Starting phenix.real_space_refine
on Thu Jun 12 09:29:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wl1_21815/06_2025/6wl1_21815.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wl1_21815/06_2025/6wl1_21815.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wl1_21815/06_2025/6wl1_21815.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wl1_21815/06_2025/6wl1_21815.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wl1_21815/06_2025/6wl1_21815.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wl1_21815/06_2025/6wl1_21815.cif"
  }
  resolution = 4.0
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    9308      2.51       5
     N    2600      2.21       5
     O    2704      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14612
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 281
          Classifications: {'peptide': 36}
          Link IDs: {'TRANS': 35}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V,
    Y, X, Z, a, c, b, e, d, g, f, i, h, k, j, m, l, o, n, q, p, s, r,
    u, t, w, v, y, x, z
  Time building chain proxies: 3.12, per 1000 atoms: 0.21
  Number of scatterers: 14612
  At special positions: 0
  Unit cell: (94.34, 94.34, 160.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    2704      8.00
     N    2600      7.00
     C    9308      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.22
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3744

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      97.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 36
      removed outlier: 3.810A  pdb=" N   LEU A   5 " --> pdb=" O   GLN A   1 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLN A  36 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN B  36 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN C  36 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN D  36 " --> pdb=" O   ILE D  32 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN E  36 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN F  36 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN G  36 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN H  36 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN I  36 " --> pdb=" O   ILE I  32 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN J  36 " --> pdb=" O   ILE J  32 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN K  36 " --> pdb=" O   ILE K  32 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN L  36 " --> pdb=" O   ILE L  32 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN M  36 " --> pdb=" O   ILE M  32 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN N  36 " --> pdb=" O   ILE N  32 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN O  36 " --> pdb=" O   ILE O  32 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN P  36 " --> pdb=" O   ILE P  32 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN Q  36 " --> pdb=" O   ILE Q  32 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN R  36 " --> pdb=" O   ILE R  32 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 2 through 36
      removed outlier: 3.603A  pdb=" N   GLN S  36 " --> pdb=" O   ILE S  32 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN T  36 " --> pdb=" O   ILE T  32 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN U  36 " --> pdb=" O   ILE U  32 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN V  36 " --> pdb=" O   ILE V  32 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN W  36 " --> pdb=" O   ILE W  32 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN X  36 " --> pdb=" O   ILE X  32 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN Y  36 " --> pdb=" O   ILE Y  32 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN Z  36 " --> pdb=" O   ILE Z  32 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN a  36 " --> pdb=" O   ILE a  32 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN b  36 " --> pdb=" O   ILE b  32 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN c  36 " --> pdb=" O   ILE c  32 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN d  36 " --> pdb=" O   ILE d  32 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN e  36 " --> pdb=" O   ILE e  32 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN f  36 " --> pdb=" O   ILE f  32 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN g  36 " --> pdb=" O   ILE g  32 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN h  36 " --> pdb=" O   ILE h  32 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN i  36 " --> pdb=" O   ILE i  32 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN j  36 " --> pdb=" O   ILE j  32 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN k  36 " --> pdb=" O   ILE k  32 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN l  36 " --> pdb=" O   ILE l  32 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN m  36 " --> pdb=" O   ILE m  32 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN n  36 " --> pdb=" O   ILE n  32 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN o  36 " --> pdb=" O   ILE o  32 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN p  36 " --> pdb=" O   ILE p  32 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN q  36 " --> pdb=" O   ILE q  32 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN r  36 " --> pdb=" O   ILE r  32 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN s  36 " --> pdb=" O   ILE s  32 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN t  36 " --> pdb=" O   ILE t  32 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN u  36 " --> pdb=" O   ILE u  32 " (cutoff:3.500A)
    Processing helix  chain 'v' and resid 2 through 36
      removed outlier: 3.601A  pdb=" N   GLN v  36 " --> pdb=" O   ILE v  32 " (cutoff:3.500A)
    Processing helix  chain 'w' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN w  36 " --> pdb=" O   ILE w  32 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN x  36 " --> pdb=" O   ILE x  32 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN y  36 " --> pdb=" O   ILE y  32 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 2 through 36
      removed outlier: 3.602A  pdb=" N   GLN z  36 " --> pdb=" O   ILE z  32 " (cutoff:3.500A)

    1560 hydrogen bonds defined for protein.
