GLU J   3 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   ARG J   5 " --> pdb=" O   HIS H   6 " (cutoff:3.500A)
      removed outlier: 8.958A  pdb=" N   SER H   8 " --> pdb=" O   ARG J   5 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   ASP J   7 " --> pdb=" O   SER H   8 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   TYR H  10 " --> pdb=" O   ASP J   7 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   GLY J   9 " --> pdb=" O   TYR H  10 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   VAL H  12 " --> pdb=" O   GLY J   9 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   GLU J  11 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ALA F   2 " --> pdb=" O   GLU H   3 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   ARG H   5 " --> pdb=" O   ALA F   2 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   PHE F   4 " --> pdb=" O   ARG H   5 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   ASP H   7 " --> pdb=" O   PHE F   4 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   HIS F   6 " --> pdb=" O   ASP H   7 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   GLY H   9 " --> pdb=" O   HIS F   6 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   SER F   8 " --> pdb=" O   GLY H   9 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   GLU H  11 " --> pdb=" O   SER F   8 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TYR F  10 " --> pdb=" O   GLU H  11 " (cutoff:3.500A)
      removed outlier: 8.517A  pdb=" N   HIS H  13 " --> pdb=" O   TYR F  10 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL F  12 " --> pdb=" O   HIS H  13 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA D   2 " --> pdb=" O   GLU F   3 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   ARG F   5 " --> pdb=" O   ALA D   2 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   PHE D   4 " --> pdb=" O   ARG F   5 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   ASP F   7 " --> pdb=" O   PHE D   4 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   HIS D   6 " --> pdb=" O   ASP F   7 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   GLY F   9 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   SER D   8 " --> pdb=" O   GLY F   9 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   GLU F  11 " --> pdb=" O   SER D   8 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   TYR D  10 " --> pdb=" O   GLU F  11 " (cutoff:3.500A)
      removed outlier: 8.469A  pdb=" N   HIS F  13 " --> pdb=" O   TYR D  10 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   VAL D  12 " --> pdb=" O   HIS F  13 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ALA B   2 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   ARG D   5 " --> pdb=" O   ALA B   2 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   PHE B   4 " --> pdb=" O   ARG D   5 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   ASP D   7 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   HIS B   6 " --> pdb=" O   ASP D   7 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   GLY D   9 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   SER B   8 " --> pdb=" O   GLY D   9 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   GLU D  11 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TYR B  10 " --> pdb=" O   GLU D  11 " (cutoff:3.500A)
      removed outlier: 8.555A  pdb=" N   HIS D  13 " --> pdb=" O   TYR B  10 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL B  12 " --> pdb=" O   HIS D  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'J' and resid 21 through 24
      removed outlier: 6.810A  pdb=" N   ALA F  21 " --> pdb=" O   GLN H  22 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   VAL H  24 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   ASN F  23 " --> pdb=" O   VAL H  24 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA D  21 " --> pdb=" O   GLN F  22 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   VAL F  24 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ASN D  23 " --> pdb=" O   VAL F  24 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ALA B  21 " --> pdb=" O   GLN D  22 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   VAL D  24 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASN B  23 " --> pdb=" O   VAL D  24 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'J' and resid 30 through 32
      removed outlier: 6.179A  pdb=" N   ILE J  31 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 18
    Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 18
      removed outlier: 3.503A  pdb=" N   VAL C  18 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 17 through 18

    36 hydrogen bonds defined for protein.
