Starting phenix.real_space_refine
on Mon Feb 10 21:41:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oln_16959/02_2025/8oln_16959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oln_16959/02_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_16959/02_2025/8oln_16959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oln_16959/02_2025/8oln_16959.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oln_16959/02_2025/8oln_16959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oln_16959/02_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-5592/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: 1.83, per 1000 atoms: 0.65
  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: 0.62
  Conformation dependent library (CDL) restraints added in 531.7 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: 0.34
  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: 0.61

  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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.890
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.230
-------------------------------------------------------------------------------
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  : 0.335 
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: 0.1819
  time to fit residues: 37.9826
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  : 0.339 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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 = 0.4380 r_free = 0.4380 target = 0.168123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.144753 restraints weight = 4790.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 4.92
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2890  Z= 0.252
  Angle     :  0.491   4.868   3870  Z= 0.284
  Chirality :  0.050   0.145    400
  Planarity :  0.003   0.014    510
  Dihedral  :  4.586  18.544    375
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 15.17 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.35 (0.34), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.26), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  13 
 PHE   0.013   0.001   PHE D   4 
 TYR   0.008   0.001   TYR G  10 
 ARG   0.005   0.001   ARG E   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
  151 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   32 ILE cc_start: 0.8073 (mm) cc_final: 0.7747 (mm)
REVERT: J   10 TYR cc_start: 0.8489 (t80) cc_final: 0.5878 (p90)
REVERT: J   19 PHE cc_start: 0.8570 (t80) cc_final: 0.7664 (t80)
REVERT: B   19 PHE cc_start: 0.8432 (t80) cc_final: 0.8155 (t80)
REVERT: B   32 ILE cc_start: 0.8044 (mm) cc_final: 0.7774 (mm)
REVERT: B   36 VAL cc_start: 0.7953 (m) cc_final: 0.7737 (t)
REVERT: C   19 PHE cc_start: 0.8525 (t80) cc_final: 0.7941 (t80)
REVERT: D   19 PHE cc_start: 0.8469 (t80) cc_final: 0.8033 (t80)
REVERT: E   19 PHE cc_start: 0.8635 (t80) cc_final: 0.8099 (t80)
REVERT: F   19 PHE cc_start: 0.8590 (t80) cc_final: 0.8131 (t80)
REVERT: H   10 TYR cc_start: 0.9090 (t80) cc_final: 0.8561 (t80)
REVERT: H   16 LYS cc_start: 0.4659 (mmtt) cc_final: 0.3766 (mttt)
REVERT: H   19 PHE cc_start: 0.8513 (t80) cc_final: 0.8026 (t80)
REVERT: I   10 TYR cc_start: 0.8592 (t80) cc_final: 0.6208 (p90)
REVERT: I   16 LYS cc_start: 0.4933 (mmtt) cc_final: 0.4016 (mttt)
  outliers start: 17
  outliers final: 10
  residues processed: 147
  average time/residue: 0.1533
  time to fit residues: 26.4708
Evaluate side-chains
  123 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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   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:    0.0980
   chunk 22 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    3.0186

-------------------------------------------------------------------------------
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 ** 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
D  13 HIS
D  22 GLN
F  22 GLN
** I  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.167452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.146103 restraints weight = 4691.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.4114 rms_B_bonded: 4.77
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2890  Z= 0.261
  Angle     :  0.488   5.451   3870  Z= 0.284
  Chirality :  0.050   0.157    400
  Planarity :  0.002   0.017    510