    4680 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: 4.35

  Time building geometry restraints manager: 3.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 2652
        1.29 -     1.35: 2392
        1.35 -     1.41: 520
        1.41 -     1.48: 2028
        1.48 -     1.54: 7072
  Bond restraints: 14664
  Sorted by residual:
  bond pdb=" CB  ARG S   6 "
       pdb=" CG  ARG S   6 "
    ideal  model  delta    sigma   weight residual
    1.520  1.479  0.041 3.00e-02 1.11e+03 1.83e+00
  bond pdb=" CB  ARG i   6 "
       pdb=" CG  ARG i   6 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.82e+00
  bond pdb=" CB  ARG C   6 "
       pdb=" CG  ARG C   6 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.81e+00
  bond pdb=" CB  ARG z   6 "
       pdb=" CG  ARG z   6 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.81e+00
  bond pdb=" CB  ARG X   6 "
       pdb=" CG  ARG X   6 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.81e+00
  ... (remaining 14659 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 16355
        0.91 -     1.81: 2411
        1.81 -     2.72: 630
        2.72 -     3.62: 208
        3.62 -     4.53: 52
  Bond angle restraints: 19656
  Sorted by residual:
  angle pdb=" N   LEU u   5 "
        pdb=" CA  LEU u   5 "
        pdb=" CB  LEU u   5 "
      ideal   model   delta    sigma   weight residual
     110.16  107.46    2.70 1.48e+00 4.57e-01 3.32e+00
  angle pdb=" N   LEU F   5 "
        pdb=" CA  LEU F   5 "
        pdb=" CB  LEU F   5 "
      ideal   model   delta    sigma   weight residual
     110.16  107.47    2.69 1.48e+00 4.57e-01 3.31e+00
  angle pdb=" N   LEU k   5 "
        pdb=" CA  LEU k   5 "
        pdb=" CB  LEU k   5 "
      ideal   model   delta    sigma   weight residual
     110.16  107.49    2.67 1.48e+00 4.57e-01 3.26e+00
  angle pdb=" N   LEU D   5 "
        pdb=" CA  LEU D   5 "
        pdb=" CB  LEU D   5 "
      ideal   model   delta    sigma   weight residual
     110.16  107.49    2.67 1.48e+00 4.57e-01 3.26e+00
  angle pdb=" N   LEU V   5 "
        pdb=" CA  LEU V   5 "
        pdb=" CB  LEU V   5 "
      ideal   model   delta    sigma   weight residual
     110.16  107.49    2.67 1.48e+00 4.57e-01 3.24e+00
  ... (remaining 19651 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     5.52: 7015
        5.52 -    11.04: 1617
       11.04 -    16.56: 520
       16.56 -    22.08: 52
       22.08 -    27.60: 156
  Dihedral angle restraints: 9360
    sinusoidal: 3744
      harmonic: 5616
  Sorted by residual:
  dihedral pdb=" CA  ALA P  28 "
           pdb=" C   ALA P  28 "
           pdb=" N   HIS P  29 "
           pdb=" CA  HIS P  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  169.45   10.55     0      5.00e+00 4.00e-02 4.45e+00
  dihedral pdb=" CA  ALA Y  28 "
           pdb=" C   ALA Y  28 "
           pdb=" N   HIS Y  29 "
           pdb=" CA  HIS Y  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  169.45   10.55     0      5.00e+00 4.00e-02 4.45e+00
  dihedral pdb=" CA  ALA X  28 "
           pdb=" C   ALA X  28 "
           pdb=" N   HIS X  29 "
           pdb=" CA  HIS X  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  169.46   10.54     0      5.00e+00 4.00e-02 4.45e+00
  ... (remaining 9357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1341
       0.031 -    0.062: 666
       0.062 -    0.093: 273
       0.093 -    0.124: 60
       0.124 -    0.156: 52
  Chirality restraints: 2392
  Sorted by residual:
  chirality pdb=" CG  LEU F   5 "
            pdb=" CB  LEU F   5 "
            pdb=" CD1 LEU F   5 "
            pdb=" CD2 LEU F   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CG  LEU q   5 "
            pdb=" CB  LEU q   5 "
            pdb=" CD1 LEU q   5 "
            pdb=" CD2 LEU q   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.16 2.00e-01 2.50e+01 6.03e-01
  chirality pdb=" CG  LEU B   5 "
            pdb=" CB  LEU B   5 "
            pdb=" CD1 LEU B   5 "
            pdb=" CD2 LEU B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.99e-01
  ... (remaining 2389 not shown)

  Planarity restraints: 2496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C   5 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.08e+00