    108 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: 0.62

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 960
        1.34 -     1.46: 655
        1.46 -     1.57: 1255
        1.57 -     1.69: 0
        1.69 -     1.80: 20
  Bond restraints: 2890
  Sorted by residual:
  bond pdb=" CA  VAL J  12 "
       pdb=" CB  VAL J  12 "
    ideal  model  delta    sigma   weight residual
    1.548  1.539  0.009 1.13e-02 7.83e+03 5.93e-01
  bond pdb=" CA  VAL I  12 "
       pdb=" CB  VAL I  12 "
    ideal  model  delta    sigma   weight residual
    1.548  1.539  0.008 1.13e-02 7.83e+03 5.38e-01
  bond pdb=" CA  VAL G  18 "
       pdb=" CB  VAL G  18 "
    ideal  model  delta    sigma   weight residual
    1.548  1.539  0.008 1.13e-02 7.83e+03 5.36e-01
  bond pdb=" CA  VAL C  18 "
       pdb=" CB  VAL C  18 "
    ideal  model  delta    sigma   weight residual
    1.548  1.539  0.008 1.13e-02 7.83e+03 5.31e-01
  bond pdb=" CA  VAL F  12 "
       pdb=" CB  VAL F  12 "
    ideal  model  delta    sigma   weight residual
    1.548  1.540  0.008 1.13e-02 7.83e+03 5.00e-01
  ... (remaining 2885 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.59: 3271
        0.59 -     1.17: 440
        1.17 -     1.76: 139
        1.76 -     2.35: 0
        2.35 -     2.94: 20
  Bond angle restraints: 3870
  Sorted by residual:
  angle pdb=" N   ALA B   2 "
        pdb=" CA  ALA B   2 "
        pdb=" C   ALA B   2 "
      ideal   model   delta    sigma   weight residual
     108.32  111.26   -2.94 1.64e+00 3.72e-01 3.20e+00
  angle pdb=" N   ALA F   2 "
        pdb=" CA  ALA F   2 "
        pdb=" C   ALA F   2 "
      ideal   model   delta    sigma   weight residual
     108.32  111.24   -2.92 1.64e+00 3.72e-01 3.18e+00
  angle pdb=" N   ALA D   2 "
        pdb=" CA  ALA D   2 "
        pdb=" C   ALA D   2 "
      ideal   model   delta    sigma   weight residual
     108.32  111.24   -2.92 1.64e+00 3.72e-01 3.17e+00
  angle pdb=" N   ALA J   2 "
        pdb=" CA  ALA J   2 "
        pdb=" C   ALA J   2 "
      ideal   model   delta    sigma   weight residual
     108.32  111.23   -2.91 1.64e+00 3.72e-01 3.14e+00
  angle pdb=" N   ALA G   2 "
        pdb=" CA  ALA G   2 "
        pdb=" C   ALA G   2 "
      ideal   model   delta    sigma   weight residual
     108.32  111.22   -2.90 1.64e+00 3.72e-01 3.14e+00
  ... (remaining 3865 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.02: 1270
        6.02 -    12.05: 220
       12.05 -    18.07: 80
       18.07 -    24.09: 30
       24.09 -    30.12: 40
  Dihedral angle restraints: 1640
    sinusoidal: 640
      harmonic: 1000
  Sorted by residual:
  dihedral pdb=" CA  LYS B  28 "
           pdb=" CB  LYS B  28 "
           pdb=" CG  LYS B  28 "
           pdb=" CD  LYS B  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -149.88  -30.12     3      1.50e+01 4.44e-03 4.77e+00
  dihedral pdb=" CA  LYS E  28 "
           pdb=" CB  LYS E  28 "
           pdb=" CG  LYS E  28 "
           pdb=" CD  LYS E  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -149.91  -30.09     3      1.50e+01 4.44e-03 4.76e+00
  dihedral pdb=" CA  LYS I  28 "
           pdb=" CB  LYS I  28 "
           pdb=" CG  LYS I  28 "
           pdb=" CD  LYS I  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -149.93  -30.07     3      1.50e+01 4.44e-03 4.76e+00
  ... (remaining 1637 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 187
       0.025 -    0.049: 143
       0.049 -    0.074: 20
       0.074 -    0.099: 27
       0.099 -    0.123: 23
  Chirality restraints: 400
  Sorted by residual:
  chirality pdb=" CA  ILE I  31 "
            pdb=" N   ILE I  31 "
            pdb=" C   ILE I  31 "
            pdb=" CB  ILE I  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  ILE F  31 "
            pdb=" N   ILE F  31 "
            pdb=" C   ILE F  31 "
            pdb=" CB  ILE F  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  chirality pdb=" CA  ILE D  31 "
            pdb=" N   ILE D  31 "
            pdb=" C   ILE D  31 "
            pdb=" CB  ILE D  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.67e-01
  ... (remaining 397 not shown)

  Planarity restraints: 510
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E   5 "   -0.002 2.00e-02 2.50e+03   3.88e-03 1.51e-01
        pdb=" C   ARG E   5 "    0.007 2.00e-02 2.50e+03
        pdb=" O   ARG E   5 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   HIS E   6 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG H   5 "   -0.002 2.00e-02 2.50e+03   3.88e-03 1.50e-01
        pdb=" C   ARG H   5 "    0.007 2.00e-02 2.50e+03
