Starting phenix.real_space_refine
on Wed Sep 17 05:25:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5fna_3241/09_2025/5fna_3241.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5fna_3241/09_2025/5fna_3241.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5fna_3241/09_2025/5fna_3241.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5fna_3241/09_2025/5fna_3241.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5fna_3241/09_2025/5fna_3241.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5fna_3241/09_2025/5fna_3241.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.718 sd=   0.877
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      48      5.16       5
     C    3312      2.51       5
     N     920      2.21       5
     O    1048      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5328
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 666
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82}
  Restraints were copied for chains:
    B, C, D, E, F, G, H
  Time building chain proxies: 0.81, per 1000 atoms: 0.15
  Number of scatterers: 5328
  At special positions: 0
  Unit cell: (80.91, 83.52, 81.78, 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      48     16.00
     O    1048      8.00
     N     920      7.00
     C    3312      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: 0.47
  Conformation dependent library (CDL) restraints added in 195.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1280

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      82.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 8
    Processing helix  chain 'A' and resid 9 through 16
      removed outlier: 3.662A  pdb=" N   ILE A  13 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ARG A  14 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 31
      removed outlier: 5.215A  pdb=" N   GLY A  23 " --> pdb=" O   GLY A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 41
    Processing helix  chain 'A' and resid 42 through 45
    Processing helix  chain 'A' and resid 48 through 50
      No H-bonds generated for 'chain 'A' and resid 48 through 50'
    Processing helix  chain 'A' and resid 51 through 59
      removed outlier: 3.805A  pdb=" N   ALA A  55 " --> pdb=" O   ASP A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 66
      No H-bonds generated for 'chain 'A' and resid 64 through 66'
    Processing helix  chain 'A' and resid 67 through 79
      removed outlier: 3.587A  pdb=" N   CYS A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1 through 8
    Processing helix  chain 'B' and resid 9 through 16
      removed outlier: 3.662A  pdb=" N   ILE B  13 " --> pdb=" O   LYS B  10 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ARG B  14 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 31
      removed outlier: 5.215A  pdb=" N   GLY B  23 " --> pdb=" O   GLY B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 41
    Processing helix  chain 'B' and resid 42 through 45
    Processing helix  chain 'B' and resid 48 through 50
      No H-bonds generated for 'chain 'B' and resid 48 through 50'
    Processing helix  chain 'B' and resid 51 through 59
      removed outlier: 3.805A  pdb=" N   ALA B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 66
      No H-bonds generated for 'chain 'B' and resid 64 through 66'
    Processing helix  chain 'B' and resid 67 through 79
      removed outlier: 3.587A  pdb=" N   CYS B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1 through 8
    Processing helix  chain 'C' and resid 9 through 16
      removed outlier: 3.662A  pdb=" N   ILE C  13 " --> pdb=" O   LYS C  10 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ARG C  14 " --> pdb=" O   LEU C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 31
      removed outlier: 5.215A  pdb=" N   GLY C  23 " --> pdb=" O   GLY C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 41
    Processing helix  chain 'C' and resid 42 through 45
    Processing helix  chain 'C' and resid 48 through 50
      No H-bonds generated for 'chain 'C' and resid 48 through 50'
    Processing helix  chain 'C' and resid 51 through 59
      removed outlier: 3.806A  pdb=" N   ALA C  55 " --> pdb=" O   ASP C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 66
      No H-bonds generated for 'chain 'C' and resid 64 through 66'
    Processing helix  chain 'C' and resid 67 through 79
      removed outlier: 3.588A  pdb=" N   CYS C  71 " --> pdb=" O   ALA C  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1 through 8
    Processing helix  chain 'D' and resid 9 through 16
      removed outlier: 3.662A  pdb=" N   ILE D  13 " --> pdb=" O   LYS D  10 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ARG D  14 " --> pdb=" O   LEU D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 31
      removed outlier: 5.214A  pdb=" N   GLY D  23 " --> pdb=" O   GLY D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 41