  Dihedral  :  4.655  19.143    373
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  7.59 %
    Allowed  : 19.31 %
    Favored  : 73.10 %
  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: -4.48 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.41 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  13 
 PHE   0.008   0.001   PHE J   4 
 TYR   0.010   0.001   TYR G  10 
 ARG   0.004   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
  150 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   32 ILE cc_start: 0.7829 (mm) cc_final: 0.7531 (mm)
REVERT: J   19 PHE cc_start: 0.8581 (t80) cc_final: 0.8068 (t80)
REVERT: J   22 GLN cc_start: 0.8789 (mt0) cc_final: 0.8529 (mt0)
REVERT: B   19 PHE cc_start: 0.8415 (t80) cc_final: 0.8171 (t80)
REVERT: B   32 ILE cc_start: 0.8043 (mm) cc_final: 0.7799 (mm)
REVERT: C   19 PHE cc_start: 0.8504 (t80) cc_final: 0.8248 (t80)
REVERT: D   19 PHE cc_start: 0.8468 (t80) cc_final: 0.8033 (t80)
REVERT: E   19 PHE cc_start: 0.8692 (t80) cc_final: 0.8194 (t80)
REVERT: F   16 LYS cc_start: 0.4648 (tttt) cc_final: 0.4171 (mttt)
REVERT: F   19 PHE cc_start: 0.8640 (t80) cc_final: 0.8185 (t80)
REVERT: G   19 PHE cc_start: 0.8576 (t80) cc_final: 0.8306 (t80)
REVERT: H   10 TYR cc_start: 0.9065 (t80) cc_final: 0.8806 (t80)
REVERT: H   16 LYS cc_start: 0.5042 (mmtt) cc_final: 0.4134 (mttt)
REVERT: H   19 PHE cc_start: 0.8516 (t80) cc_final: 0.8164 (t80)
REVERT: I   19 PHE cc_start: 0.8494 (t80) cc_final: 0.8020 (t80)
REVERT: I   22 GLN cc_start: 0.8903 (mt0) cc_final: 0.8634 (mt0)
  outliers start: 22
  outliers final: 16
  residues processed: 144
  average time/residue: 0.1344
  time to fit residues: 23.0198
Evaluate side-chains
  128 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain H 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:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0970
   chunk 12 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    3.2186

-------------------------------------------------------------------------------
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  22 GLN
** J  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  23 ASN
** D  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  22 GLN
F  22 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.166941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.145414 restraints weight = 4859.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 5.01
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2890  Z= 0.275
  Angle     :  0.481   5.066   3870  Z= 0.280
  Chirality :  0.049   0.143    400
  Planarity :  0.002   0.007    510
  Dihedral  :  4.672  19.576    373
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  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 : -3.48 (0.24), 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   0.013   0.001   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
  133 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A   19 PHE cc_start: 0.8577 (t80) cc_final: 0.8240 (t80)
REVERT: A   32 ILE cc_start: 0.7876 (mm) cc_final: 0.7561 (mm)
REVERT: J   19 PHE cc_start: 0.8573 (t80) cc_final: 0.8156 (t80)
REVERT: J   22 GLN cc_start: 0.8807 (mt0) cc_final: 0.8508 (mt0)
REVERT: B   32 ILE cc_start: 0.8060 (mm) cc_final: 0.7816 (mm)
REVERT: D   19 PHE cc_start: 0.8483 (t80) cc_final: 0.7959 (t80)
REVERT: F   16 LYS cc_start: 0.4592 (tttt) cc_final: 0.4203 (mttt)
REVERT: F   19 PHE cc_start: 0.8731 (t80) cc_final: 0.8264 (t80)
REVERT: H   10 TYR cc_start: 0.9054 (t80) cc_final: 0.8778 (t80)
REVERT: H   16 LYS cc_start: 0.4783 (mmtt) cc_final: 0.3921 (mttt)
REVERT: H   19 PHE cc_start: 0.8431 (t80) cc_final: 0.7979 (t80)
REVERT: I   10 TYR cc_start: 0.8451 (t80) cc_final: 0.6082 (p90)
REVERT: I   19 PHE cc_start: 0.8622 (t80) cc_final: 0.8259 (t80)
REVERT: I   22 GLN cc_start: 0.8868 (mt0) cc_final: 0.8585 (mt0)
  outliers start: 19
  outliers final: 18
  residues processed: 130
  average time/residue: 0.1344
  time to fit residues: 20.9359
Evaluate side-chains
  126 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  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 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
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:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    6.9990