        pdb=" O   ARG H   5 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   HIS H   6 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG J   5 "   -0.002 2.00e-02 2.50e+03   3.68e-03 1.36e-01
        pdb=" C   ARG J   5 "    0.006 2.00e-02 2.50e+03
        pdb=" O   ARG J   5 "   -0.002 2.00e-02 2.50e+03
        pdb=" N   HIS J   6 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 507 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 611
        2.80 -     3.32: 2443
        3.32 -     3.85: 4757
        3.85 -     4.37: 5160
        4.37 -     4.90: 9774
  Nonbonded interactions: 22745
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP F   1 "
            pdb=" N   ASP H   1 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OD1 ASP C   1 "
            pdb=" N   ASP E   1 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" O   ASN D  23 "
            pdb=" OH  TYR F  10 "
     model   vdw
     2.430 3.040
  nonbonded pdb=" OD1 ASP B   1 "
            pdb=" N   ASP D   1 "
     model   vdw
     2.439 3.120
  nonbonded pdb=" O   ASN G  23 "
            pdb=" OH  TYR I  10 "
     model   vdw
     2.455 3.040
  ... (remaining 22740 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 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:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     12.740
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.009   2890  Z= 0.148
  Angle     :  0.479   2.936   3870  Z= 0.307
  Chirality :  0.044   0.123    400
  Planarity :  0.001   0.005    510
  Dihedral  :  9.035  30.117   1000
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  :  4.48 %
    Favored  : 93.10 %
  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: -4.24 (0.32), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  13 
 PHE   0.003   0.001   PHE G   4 
 TYR   0.004   0.001   TYR A  10 
 ARG   0.001   0.000   ARG G   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 177
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.5642 (ptm-80) cc_final: 0.5275 (ptt90)
REVERT: J    5 ARG cc_start: 0.7146 (ptm-80) cc_final: 0.5757 (mmm160)
REVERT: J   10 TYR cc_start: 0.8407 (t80) cc_final: 0.5764 (p90)
REVERT: J   19 PHE cc_start: 0.8262 (t80) cc_final: 0.7953 (t80)
REVERT: B    5 ARG cc_start: 0.6090 (ptm-80) cc_final: 0.5215 (ptt-90)
REVERT: B   19 PHE cc_start: 0.8523 (t80) cc_final: 0.8154 (t80)
REVERT: B   22 GLN cc_start: 0.8531 (mt0) cc_final: 0.7526 (pm20)
REVERT: C   19 PHE cc_start: 0.8513 (t80) cc_final: 0.7923 (t80)
REVERT: D   19 PHE cc_start: 0.8452 (t80) cc_final: 0.7837 (t80)
REVERT: E   19 PHE cc_start: 0.8587 (t80) cc_final: 0.8037 (t80)
REVERT: F   19 PHE cc_start: 0.8532 (t80) cc_final: 0.8058 (t80)
REVERT: G   19 PHE cc_start: 0.8557 (t80) cc_final: 0.8183 (t80)
REVERT: H    5 ARG cc_start: 0.7493 (ptm-80) cc_final: 0.7143 (ttp-110)
REVERT: H   19 PHE cc_start: 0.8602 (t80) cc_final: 0.8302 (t80)
REVERT: I   10 TYR cc_start: 0.8295 (t80) cc_final: 0.5903 (p90)
REVERT: I   19 PHE cc_start: 0.8176 (t80) cc_final: 0.7527 (t80)
REVERT: I   23 ASN cc_start: 0.8235 (m-40) cc_final: 0.7873 (m-40)
  outliers start: 7
  outliers final: 5
  residues processed: 183
  average time/residue: 0.1836
  time to fit residues: 38.2918
Evaluate side-chains
  139 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain F residue   12 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A  14 HIS
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  13 HIS
J  14 HIS
J  22 GLN
** J  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  13 HIS
B  14 HIS
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 HIS
C  14 HIS
D  14 HIS
D  22 GLN
** D  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 HIS
E  14 HIS
E  22 GLN
F  13 HIS
F  14 HIS
F  22 GLN
G  13 HIS
G  14 HIS
H  13 HIS
H  14 HIS
H  22 GLN
I  13 HIS
I  14 HIS
I  22 GLN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.167825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.144698 restraints weight = 4797.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 4.89
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2890  Z= 0.260
  Angle     :  0.495   4.851   3870  Z= 0.286
  Chirality :  0.050   0.141    400
  Planarity :  0.003   0.018    510
  Dihedral  :  4.662  19.334    375
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 14.48 %
    Favored  : 78.62 %
  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: -4.37 (0.34), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.26), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  13 
 PHE   0.013   0.002   PHE C   4 
 TYR   0.009   0.001   TYR G  10 
 ARG   0.006   0.001   ARG F   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   32 ILE cc_start: 0.7903 (mm) cc_final: 0.7561 (mm)