    Processing helix  chain 'D' and resid 42 through 45
    Processing helix  chain 'D' and resid 48 through 50
      No H-bonds generated for 'chain 'D' and resid 48 through 50'
    Processing helix  chain 'D' and resid 51 through 59
      removed outlier: 3.805A  pdb=" N   ALA D  55 " --> pdb=" O   ASP D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 66
      No H-bonds generated for 'chain 'D' and resid 64 through 66'
    Processing helix  chain 'D' and resid 67 through 79
      removed outlier: 3.587A  pdb=" N   CYS D  71 " --> pdb=" O   ALA D  67 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1 through 8
    Processing helix  chain 'E' and resid 9 through 16
      removed outlier: 3.662A  pdb=" N   ILE E  13 " --> pdb=" O   LYS E  10 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ARG E  14 " --> pdb=" O   LEU E  11 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 31
      removed outlier: 5.215A  pdb=" N   GLY E  23 " --> pdb=" O   GLY E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 41
    Processing helix  chain 'E' and resid 42 through 45
    Processing helix  chain 'E' and resid 48 through 50
      No H-bonds generated for 'chain 'E' and resid 48 through 50'
    Processing helix  chain 'E' and resid 51 through 59
      removed outlier: 3.806A  pdb=" N   ALA E  55 " --> pdb=" O   ASP E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 66
      No H-bonds generated for 'chain 'E' and resid 64 through 66'
    Processing helix  chain 'E' and resid 67 through 79
      removed outlier: 3.587A  pdb=" N   CYS E  71 " --> pdb=" O   ALA E  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1 through 8
    Processing helix  chain 'F' and resid 9 through 16
      removed outlier: 3.662A  pdb=" N   ILE F  13 " --> pdb=" O   LYS F  10 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ARG F  14 " --> pdb=" O   LEU F  11 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 17 through 31
      removed outlier: 5.215A  pdb=" N   GLY F  23 " --> pdb=" O   GLY F  19 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 41
    Processing helix  chain 'F' and resid 42 through 45
    Processing helix  chain 'F' and resid 48 through 50
      No H-bonds generated for 'chain 'F' and resid 48 through 50'
    Processing helix  chain 'F' and resid 51 through 59
      removed outlier: 3.806A  pdb=" N   ALA F  55 " --> pdb=" O   ASP F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 64 through 66
      No H-bonds generated for 'chain 'F' and resid 64 through 66'
    Processing helix  chain 'F' and resid 67 through 79
      removed outlier: 3.587A  pdb=" N   CYS F  71 " --> pdb=" O   ALA F  67 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1 through 8
    Processing helix  chain 'G' and resid 9 through 16
      removed outlier: 3.662A  pdb=" N   ILE G  13 " --> pdb=" O   LYS G  10 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ARG G  14 " --> pdb=" O   LEU G  11 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 31
      removed outlier: 5.214A  pdb=" N   GLY G  23 " --> pdb=" O   GLY G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 35 through 41
    Processing helix  chain 'G' and resid 42 through 45
    Processing helix  chain 'G' and resid 48 through 50
      No H-bonds generated for 'chain 'G' and resid 48 through 50'
    Processing helix  chain 'G' and resid 51 through 59
      removed outlier: 3.806A  pdb=" N   ALA G  55 " --> pdb=" O   ASP G  51 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 64 through 66
      No H-bonds generated for 'chain 'G' and resid 64 through 66'
    Processing helix  chain 'G' and resid 67 through 79
      removed outlier: 3.587A  pdb=" N   CYS G  71 " --> pdb=" O   ALA G  67 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1 through 8
    Processing helix  chain 'H' and resid 9 through 16
      removed outlier: 3.662A  pdb=" N   ILE H  13 " --> pdb=" O   LYS H  10 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ARG H  14 " --> pdb=" O   LEU H  11 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 17 through 31
      removed outlier: 5.215A  pdb=" N   GLY H  23 " --> pdb=" O   GLY H  19 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 35 through 41
    Processing helix  chain 'H' and resid 42 through 45
    Processing helix  chain 'H' and resid 48 through 50
      No H-bonds generated for 'chain 'H' and resid 48 through 50'
    Processing helix  chain 'H' and resid 51 through 59
      removed outlier: 3.805A  pdb=" N   ALA H  55 " --> pdb=" O   ASP H  51 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 64 through 66
      No H-bonds generated for 'chain 'H' and resid 64 through 66'
    Processing helix  chain 'H' and resid 67 through 79
      removed outlier: 3.587A  pdb=" N   CYS H  71 " --> pdb=" O   ALA H  67 " (cutoff:3.500A)