-------------------------------------------------------------------------------
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**
** B  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 ** 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 = 0.4288 r_free = 0.4288 target = 0.157092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.138153 restraints weight = 5116.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 4.72
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.5280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.041   2890  Z= 0.547
  Angle     :  0.648   6.741   3870  Z= 0.371
  Chirality :  0.051   0.135    400
  Planarity :  0.003   0.016    510
  Dihedral  :  5.478  28.118    373
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  9.66 %
    Allowed  : 26.21 %
    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: -4.54 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.46 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B  13 
 PHE   0.016   0.002   PHE H   4 
 TYR   0.014   0.002   TYR G  10 
 ARG   0.003   0.001   ARG B   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
  150 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   19 PHE cc_start: 0.8520 (t80) cc_final: 0.8238 (t80)
REVERT: A   32 ILE cc_start: 0.8532 (mm) cc_final: 0.8280 (mm)
REVERT: J    7 ASP cc_start: 0.7386 (t0) cc_final: 0.7098 (t70)
REVERT: J   19 PHE cc_start: 0.8626 (t80) cc_final: 0.8200 (t80)
REVERT: J   22 GLN cc_start: 0.8806 (mt0) cc_final: 0.8510 (mt0)
REVERT: C   19 PHE cc_start: 0.8542 (t80) cc_final: 0.8106 (t80)
REVERT: F   19 PHE cc_start: 0.8675 (t80) cc_final: 0.7907 (t80)
REVERT: F   20 PHE cc_start: 0.8859 (m-80) cc_final: 0.7914 (m-80)
REVERT: H   19 PHE cc_start: 0.8537 (t80) cc_final: 0.8175 (t80)
REVERT: I    7 ASP cc_start: 0.7378 (t0) cc_final: 0.7144 (t70)
REVERT: I   20 PHE cc_start: 0.8780 (m-10) cc_final: 0.8521 (m-10)
REVERT: I   22 GLN cc_start: 0.8828 (mt0) cc_final: 0.8532 (mt0)
  outliers start: 28
  outliers final: 24
  residues processed: 143
  average time/residue: 0.1545
  time to fit residues: 26.2336
Evaluate side-chains
  144 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
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 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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
** J  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 ** 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 = 0.4331 r_free = 0.4331 target = 0.162403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.143199 restraints weight = 5000.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.4104 rms_B_bonded: 4.77
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.5463

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= 0.284
  Angle     :  0.508   6.595   3870  Z= 0.287
  Chirality :  0.050   0.142    400
  Planarity :  0.002   0.008    510
  Dihedral  :  4.852  18.933    373
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  7.59 %
    Allowed  : 28.28 %
    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: -4.50 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.25), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS I   6 
 PHE   0.009   0.001   PHE E   4 
 TYR   0.009   0.001   TYR H  10 
 ARG   0.001   0.000   ARG B   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
  145 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.8700 (t80) cc_final: 0.8409 (t80)
REVERT: A   32 ILE cc_start: 0.7848 (mm) cc_final: 0.7556 (mm)
REVERT: J    7 ASP cc_start: 0.7252 (t0) cc_final: 0.6893 (t70)
REVERT: J   19 PHE cc_start: 0.8599 (t80) cc_final: 0.7935 (t80)
REVERT: J   20 PHE cc_start: 0.8638 (m-80) cc_final: 0.7921 (m-80)
REVERT: J   22 GLN cc_start: 0.8826 (mt0) cc_final: 0.8518 (mt0)
REVERT: C   19 PHE cc_start: 0.8544 (t80) cc_final: 0.8136 (t80)
REVERT: D   19 PHE cc_start: 0.8285 (t80) cc_final: 0.7865 (t80)
REVERT: E   19 PHE cc_start: 0.8516 (t80) cc_final: 0.7897 (t80)
REVERT: F   19 PHE cc_start: 0.8710 (t80) cc_final: 0.7987 (t80)
REVERT: F   20 PHE cc_start: 0.8889 (m-80) cc_final: 0.8047 (m-80)
REVERT: G   19 PHE cc_start: 0.8590 (t80) cc_final: 0.8330 (t80)
REVERT: H   16 LYS cc_start: 0.4744 (mmtt) cc_final: 0.3949 (mttt)
REVERT: H   19 PHE cc_start: 0.8545 (t80) cc_final: 0.8109 (t80)
REVERT: I    7 ASP cc_start: 0.7247 (t0) cc_final: 0.6926 (t70)