REVERT: J   10 TYR cc_start: 0.8541 (t80) cc_final: 0.5914 (p90)
REVERT: J   19 PHE cc_start: 0.8601 (t80) cc_final: 0.7712 (t80)
REVERT: B   19 PHE cc_start: 0.8467 (t80) cc_final: 0.8209 (t80)
REVERT: B   32 ILE cc_start: 0.7698 (mm) cc_final: 0.7404 (mm)
REVERT: C   19 PHE cc_start: 0.8549 (t80) cc_final: 0.7974 (t80)
REVERT: D   19 PHE cc_start: 0.8501 (t80) cc_final: 0.8077 (t80)
REVERT: E   19 PHE cc_start: 0.8655 (t80) cc_final: 0.8136 (t80)
REVERT: F   19 PHE cc_start: 0.8607 (t80) cc_final: 0.8157 (t80)
REVERT: H   10 TYR cc_start: 0.9082 (t80) cc_final: 0.8583 (t80)
REVERT: H   16 LYS cc_start: 0.4826 (mmtt) cc_final: 0.3885 (mttt)
REVERT: H   19 PHE cc_start: 0.8537 (t80) cc_final: 0.8041 (t80)
REVERT: I   10 TYR cc_start: 0.8607 (t80) cc_final: 0.6235 (p90)
  outliers start: 20
  outliers final: 11
  residues processed: 152
  average time/residue: 0.1488
  time to fit residues: 26.6272
Evaluate side-chains
  125 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    8 SER
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain H residue    8 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 4 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    4.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  13 HIS
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  22 GLN
** J  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 GLN
C  23 ASN
D  13 HIS
D  22 GLN
** E  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.163501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.142433 restraints weight = 4826.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 4.82
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   2890  Z= 0.337
  Angle     :  0.526   5.461   3870  Z= 0.307
  Chirality :  0.050   0.155    400
  Planarity :  0.003   0.021    510
  Dihedral  :  4.988  20.283    374
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  7.59 %
    Allowed  : 21.72 %
    Favored  : 70.69 %
  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: -4.57 (0.32), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  13 
 PHE   0.009   0.001   PHE E   4 
 TYR   0.007   0.001   TYR G  10 
 ARG   0.003   0.001   ARG E   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   32 ILE cc_start: 0.8255 (mm) cc_final: 0.7962 (mm)
REVERT: J   19 PHE cc_start: 0.8634 (t80) cc_final: 0.8059 (t80)
REVERT: J   22 GLN cc_start: 0.8819 (mt0) cc_final: 0.8510 (mt0)
REVERT: B   19 PHE cc_start: 0.8419 (t80) cc_final: 0.8169 (t80)
REVERT: B   32 ILE cc_start: 0.8301 (mm) cc_final: 0.8052 (mm)
REVERT: D   19 PHE cc_start: 0.8507 (t80) cc_final: 0.8075 (t80)
REVERT: F   19 PHE cc_start: 0.8671 (t80) cc_final: 0.8235 (t80)
REVERT: H   16 LYS cc_start: 0.4899 (mmtt) cc_final: 0.3924 (mttt)
REVERT: H   19 PHE cc_start: 0.8557 (t80) cc_final: 0.8204 (t80)
REVERT: I   19 PHE cc_start: 0.8534 (t80) cc_final: 0.8072 (t80)
REVERT: I   22 GLN cc_start: 0.8878 (mt0) cc_final: 0.8634 (mt0)
  outliers start: 22
  outliers final: 18
  residues processed: 136
  average time/residue: 0.1416
  time to fit residues: 22.7549
Evaluate side-chains
  127 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   26 SER
Chi-restraints excluded: chain J residue    8 SER
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue    8 SER
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   23 ASN
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain G residue    8 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0020
   overall best weight:    2.3594

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 GLN
C  23 ASN
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  22 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.166965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.146199 restraints weight = 4734.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 4.87
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2890  Z= 0.216
  Angle     :  0.457   5.142   3870  Z= 0.266
  Chirality :  0.049   0.140    400
  Planarity :  0.002   0.007    510
  Dihedral  :  4.635  18.308    374
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 26.55 %
    Favored  : 66.90 %
  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: -4.57 (0.32), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C  13 
 PHE   0.007   0.001   PHE J   4 
 TYR   0.012   0.002   TYR G  10 
 ARG   0.002   0.000   ARG E   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A   19 PHE cc_start: 0.8575 (t80) cc_final: 0.8208 (t80)
REVERT: A   32 ILE cc_start: 0.7824 (mm) cc_final: 0.7535 (mm)
REVERT: J   19 PHE cc_start: 0.8675 (t80) cc_final: 0.8144 (t80)
REVERT: J   22 GLN cc_start: 0.8785 (mt0) cc_final: 0.8490 (mt0)