    272 hydrogen bonds defined for protein.
    600 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: 0.95

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1143
        1.32 -     1.44: 1112
        1.44 -     1.57: 3025
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 5352
  Sorted by residual:
  bond pdb=" CA  VAL B  42 "
       pdb=" C   VAL B  42 "
    ideal  model  delta    sigma   weight residual
    1.523  1.467  0.056 1.46e-02 4.69e+03 1.47e+01
  bond pdb=" CA  VAL C  42 "
       pdb=" C   VAL C  42 "
    ideal  model  delta    sigma   weight residual
    1.523  1.467  0.056 1.46e-02 4.69e+03 1.45e+01
  bond pdb=" CA  VAL F  42 "
       pdb=" C   VAL F  42 "
    ideal  model  delta    sigma   weight residual
    1.523  1.468  0.055 1.46e-02 4.69e+03 1.43e+01
  bond pdb=" CA  VAL D  42 "
       pdb=" C   VAL D  42 "
    ideal  model  delta    sigma   weight residual
    1.523  1.468  0.055 1.46e-02 4.69e+03 1.43e+01
  bond pdb=" CA  VAL H  42 "
       pdb=" C   VAL H  42 "
    ideal  model  delta    sigma   weight residual
    1.523  1.468  0.055 1.46e-02 4.69e+03 1.42e+01
  ... (remaining 5347 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 6588
        2.38 -     4.75: 449
        4.75 -     7.13: 83
        7.13 -     9.51: 24
        9.51 -    11.88: 16
  Bond angle restraints: 7160
  Sorted by residual:
  angle pdb=" N   LYS E   8 "
        pdb=" CA  LYS E   8 "
        pdb=" C   LYS E   8 "
      ideal   model   delta    sigma   weight residual
     111.36  123.24  -11.88 1.09e+00 8.42e-01 1.19e+02
  angle pdb=" N   LYS H   8 "
        pdb=" CA  LYS H   8 "
        pdb=" C   LYS H   8 "
      ideal   model   delta    sigma   weight residual
     111.36  123.24  -11.88 1.09e+00 8.42e-01 1.19e+02
  angle pdb=" N   LYS C   8 "
        pdb=" CA  LYS C   8 "
        pdb=" C   LYS C   8 "
      ideal   model   delta    sigma   weight residual
     111.36  123.23  -11.87 1.09e+00 8.42e-01 1.18e+02
  angle pdb=" N   LYS A   8 "
        pdb=" CA  LYS A   8 "
        pdb=" C   LYS A   8 "
      ideal   model   delta    sigma   weight residual
     111.36  123.22  -11.86 1.09e+00 8.42e-01 1.18e+02
  angle pdb=" N   LYS B   8 "
        pdb=" CA  LYS B   8 "
        pdb=" C   LYS B   8 "
      ideal   model   delta    sigma   weight residual
     111.36  123.21  -11.85 1.09e+00 8.42e-01 1.18e+02
  ... (remaining 7155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 3184
       17.63 -    35.26: 192
       35.26 -    52.89: 24
       52.89 -    70.52: 8
       70.52 -    88.16: 8
  Dihedral angle restraints: 3416
    sinusoidal: 1448
      harmonic: 1968
  Sorted by residual:
  dihedral pdb=" CA  LYS D   8 "
           pdb=" C   LYS D   8 "
           pdb=" N   ARG D   9 "
           pdb=" CA  ARG D   9 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   15.63  -15.63     0      5.00e+00 4.00e-02 9.77e+00
  dihedral pdb=" CA  LYS B   8 "
           pdb=" C   LYS B   8 "
           pdb=" N   ARG B   9 "
           pdb=" CA  ARG B   9 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   15.61  -15.61     0      5.00e+00 4.00e-02 9.75e+00
  dihedral pdb=" CA  LYS H   8 "
           pdb=" C   LYS H   8 "
           pdb=" N   ARG H   9 "
           pdb=" CA  ARG H   9 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   15.56  -15.56     0      5.00e+00 4.00e-02 9.69e+00
  ... (remaining 3413 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 595
       0.077 -    0.154: 226
       0.154 -    0.231: 19
       0.231 -    0.308: 8
       0.308 -    0.385: 8
  Chirality restraints: 856
  Sorted by residual:
  chirality pdb=" CA  LYS H   8 "
            pdb=" N   LYS H   8 "
            pdb=" C   LYS H   8 "
            pdb=" CB  LYS H   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.70e+00
  chirality pdb=" CA  LYS B   8 "
            pdb=" N   LYS B   8 "
            pdb=" C   LYS B   8 "
            pdb=" CB  LYS B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.67e+00
  chirality pdb=" CA  LYS A   8 "
            pdb=" N   LYS A   8 "
            pdb=" C   LYS A   8 "
            pdb=" CB  LYS A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.65e+00
  ... (remaining 853 not shown)