REVERT: I   19 PHE cc_start: 0.8690 (t80) cc_final: 0.8447 (t80)
REVERT: I   22 GLN cc_start: 0.8810 (mt0) cc_final: 0.8521 (mt0)
  outliers start: 22
  outliers final: 18
  residues processed: 140
  average time/residue: 0.1419
  time to fit residues: 23.6148
Evaluate side-chains
  138 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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   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 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:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:   30.0000
   chunk 24 optimal weight:   20.0000
   chunk 14 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0970
   chunk 22 optimal weight:    9.9990
   overall best weight:    2.8184

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

Flipped N/Q/H residues before XYZ refinement:
** J  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**
D  22 GLN
** F   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 = 0.4370 r_free = 0.4370 target = 0.165289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.146065 restraints weight = 4895.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.4129 rms_B_bonded: 4.70
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.5549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2890  Z= 0.245
  Angle     :  0.484   6.232   3870  Z= 0.275
  Chirality :  0.049   0.140    400
  Planarity :  0.002   0.008    510
  Dihedral  :  4.738  18.246    373
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  8.97 %
    Allowed  : 27.59 %
    Favored  : 63.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.50 (0.33), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.43 (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   0.011   0.002   TYR F  10 
 ARG   0.001   0.000   ARG B   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: 26
    poor density    : 119
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   19 PHE cc_start: 0.8657 (t80) cc_final: 0.8367 (t80)
REVERT: A   32 ILE cc_start: 0.7839 (mm) cc_final: 0.7529 (mm)
REVERT: J    7 ASP cc_start: 0.7180 (t0) cc_final: 0.6810 (t70)
REVERT: J   19 PHE cc_start: 0.8620 (t80) cc_final: 0.7934 (t80)
REVERT: J   20 PHE cc_start: 0.8647 (m-80) cc_final: 0.7934 (m-80)
REVERT: J   22 GLN cc_start: 0.8798 (mt0) cc_final: 0.8489 (mt0)
REVERT: C   19 PHE cc_start: 0.8387 (t80) cc_final: 0.7832 (t80)
REVERT: D   19 PHE cc_start: 0.8209 (t80) cc_final: 0.7764 (t80)
REVERT: E   19 PHE cc_start: 0.8506 (t80) cc_final: 0.7639 (t80)
REVERT: E   20 PHE cc_start: 0.8755 (m-80) cc_final: 0.7889 (m-80)
REVERT: F   19 PHE cc_start: 0.8718 (t80) cc_final: 0.8000 (t80)
REVERT: F   20 PHE cc_start: 0.8843 (m-80) cc_final: 0.7959 (m-80)
REVERT: G   19 PHE cc_start: 0.8604 (t80) cc_final: 0.8335 (t80)
REVERT: H   16 LYS cc_start: 0.4862 (mmtt) cc_final: 0.4009 (mttt)
REVERT: H   19 PHE cc_start: 0.8501 (t80) cc_final: 0.8067 (t80)
REVERT: I    7 ASP cc_start: 0.7209 (t0) cc_final: 0.6884 (t70)
REVERT: I   19 PHE cc_start: 0.8706 (t80) cc_final: 0.8468 (t80)
REVERT: I   22 GLN cc_start: 0.8809 (mt0) cc_final: 0.8517 (mt0)
  outliers start: 26
  outliers final: 23
  residues processed: 138
  average time/residue: 0.1292
  time to fit residues: 21.4920
Evaluate side-chains
  140 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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 J residue   35 MET
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   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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 8 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 3 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** F   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  23 ASN
** G  23 ASN ** 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 = 0.4291 r_free = 0.4291 target = 0.157972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.139122 restraints weight = 5082.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 4.69
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.5699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   2890  Z= 0.444
  Angle     :  0.592   7.296   3870  Z= 0.336
  Chirality :  0.051   0.161    400
  Planarity :  0.003   0.015    510
  Dihedral  :  5.275  24.028    373
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 27.59 %