REVERT: B   19 PHE cc_start: 0.8375 (t80) cc_final: 0.8165 (t80)
REVERT: B   32 ILE cc_start: 0.7623 (mm) cc_final: 0.7368 (mm)
REVERT: C   19 PHE cc_start: 0.8519 (t80) cc_final: 0.8167 (t80)
REVERT: D   19 PHE cc_start: 0.8457 (t80) cc_final: 0.8008 (t80)
REVERT: F   16 LYS cc_start: 0.4813 (tttt) cc_final: 0.4516 (mttt)
REVERT: F   19 PHE cc_start: 0.8680 (t80) cc_final: 0.8249 (t80)
REVERT: H   16 LYS cc_start: 0.5120 (mmtt) cc_final: 0.4127 (mttt)
REVERT: H   19 PHE cc_start: 0.8523 (t80) cc_final: 0.8202 (t80)
REVERT: I   10 TYR cc_start: 0.8337 (t80) cc_final: 0.6005 (p90)
REVERT: I   19 PHE cc_start: 0.8648 (t80) cc_final: 0.8277 (t80)
REVERT: I   22 GLN cc_start: 0.8875 (mt0) cc_final: 0.8602 (mt0)
  outliers start: 19
  outliers final: 18
  residues processed: 132
  average time/residue: 0.1424
  time to fit residues: 22.3303
Evaluate side-chains
  127 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain J residue    8 SER
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   35 MET
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue    8 SER
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   23 ASN
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain H residue    8 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 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 = 0.4278 r_free = 0.4278 target = 0.157314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.138651 restraints weight = 5036.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 4.61
r_work: 0.3894 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.5259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   2890  Z= 0.499
  Angle     :  0.615   7.682   3870  Z= 0.351
  Chirality :  0.050   0.141    400
  Planarity :  0.003   0.025    510
  Dihedral  :  5.337  25.872    373
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  9.66 %
    Allowed  : 23.10 %
    Favored  : 67.24 %
  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: -4.57 (0.32), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  13 
 PHE   0.015   0.002   PHE E   4 
 TYR   0.013   0.002   TYR G  10 
 ARG   0.002   0.001   ARG D   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   19 PHE cc_start: 0.8518 (t80) cc_final: 0.8212 (t80)
REVERT: J    7 ASP cc_start: 0.7475 (t0) cc_final: 0.7212 (t70)
REVERT: J   19 PHE cc_start: 0.8591 (t80) cc_final: 0.8145 (t80)
REVERT: J   22 GLN cc_start: 0.9095 (mt0) cc_final: 0.8837 (mt0)
REVERT: B   19 PHE cc_start: 0.8432 (t80) cc_final: 0.8215 (t80)
REVERT: C   19 PHE cc_start: 0.8543 (t80) cc_final: 0.8098 (t80)
REVERT: D   19 PHE cc_start: 0.8492 (t80) cc_final: 0.7995 (t80)
REVERT: F   19 PHE cc_start: 0.8722 (t80) cc_final: 0.8294 (t80)
REVERT: H   19 PHE cc_start: 0.8520 (t80) cc_final: 0.8146 (t80)
REVERT: I    7 ASP cc_start: 0.7382 (t0) cc_final: 0.7098 (t70)
REVERT: I   20 PHE cc_start: 0.8820 (m-10) cc_final: 0.8487 (m-10)
REVERT: I   22 GLN cc_start: 0.9105 (mt0) cc_final: 0.8853 (mt0)
  outliers start: 28
  outliers final: 24
  residues processed: 142
  average time/residue: 0.1492
  time to fit residues: 24.9956
Evaluate side-chains
  142 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 HIS
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain J residue    8 SER
Chi-restraints excluded: chain J residue   12 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   35 MET
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   23 ASN
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue    8 SER
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   23 ASN
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain H residue    8 SER
Chi-restraints excluded: chain I residue    8 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  23 ASN
** D   6 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 = 0.4323 r_free = 0.4323 target = 0.160743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.142302 restraints weight = 5011.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 4.44
r_work: 0.3934 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.5467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   2890  Z= 0.352
  Angle     :  0.541   7.031   3870  Z= 0.305
  Chirality :  0.049   0.139    400
  Planarity :  0.002   0.019    510
  Dihedral  :  5.002  20.576    373
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  8.97 %
    Allowed  : 26.90 %
    Favored  : 64.14 %
  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: -4.56 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  13 
 PHE   0.011   0.002   PHE E   4 
 TYR   0.009   0.001   TYR H  10 
 ARG   0.001   0.000   ARG J   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   19 PHE cc_start: 0.8688 (t80) cc_final: 0.8415 (t80)