  Planarity restraints: 912
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET F  50 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   MET F  50 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   MET F  50 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASP F  51 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET H  50 "    0.013 2.00e-02 2.50e+03   2.69e-02 7.24e+00
        pdb=" C   MET H  50 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   MET H  50 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASP H  51 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET G  50 "   -0.013 2.00e-02 2.50e+03   2.68e-02 7.17e+00
        pdb=" C   MET G  50 "    0.046 2.00e-02 2.50e+03
        pdb=" O   MET G  50 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP G  51 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 909 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1092
        2.76 -     3.29: 6049
        3.29 -     3.83: 8159
        3.83 -     4.36: 11768
        4.36 -     4.90: 15435
  Nonbonded interactions: 42503
  Sorted by model distance:
  nonbonded pdb=" CB  ALA D  83 "
            pdb=" CD  LYS H  63 "
     model   vdw
     2.219 3.860
  nonbonded pdb=" CB  ALA A  83 "
            pdb=" CD  LYS E  63 "
     model   vdw
     2.256 3.860
  nonbonded pdb=" CB  ALA C  83 "
            pdb=" CD  LYS G  63 "
     model   vdw
     2.299 3.860
  nonbonded pdb=" CB  ALA B  83 "
            pdb=" CD  LYS F  63 "
     model   vdw
     2.318 3.860
  nonbonded pdb=" CB  ALA D  83 "
            pdb=" CG  LYS H  63 "
     model   vdw
     2.354 3.860
  ... (remaining 42498 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.890
  Find NCS groups from input model:        0.060
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
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      :  0.013   0.056   5352  Z= 0.837
  Angle     :  1.513  11.882   7160  Z= 1.126
  Chirality :  0.078   0.385    856
  Planarity :  0.006   0.027    912
  Dihedral  : 12.323  88.156   2136
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 36.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.32), residues: 664
  helix: -2.44 (0.21), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.96 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  32 
 TYR   0.001   0.000   TYR A  74 
 PHE   0.001   0.000   PHE A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.01279 ( 5352)
  covalent geometry    : angle       1.51269 ( 7160)
  hydrogen bonds       : bond        0.18376 (  272)
  hydrogen bonds       : angle       7.27710 (  600)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8447 (m-80) cc_final: 0.8245 (m-80)
REVERT: A   18 GLU cc_start: 0.8770 (pm20) cc_final: 0.8143 (pp20)
REVERT: A   41 LYS cc_start: 0.8697 (mttm) cc_final: 0.8312 (ttpt)
REVERT: A   66 GLN cc_start: 0.7935 (pm20) cc_final: 0.7703 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1114
  time to fit residues: 3.3617
Evaluate side-chains
  16 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0040
   chunk 17 optimal weight:   20.0000
   overall best weight:    0.5792
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.057460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.048934 restraints weight = 5468.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.049633 restraints weight = 4643.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.050205 restraints weight = 4031.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.050658 restraints weight = 3573.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.050980 restraints weight = 3226.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.6357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5352  Z= 0.187
  Angle     :  0.823   5.586   7160  Z= 0.464
  Chirality :  0.061   0.377    856
  Planarity :  0.005   0.037    912
  Dihedral  :  9.854  66.525    736
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  :  4.05 %
    Favored  : 91.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.34), residues: 664
  helix: -1.29 (0.24), residues: 440
  sheet:  None (None), residues: 0
  loop :  3.16 (0.45), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  44 
 TYR   0.006   0.001   TYR A  74 
 PHE   0.002   0.001   PHE H  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 5352)
  covalent geometry    : angle       0.82269 ( 7160)
  hydrogen bonds       : bond        0.05747 (  272)
  hydrogen bonds       : angle       5.24484 (  600)