    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: -4.54 (0.34), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.45 (0.26), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I  13 
 PHE   0.012   0.002   PHE E   4 
 TYR   0.016   0.002   TYR F  10 
 ARG   0.002   0.001   ARG B   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
  148 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   32 ILE cc_start: 0.8248 (mm) cc_final: 0.7963 (mm)
REVERT: J    7 ASP cc_start: 0.7110 (t0) cc_final: 0.6740 (t70)
REVERT: J   19 PHE cc_start: 0.8640 (t80) cc_final: 0.8152 (t80)
REVERT: J   20 PHE cc_start: 0.8638 (m-80) cc_final: 0.8223 (m-10)
REVERT: J   22 GLN cc_start: 0.8803 (mt0) cc_final: 0.8492 (mt0)
REVERT: D   19 PHE cc_start: 0.8311 (t80) cc_final: 0.7795 (t80)
REVERT: E   20 PHE cc_start: 0.8825 (m-80) cc_final: 0.8445 (m-80)
REVERT: F   19 PHE cc_start: 0.8697 (t80) cc_final: 0.7953 (t80)
REVERT: F   20 PHE cc_start: 0.8849 (m-80) cc_final: 0.7862 (m-80)
REVERT: G   19 PHE cc_start: 0.8621 (t80) cc_final: 0.8362 (t80)
REVERT: H   16 LYS cc_start: 0.4524 (mmtt) cc_final: 0.3773 (mttt)
REVERT: H   19 PHE cc_start: 0.8539 (t80) cc_final: 0.8119 (t80)
REVERT: I    7 ASP cc_start: 0.7241 (t0) cc_final: 0.6896 (t70)
REVERT: I   19 PHE cc_start: 0.8711 (t80) cc_final: 0.8166 (t80)
REVERT: I   20 PHE cc_start: 0.8758 (m-10) cc_final: 0.8254 (m-10)
REVERT: I   22 GLN cc_start: 0.8781 (mt0) cc_final: 0.8497 (mt0)
  outliers start: 29
  outliers final: 27
  residues processed: 140
  average time/residue: 0.1448
  time to fit residues: 24.0318
Evaluate side-chains
  143 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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 J residue   12 VAL
Chi-restraints excluded: chain J residue   35 MET
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   23 ASN
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:    6.9990
   chunk 6 optimal weight:   30.0000
   chunk 5 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** F   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  23 ASN ** 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 = 0.4300 r_free = 0.4300 target = 0.158680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.140094 restraints weight = 5008.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 4.57
r_work: 0.3917 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.5821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   2890  Z= 0.434
  Angle     :  0.580   7.090   3870  Z= 0.329
  Chirality :  0.051   0.159    400
  Planarity :  0.002   0.013    510
  Dihedral  :  5.277  22.743    373
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 27.59 %
    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: -4.50 (0.34), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.26), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I  13 
 PHE   0.015   0.002   PHE C  20 
 TYR   0.018   0.002   TYR F  10 
 ARG   0.002   0.001   ARG B   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
  144 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A    4 PHE cc_start: 0.4878 (OUTLIER) cc_final: 0.2721 (t80)
REVERT: A   32 ILE cc_start: 0.7815 (mm) cc_final: 0.7578 (mm)
REVERT: J    7 ASP cc_start: 0.7245 (t0) cc_final: 0.6861 (t70)
REVERT: J   19 PHE cc_start: 0.8629 (t80) cc_final: 0.8119 (t80)
REVERT: J   20 PHE cc_start: 0.8746 (m-80) cc_final: 0.8332 (m-10)
REVERT: J   22 GLN cc_start: 0.9085 (mt0) cc_final: 0.8818 (mt0)
REVERT: C   19 PHE cc_start: 0.8313 (t80) cc_final: 0.7797 (t80)
REVERT: D   19 PHE cc_start: 0.8327 (t80) cc_final: 0.7851 (t80)
REVERT: E   19 PHE cc_start: 0.8535 (t80) cc_final: 0.7675 (t80)
REVERT: E   20 PHE cc_start: 0.8855 (m-80) cc_final: 0.7966 (m-80)
REVERT: F   19 PHE cc_start: 0.8707 (t80) cc_final: 0.7998 (t80)
REVERT: F   20 PHE cc_start: 0.8897 (m-80) cc_final: 0.8003 (m-80)
REVERT: G   19 PHE cc_start: 0.8633 (t80) cc_final: 0.8334 (t80)
REVERT: H   16 LYS cc_start: 0.5017 (mmtt) cc_final: 0.4005 (mttt)
REVERT: H   19 PHE cc_start: 0.8533 (t80) cc_final: 0.8125 (t80)
REVERT: I    7 ASP cc_start: 0.7287 (t0) cc_final: 0.6910 (t70)
REVERT: I   19 PHE cc_start: 0.8733 (t80) cc_final: 0.8205 (t80)
REVERT: I   20 PHE cc_start: 0.8836 (m-10) cc_final: 0.8392 (m-10)
REVERT: I   22 GLN cc_start: 0.9013 (mt0) cc_final: 0.8754 (mt0)
  outliers start: 29
  outliers final: 26