REVERT: J    7 ASP cc_start: 0.7407 (t0) cc_final: 0.7034 (t70)
REVERT: J   19 PHE cc_start: 0.8592 (t80) cc_final: 0.7820 (t80)
REVERT: J   20 PHE cc_start: 0.8680 (m-10) cc_final: 0.7994 (m-80)
REVERT: J   22 GLN cc_start: 0.9080 (mt0) cc_final: 0.8801 (mt0)
REVERT: C   19 PHE cc_start: 0.8543 (t80) cc_final: 0.8209 (t80)
REVERT: D   19 PHE cc_start: 0.8478 (t80) cc_final: 0.7903 (t80)
REVERT: E   19 PHE cc_start: 0.8397 (t80) cc_final: 0.7998 (t80)
REVERT: F   19 PHE cc_start: 0.8706 (t80) cc_final: 0.8095 (t80)
REVERT: F   20 PHE cc_start: 0.8876 (m-80) cc_final: 0.8377 (m-80)
REVERT: G   19 PHE cc_start: 0.8534 (t80) cc_final: 0.8234 (t80)
REVERT: H   16 LYS cc_start: 0.5063 (mmtt) cc_final: 0.4035 (mttt)
REVERT: H   19 PHE cc_start: 0.8514 (t80) cc_final: 0.8076 (t80)
REVERT: I    7 ASP cc_start: 0.7198 (t0) cc_final: 0.6748 (t70)
REVERT: I   19 PHE cc_start: 0.8702 (t80) cc_final: 0.8458 (t80)
REVERT: I   22 GLN cc_start: 0.9053 (mt0) cc_final: 0.8793 (mt0)
  outliers start: 26
  outliers final: 23
  residues processed: 140
  average time/residue: 0.1260
  time to fit residues: 21.2352
Evaluate side-chains
  141 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 HIS
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain J residue    8 SER
Chi-restraints excluded: chain B residue    6 HIS
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   35 MET
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   23 ASN
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue    8 SER
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain H residue    8 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 6 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  23 ASN
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 GLN
** F   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.159475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.140634 restraints weight = 5020.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 4.65
r_work: 0.3921 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.5595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2890  Z= 0.368
  Angle     :  0.539   6.493   3870  Z= 0.307
  Chirality :  0.049   0.142    400
  Planarity :  0.002   0.013    510
  Dihedral  :  5.076  22.060    373
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  9.66 %
    Allowed  : 26.55 %
    Favored  : 63.79 %
  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: -4.61 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  13 
 PHE   0.011   0.002   PHE E   4 
 TYR   0.012   0.002   TYR I  10 
 ARG   0.001   0.000   ARG J   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.324 
Fit side-chains
REVERT: J    7 ASP cc_start: 0.7300 (t0) cc_final: 0.6939 (t70)
REVERT: J   19 PHE cc_start: 0.8602 (t80) cc_final: 0.7783 (t80)
REVERT: J   20 PHE cc_start: 0.8706 (m-10) cc_final: 0.8015 (m-80)
REVERT: J   22 GLN cc_start: 0.9091 (mt0) cc_final: 0.8826 (mt0)
REVERT: D   19 PHE cc_start: 0.8275 (t80) cc_final: 0.7880 (t80)
REVERT: F   19 PHE cc_start: 0.8696 (t80) cc_final: 0.8338 (t80)
REVERT: G   19 PHE cc_start: 0.8610 (t80) cc_final: 0.8347 (t80)
REVERT: H   16 LYS cc_start: 0.5075 (mmtt) cc_final: 0.3906 (mttt)
REVERT: H   19 PHE cc_start: 0.8510 (t80) cc_final: 0.8069 (t80)
REVERT: I    7 ASP cc_start: 0.7184 (t0) cc_final: 0.6746 (t70)
REVERT: I   19 PHE cc_start: 0.8717 (t80) cc_final: 0.8126 (t80)
REVERT: I   20 PHE cc_start: 0.8811 (m-10) cc_final: 0.8288 (m-80)
REVERT: I   22 GLN cc_start: 0.9066 (mt0) cc_final: 0.8821 (mt0)
  outliers start: 28
  outliers final: 25
  residues processed: 139
  average time/residue: 0.1307
  time to fit residues: 21.7408
Evaluate side-chains
  140 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 HIS
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain J residue    8 SER
Chi-restraints excluded: chain B residue    6 HIS
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   35 MET
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   23 ASN
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue    8 SER
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   23 ASN
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain H residue    8 SER
Chi-restraints excluded: chain I residue    8 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 12 optimal weight:   20.0000
   chunk 8 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 GLN
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.157450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.138932 restraints weight = 5060.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 4.60