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

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

  1162 Ramachandran restraints generated.
    581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1162 Ramachandran restraints generated.
    581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   18 GLU cc_start: 0.8714 (pm20) cc_final: 0.8257 (pp20)
REVERT: H   39 MET cc_start: 0.9119 (tmm) cc_final: 0.8811 (tmm)
REVERT: H   58 ASP cc_start: 0.8123 (m-30) cc_final: 0.7872 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0710
  time to fit residues: 1.9563
Evaluate side-chains
  15 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 3 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    4.3388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.057782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.049324 restraints weight = 5313.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.049791 restraints weight = 4715.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.050313 restraints weight = 4279.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.050599 restraints weight = 3906.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.050966 restraints weight = 3637.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.8683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5352  Z= 0.181
  Angle     :  0.782   5.506   7160  Z= 0.424
  Chirality :  0.050   0.258    856
  Planarity :  0.005   0.024    912
  Dihedral  :  8.007  36.879    736
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.35), residues: 664
  helix: -0.86 (0.26), residues: 392
  sheet:  None (None), residues: 0
  loop :  2.16 (0.45), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG G   9 
 TYR   0.007   0.002   TYR F  81 
 PHE   0.004   0.001   PHE A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5352)
  covalent geometry    : angle       0.78162 ( 7160)
  hydrogen bonds       : bond        0.04931 (  272)
  hydrogen bonds       : angle       5.49611 (  600)

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

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

  1162 Ramachandran restraints generated.
    581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1162 Ramachandran restraints generated.
    581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.029 
Fit side-chains
   revert: symmetry clash
REVERT: H   16 MET cc_start: 0.7612 (tpt) cc_final: 0.7365 (tpt)
REVERT: H   18 GLU cc_start: 0.8847 (pm20) cc_final: 0.8384 (pp20)
REVERT: H   39 MET cc_start: 0.8968 (tmm) cc_final: 0.8755 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0866
  time to fit residues: 1.5654
Evaluate side-chains
  10 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    4.3388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
H  30 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.059661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.050755 restraints weight = 5220.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.051408 restraints weight = 4416.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.052045 restraints weight = 3876.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.052468 restraints weight = 3434.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.052833 restraints weight = 3116.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.9347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5352  Z= 0.161
  Angle     :  0.693   5.557   7160  Z= 0.382
  Chirality :  0.045   0.129    856
  Planarity :  0.006   0.040    912
  Dihedral  :  6.978  20.394    736
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 18.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.34), residues: 664
  helix: -0.63 (0.27), residues: 336
  sheet:  None (None), residues: 0
  loop :  1.71 (0.39), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG D   9 
 TYR   0.006   0.002   TYR F  81 
 PHE   0.005   0.002   PHE C  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5352)
  covalent geometry    : angle       0.69280 ( 7160)
  hydrogen bonds       : bond        0.03847 (  272)
  hydrogen bonds       : angle       5.61495 (  600)