  residues processed: 138
  average time/residue: 0.1359
  time to fit residues: 22.3535
Evaluate side-chains
  141 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 114
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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 J residue   35 MET
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 15 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:   20.0000
   chunk 9 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4299 r_free = 0.4299 target = 0.158758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.139302 restraints weight = 5184.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.4042 rms_B_bonded: 4.77
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.5998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   2890  Z= 0.433
  Angle     :  0.584   7.266   3870  Z= 0.331
  Chirality :  0.051   0.159    400
  Planarity :  0.003   0.013    510
  Dihedral  :  5.354  23.508    373
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  9.31 %
    Allowed  : 28.62 %
    Favored  : 62.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.54 (0.34), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.45 (0.26), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J   6 
 PHE   0.015   0.002   PHE C  20 
 TYR   0.019   0.003   TYR F  10 
 ARG   0.002   0.001   ARG B   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
  143 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A    4 PHE cc_start: 0.4577 (OUTLIER) cc_final: 0.2671 (t80)
REVERT: A   32 ILE cc_start: 0.7802 (mm) cc_final: 0.7499 (mm)
REVERT: J   19 PHE cc_start: 0.8625 (t80) cc_final: 0.8106 (t80)
REVERT: J   20 PHE cc_start: 0.8662 (m-80) cc_final: 0.8202 (m-10)
REVERT: J   22 GLN cc_start: 0.8823 (mt0) cc_final: 0.8526 (mt0)
REVERT: D   19 PHE cc_start: 0.8338 (t80) cc_final: 0.7834 (t80)
REVERT: E   20 PHE cc_start: 0.8814 (m-80) cc_final: 0.8524 (m-80)
REVERT: F   19 PHE cc_start: 0.8675 (t80) cc_final: 0.7997 (t80)
REVERT: F   20 PHE cc_start: 0.8829 (m-80) cc_final: 0.7933 (m-80)
REVERT: G    6 HIS cc_start: 0.7773 (t70) cc_final: 0.6384 (p90)
REVERT: G   19 PHE cc_start: 0.8634 (t80) cc_final: 0.8321 (t80)
REVERT: H    6 HIS cc_start: 0.7421 (t70) cc_final: 0.6418 (p90)
REVERT: H   16 LYS cc_start: 0.4648 (mmtt) cc_final: 0.3807 (mttt)
REVERT: H   19 PHE cc_start: 0.8496 (t80) cc_final: 0.8097 (t80)
REVERT: I   19 PHE cc_start: 0.8767 (t80) cc_final: 0.8276 (t80)
REVERT: I   20 PHE cc_start: 0.8784 (m-10) cc_final: 0.8339 (m-10)
REVERT: I   22 GLN cc_start: 0.8798 (mt0) cc_final: 0.8507 (mt0)
  outliers start: 27
  outliers final: 25
  residues processed: 136
  average time/residue: 0.1418
  time to fit residues: 22.9183
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  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 PHE
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 J residue   35 MET
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:    9.9990
   chunk 7 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 3 optimal weight:   20.0000
   chunk 20 optimal weight:    8.9990
   chunk 8 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 6 optimal weight:   30.0000
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    2.8786

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 GLN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.163867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.144165 restraints weight = 4941.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.4097 rms_B_bonded: 4.68
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.5948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2890  Z= 0.258
  Angle     :  0.508   7.316   3870  Z= 0.287
  Chirality :  0.051   0.155    400
  Planarity :  0.002   0.010    510
  Dihedral  :  4.986  18.761    373
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  8.28 %
    Allowed  : 31.03 %
    Favored  : 60.69 %
  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: -4.47 (0.34), residues: 340
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.26), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I  13 
 PHE   0.024   0.002   PHE B  19 
 TYR   0.018   0.002   TYR H  10 
 ARG   0.001   0.000   ARG B   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1409.40 seconds
wall clock time: 26 minutes 24.80 seconds (1584.80 seconds total)