r_work: 0.3910 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.5722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   2890  Z= 0.468
  Angle     :  0.592   6.145   3870  Z= 0.337
  Chirality :  0.050   0.140    400
  Planarity :  0.003   0.014    510
  Dihedral  :  5.345  24.580    373
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  9.31 %
    Allowed  : 26.90 %
    Favored  : 63.79 %
  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: -4.62 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  13 
 PHE   0.012   0.002   PHE H   4 
 TYR   0.009   0.001   TYR F  10 
 ARG   0.002   0.000   ARG J   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.335 
Fit side-chains
REVERT: J    7 ASP cc_start: 0.7214 (t0) cc_final: 0.6792 (t70)
REVERT: J   20 PHE cc_start: 0.8703 (m-10) cc_final: 0.8317 (m-80)
REVERT: J   22 GLN cc_start: 0.9068 (mt0) cc_final: 0.8796 (mt0)
REVERT: C   19 PHE cc_start: 0.8301 (t80) cc_final: 0.7876 (t80)
REVERT: F   19 PHE cc_start: 0.8599 (t80) cc_final: 0.8170 (t80)
REVERT: F   20 PHE cc_start: 0.8829 (m-80) cc_final: 0.8376 (m-80)
REVERT: G   19 PHE cc_start: 0.8640 (t80) cc_final: 0.8372 (t80)
REVERT: H   19 PHE cc_start: 0.8489 (t80) cc_final: 0.8171 (t80)
REVERT: I    7 ASP cc_start: 0.7186 (t0) cc_final: 0.6766 (t70)
REVERT: I   19 PHE cc_start: 0.8721 (t80) cc_final: 0.8180 (t80)
REVERT: I   20 PHE cc_start: 0.8825 (m-10) cc_final: 0.8379 (m-10)
REVERT: I   22 GLN cc_start: 0.9084 (mt0) cc_final: 0.8823 (mt0)
  outliers start: 27
  outliers final: 26
  residues processed: 139
  average time/residue: 0.1461
  time to fit residues: 23.9839
Evaluate side-chains
  142 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 HIS
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain J residue    8 SER
Chi-restraints excluded: chain B residue    6 HIS
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   35 MET
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   23 ASN
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue    8 SER
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   23 ASN
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain H residue    8 SER
Chi-restraints excluded: chain I residue    8 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:   30.0000
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 GLN
C  23 ASN
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 GLN
** F   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.163054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.144407 restraints weight = 4922.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.4105 rms_B_bonded: 4.58
r_work: 0.3960 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.5819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2890  Z= 0.274
  Angle     :  0.493   6.091   3870  Z= 0.279
  Chirality :  0.050   0.144    400
  Planarity :  0.002   0.011    510
  Dihedral  :  4.911  19.630    373
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  9.31 %
    Allowed  : 27.59 %
    Favored  : 63.10 %
  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: -4.63 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  13 
 PHE   0.009   0.001   PHE C  19 
 TYR   0.018   0.002   TYR H  10 
 ARG   0.001   0.000   ARG J   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A    4 PHE cc_start: 0.4987 (OUTLIER) cc_final: 0.2824 (t80)
REVERT: J    7 ASP cc_start: 0.7166 (t0) cc_final: 0.6782 (t70)
REVERT: J   19 PHE cc_start: 0.8627 (t80) cc_final: 0.7829 (t80)
REVERT: J   20 PHE cc_start: 0.8596 (m-10) cc_final: 0.7924 (m-80)
REVERT: J   22 GLN cc_start: 0.9041 (mt0) cc_final: 0.8777 (mt0)
REVERT: C   19 PHE cc_start: 0.8330 (t80) cc_final: 0.7917 (t80)
REVERT: D   19 PHE cc_start: 0.8255 (t80) cc_final: 0.7918 (t80)
REVERT: F   19 PHE cc_start: 0.8633 (t80) cc_final: 0.8274 (t80)
REVERT: F   20 PHE cc_start: 0.8739 (m-80) cc_final: 0.8482 (m-10)
REVERT: G   19 PHE cc_start: 0.8588 (t80) cc_final: 0.8230 (t80)
REVERT: H   16 LYS cc_start: 0.5100 (mmtt) cc_final: 0.4116 (mttt)
REVERT: H   19 PHE cc_start: 0.8498 (t80) cc_final: 0.8085 (t80)
REVERT: I    7 ASP cc_start: 0.7132 (t0) cc_final: 0.6721 (t70)
REVERT: I   19 PHE cc_start: 0.8766 (t80) cc_final: 0.8081 (t80)
REVERT: I   20 PHE cc_start: 0.8817 (m-10) cc_final: 0.8207 (m-80)
REVERT: I   22 GLN cc_start: 0.9044 (mt0) cc_final: 0.8783 (mt0)
  outliers start: 27
  outliers final: 25
  residues processed: 140
  average time/residue: 0.1293
  time to fit residues: 21.8434
Evaluate side-chains
  142 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 PHE
Chi-restraints excluded: chain A residue    6 HIS
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain J residue    8 SER