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

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

  1162 Ramachandran restraints generated.
    581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1162 Ramachandran restraints generated.
    581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.026 
Fit side-chains
   revert: symmetry clash
REVERT: H   18 GLU cc_start: 0.8806 (pm20) cc_final: 0.8153 (pp20)
REVERT: H   39 MET cc_start: 0.8929 (tmm) cc_final: 0.8597 (tmm)
REVERT: H   50 MET cc_start: 0.7579 (ppp) cc_final: 0.6884 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0728
  time to fit residues: 1.1795
Evaluate side-chains
  10 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 48 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 49 optimal weight:    3.9990
   chunk 60 optimal weight:   20.0000
   chunk 52 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0370
   chunk 18 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   overall best weight:    6.0070
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.057765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.048390 restraints weight = 5230.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.049077 restraints weight = 4560.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.049582 restraints weight = 4053.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.050036 restraints weight = 3683.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.050332 restraints weight = 3382.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          1.0094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5352  Z= 0.144
  Angle     :  0.661   5.305   7160  Z= 0.370
  Chirality :  0.044   0.126    856
  Planarity :  0.006   0.048    912
  Dihedral  :  6.658  19.403    736
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.36), residues: 664
  helix: -1.07 (0.26), residues: 416
  sheet:  None (None), residues: 0
  loop :  1.63 (0.48), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E   9 
 TYR   0.006   0.002   TYR G  74 
 PHE   0.003   0.001   PHE A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5352)
  covalent geometry    : angle       0.66093 ( 7160)
  hydrogen bonds       : bond        0.03349 (  272)
  hydrogen bonds       : angle       5.60108 (  600)

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

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

  1162 Ramachandran restraints generated.
    581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1162 Ramachandran restraints generated.
    581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.028 
Fit side-chains
REVERT: H   18 GLU cc_start: 0.8903 (pm20) cc_final: 0.8073 (pp20)
REVERT: H   39 MET cc_start: 0.8968 (tmm) cc_final: 0.8581 (tmm)
REVERT: H   40 GLU cc_start: 0.8863 (pm20) cc_final: 0.8458 (pm20)
REVERT: H   50 MET cc_start: 0.7592 (ppp) cc_final: 0.6889 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0664
  time to fit residues: 1.0162
Evaluate side-chains
  10 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 36 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 35 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 32 optimal weight:   20.0000
   overall best weight:    7.1994
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.057350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.048808 restraints weight = 5372.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.049485 restraints weight = 4631.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.049949 restraints weight = 4067.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.050484 restraints weight = 3668.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.050798 restraints weight = 3337.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          1.0362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5352  Z= 0.138
  Angle     :  0.632   5.337   7160  Z= 0.355
  Chirality :  0.043   0.126    856
  Planarity :  0.004   0.024    912
  Dihedral  :  6.220  18.130    736
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.37), residues: 664
  helix: -0.09 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop :  1.53 (0.45), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  44 
 TYR   0.010   0.002   TYR D  74 
 PHE   0.004   0.001   PHE G  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5352)
  covalent geometry    : angle       0.63240 ( 7160)
  hydrogen bonds       : bond        0.02589 (  272)
  hydrogen bonds       : angle       5.17913 (  600)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.028 
Fit side-chains
REVERT: E   18 GLU cc_start: 0.9044 (pm20) cc_final: 0.8281 (pp20)
REVERT: E   39 MET cc_start: 0.9052 (tmm) cc_final: 0.8638 (tmm)
REVERT: E   40 GLU cc_start: 0.8808 (pm20) cc_final: 0.8270 (tm-30)
REVERT: E   50 MET cc_start: 0.7440 (ppp) cc_final: 0.6679 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0642
  time to fit residues: 1.0478
Evaluate side-chains
  8 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 18 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 17 optimal weight:    0.3980
   chunk 52 optimal weight:   20.0000
   chunk 23 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0670
   chunk 2 optimal weight:    6.9990
   chunk 44 optimal weight:   20.0000
   overall best weight:    3.0122
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.058508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.049492 restraints weight = 4983.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.050334 restraints weight = 4223.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.050950 restraints weight = 3670.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.051302 restraints weight = 3273.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.051822 restraints weight = 2992.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          1.0817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5352  Z= 0.124
  Angle     :  0.651   5.745   7160  Z= 0.356
  Chirality :  0.045   0.122    856
  Planarity :  0.003   0.025    912
  Dihedral  :  6.087  16.852    736
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.36), residues: 664
  helix: -0.23 (0.27), residues: 360
  sheet:  None (None), residues: 0
  loop :  1.46 (0.45), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  44 
 TYR   0.004   0.001   TYR B  74 
 PHE   0.007   0.002   PHE E  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 5352)
  covalent geometry    : angle       0.65071 ( 7160)
  hydrogen bonds       : bond        0.02930 (  272)
  hydrogen bonds       : angle       5.43843 (  600)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.031 
Fit side-chains
REVERT: H   18 GLU cc_start: 0.8864 (pm20) cc_final: 0.8593 (pp20)
REVERT: H   39 MET cc_start: 0.9023 (tmm) cc_final: 0.8468 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0538
  time to fit residues: 0.9486
Evaluate side-chains
  8 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 38 optimal weight:   40.0000
   chunk 60 optimal weight:   30.0000
   chunk 47 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 44 optimal weight:   30.0000
   chunk 4 optimal weight:   30.0000
   chunk 54 optimal weight:   20.0000
   chunk 56 optimal weight:   20.0000
   chunk 39 optimal weight:    8.9990
   chunk 8 optimal weight:   20.0000
   overall best weight:    9.5992
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.057894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.048818 restraints weight = 5329.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.049541 restraints weight = 4552.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.050102 restraints weight = 3988.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.050536 restraints weight = 3559.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.050837 restraints weight = 3234.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          1.1026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   5352  Z= 0.156
  Angle     :  0.685   5.225   7160  Z= 0.384
  Chirality :  0.044   0.117    856
  Planarity :  0.004   0.025    912
  Dihedral  :  6.079  16.780    736
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.35), residues: 664
  helix: -0.35 (0.27), residues: 360
  sheet:  None (None), residues: 0
  loop :  1.41 (0.43), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  44 
 TYR   0.012   0.002   TYR G  74 
 PHE   0.003   0.001   PHE E  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5352)
  covalent geometry    : angle       0.68475 ( 7160)
  hydrogen bonds       : bond        0.02741 (  272)