Chi-restraints excluded: chain B residue    6 HIS
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   23 ASN
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue    8 SER
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   23 ASN
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain H residue    8 SER
Chi-restraints excluded: chain I residue    8 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 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 = 0.4316 r_free = 0.4316 target = 0.159294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.140865 restraints weight = 5044.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 4.58
r_work: 0.3922 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.5894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   2890  Z= 0.417
  Angle     :  0.572   7.647   3870  Z= 0.324
  Chirality :  0.050   0.145    400
  Planarity :  0.003   0.014    510
  Dihedral  :  5.259  23.543    373
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  9.31 %
    Allowed  : 27.59 %
    Favored  : 63.10 %
  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: -4.63 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.52 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J   6 
 PHE   0.011   0.002   PHE E   4 
 TYR   0.021   0.002   TYR H  10 
 ARG   0.002   0.000   ARG J   5 

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

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

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  680 Ramachandran restraints generated.
    340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A    4 PHE cc_start: 0.4818 (OUTLIER) cc_final: 0.2480 (t80)
REVERT: J   19 PHE cc_start: 0.8659 (t80) cc_final: 0.7983 (t80)
REVERT: J   20 PHE cc_start: 0.8618 (m-10) cc_final: 0.8087 (m-80)
REVERT: J   22 GLN cc_start: 0.9050 (mt0) cc_final: 0.8783 (mt0)
REVERT: C   19 PHE cc_start: 0.8341 (t80) cc_final: 0.7953 (t80)
REVERT: D   19 PHE cc_start: 0.8300 (t80) cc_final: 0.7890 (t80)
REVERT: F   19 PHE cc_start: 0.8657 (t80) cc_final: 0.8241 (t80)
REVERT: F   20 PHE cc_start: 0.8803 (m-80) cc_final: 0.8466 (m-10)
REVERT: G   19 PHE cc_start: 0.8663 (t80) cc_final: 0.8347 (t80)
REVERT: H    6 HIS cc_start: 0.7575 (t70) cc_final: 0.6396 (p90)
REVERT: H   16 LYS cc_start: 0.4918 (mmtt) cc_final: 0.3939 (mttt)
REVERT: H   19 PHE cc_start: 0.8477 (t80) cc_final: 0.8079 (t80)
REVERT: I    7 ASP cc_start: 0.7200 (t0) cc_final: 0.6792 (t70)
REVERT: I   19 PHE cc_start: 0.8762 (t80) cc_final: 0.8158 (t80)
REVERT: I   20 PHE cc_start: 0.8821 (m-10) cc_final: 0.8313 (m-80)
REVERT: I   22 GLN cc_start: 0.9067 (mt0) cc_final: 0.8811 (mt0)
  outliers start: 27
  outliers final: 25
  residues processed: 137
  average time/residue: 0.1412
  time to fit residues: 23.0055
Evaluate side-chains
  139 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 PHE
Chi-restraints excluded: chain A residue    6 HIS
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain J residue    8 SER
Chi-restraints excluded: chain B residue    6 HIS
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   35 MET
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   23 ASN
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue    8 SER
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   23 ASN
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain H residue    8 SER
Chi-restraints excluded: chain I residue    8 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:   20.0000
   chunk 2 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   overall best weight:    3.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 GLN
C  23 ASN
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 GLN
** F   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.162386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.143083 restraints weight = 4931.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 4.71
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.5965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   2890  Z= 0.327
  Angle     :  0.529   7.782   3870  Z= 0.298
  Chirality :  0.050   0.144    400
  Planarity :  0.002   0.009    510
  Dihedral  :  5.090  20.686    373
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  8.97 %
    Allowed  : 28.62 %
    Favored  : 62.41 %
  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: -4.58 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  13 
 PHE   0.010   0.002   PHE E   4 
 TYR   0.020   0.002   TYR H  10 
 ARG   0.001   0.000   ARG I   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1615.50 seconds
wall clock time: 28 minutes 46.64 seconds (1726.64 seconds total)