  hydrogen bonds       : angle       5.60570 (  600)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.035 
Fit side-chains
REVERT: H   16 MET cc_start: 0.7900 (tpt) cc_final: 0.7669 (tpt)
REVERT: H   18 GLU cc_start: 0.8825 (pm20) cc_final: 0.8607 (pp20)
REVERT: H   39 MET cc_start: 0.8921 (tmm) cc_final: 0.8259 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0702
  time to fit residues: 1.2070
Evaluate side-chains
  7 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 7
  time to evaluate  : 0.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 41 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   chunk 24 optimal weight:   30.0000
   chunk 8 optimal weight:   20.0000
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 46 optimal weight:   20.0000
   overall best weight:    6.3990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.057292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.046965 restraints weight = 4948.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.047774 restraints weight = 4192.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.048463 restraints weight = 3645.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.048957 restraints weight = 3220.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.049428 restraints weight = 2915.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          1.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   5352  Z= 0.127
  Angle     :  0.658   5.645   7160  Z= 0.369
  Chirality :  0.043   0.119    856
  Planarity :  0.004   0.026    912
  Dihedral  :  6.046  16.807    736
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.34), residues: 664
  helix: -0.44 (0.27), residues: 352
  sheet:  None (None), residues: 0
  loop :  0.87 (0.41), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B   9 
 TYR   0.007   0.001   TYR D  74 
 PHE   0.003   0.001   PHE A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5352)
  covalent geometry    : angle       0.65758 ( 7160)
  hydrogen bonds       : bond        0.02342 (  272)
  hydrogen bonds       : angle       5.43982 (  600)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.043 
Fit side-chains
REVERT: H   16 MET cc_start: 0.7920 (tpt) cc_final: 0.7632 (tpt)
REVERT: H   18 GLU cc_start: 0.8868 (pm20) cc_final: 0.8625 (pp20)
REVERT: H   39 MET cc_start: 0.8940 (tmm) cc_final: 0.8238 (tmm)
REVERT: H   41 LYS cc_start: 0.9253 (tptp) cc_final: 0.8797 (tppp)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0691
  time to fit residues: 1.2824
Evaluate side-chains
  8 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 33 optimal weight:    0.0020
   chunk 8 optimal weight:   20.0000
   chunk 57 optimal weight:    0.0020
   chunk 16 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 56 optimal weight:   30.0000
   chunk 35 optimal weight:    0.4980
   chunk 42 optimal weight:    6.9990
   chunk 32 optimal weight:   30.0000
   chunk 2 optimal weight:    9.9990
   overall best weight:    3.5000
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.058324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.049216 restraints weight = 4963.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.049950 restraints weight = 4269.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.050425 restraints weight = 3732.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.051016 restraints weight = 3354.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.051334 restraints weight = 3037.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          1.1413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5352  Z= 0.121
  Angle     :  0.673   5.639   7160  Z= 0.370
  Chirality :  0.043   0.117    856
  Planarity :  0.003   0.028    912
  Dihedral  :  5.780  16.807    736
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.35), residues: 664
  helix: -0.78 (0.26), residues: 360
  sheet:  None (None), residues: 0
  loop :  0.69 (0.43), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D   9 
 TYR   0.002   0.001   TYR H  81 
 PHE   0.001   0.000   PHE A  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 5352)
  covalent geometry    : angle       0.67293 ( 7160)
  hydrogen bonds       : bond        0.02426 (  272)
  hydrogen bonds       : angle       5.05429 (  600)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.026 
Fit side-chains
REVERT: H   18 GLU cc_start: 0.8858 (pm20) cc_final: 0.8627 (pp20)
REVERT: H   39 MET cc_start: 0.8923 (tmm) cc_final: 0.8191 (tmm)
REVERT: H   41 LYS cc_start: 0.9211 (tptp) cc_final: 0.8811 (tppp)
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0603
  time to fit residues: 0.9254
Evaluate side-chains
  9 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0070
   chunk 11 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:    8.9990
   chunk 30 optimal weight:   40.0000
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    1.3402
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.060182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.050322 restraints weight = 4930.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.051117 restraints weight = 4213.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.051773 restraints weight = 3673.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.052201 restraints weight = 3251.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.052669 restraints weight = 2958.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          1.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5352  Z= 0.121
  Angle     :  0.643   5.823   7160  Z= 0.352
  Chirality :  0.042   0.120    856
  Planarity :  0.003   0.029    912
  Dihedral  :  5.503  15.843    736
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.34), residues: 664
  helix: -0.76 (0.27), residues: 352
  sheet:  None (None), residues: 0
  loop :  0.34 (0.40), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  44 
 TYR   0.004   0.001   TYR C  74 
 PHE   0.001   0.000   PHE C  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5352)
  covalent geometry    : angle       0.64304 ( 7160)
  hydrogen bonds       : bond        0.02238 (  272)
  hydrogen bonds       : angle       4.80786 (  600)

===============================================================================
Job complete
usr+sys time: 574.61 seconds
wall clock time: 10 minutes 47.53 seconds (647.53 seconds total)