        pdb=" C   LEU C   5 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LEU C   5 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ARG C   6 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU f   5 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   LEU f   5 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LEU f   5 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ARG f   6 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU N   5 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   LEU N   5 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LEU N   5 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ARG N   6 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2493 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 4880
        2.91 -     3.41: 14842
        3.41 -     3.91: 23752
        3.91 -     4.40: 26056
        4.40 -     4.90: 43163
  Nonbonded interactions: 112693
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG o   6 "
            pdb=" OE2 GLU u   3 "
     model   vdw
     2.413 3.120
  nonbonded pdb=" NH2 ARG e   6 "
            pdb=" OE2 GLU k   3 "
     model   vdw
     2.413 3.120
  nonbonded pdb=" OE2 GLU Z   3 "
            pdb=" NH2 ARG f   6 "
     model   vdw
     2.414 3.120
  nonbonded pdb=" OE2 GLU t   3 "
            pdb=" NH2 ARG z   6 "
     model   vdw
     2.414 3.120
  nonbonded pdb=" NH2 ARG O   6 "
            pdb=" OE2 GLU U   3 "
     model   vdw
     2.414 3.120
  ... (remaining 112688 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: 0.16
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 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'R'
  selection = chain 'U'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'V'
  selection = chain 'Y'
  selection = chain 'X'
  selection = chain 'Z'
  selection = 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 'k'
  selection = chain 'j'
  selection = chain 'm'
  selection = chain 'l'
  selection = chain 'o'
  selection = chain 'n'
  selection = chain 'q'
  selection = chain 'p'
  selection = chain 's'
  selection = chain 'r'
  selection = chain 'u'
  selection = chain 't'
  selection = chain 'w'
  selection = chain 'v'
  selection = chain 'y'
  selection = chain 'x'
  selection = chain 'z'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     27.460
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
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      :  0.007   0.041  14664  Z= 0.349
  Angle     :  0.811   4.525  19656  Z= 0.462
  Chirality :  0.047   0.156   2392
  Planarity :  0.005   0.014   2496
  Dihedral  :  7.850  27.597   5616
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.15), residues: 1768
  helix: -0.52 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS V  29 
 TYR   0.016   0.004   TYR j   8 
 ARG   0.008   0.003   ARG p   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12388 ( 1560)
  hydrogen bonds       : angle       5.55268 ( 4680)
  covalent geometry    : bond        0.00715 (14664)
  covalent geometry    : angle       0.81077 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 373
  time to evaluate  : 1.552 
Fit side-chains
REVERT: a   22 GLN cc_start: 0.8624 (mt0) cc_final: 0.8422 (mt0)
REVERT: w   33 LEU cc_start: 0.8609 (mt) cc_final: 0.8390 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 373
  average time/residue: 0.3351
  time to fit residues: 170.3280
Evaluate side-chains
  152 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    0.9980
   chunk 118 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 141 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
G  22 GLN
J  22 GLN
K  22 GLN
Q  36 GLN
X  29 HIS
Y  22 GLN
k  22 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.123694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.117265 restraints weight = 19817.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.117945 restraints weight = 16780.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.118234 restraints weight = 15725.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013  14664  Z= 0.138
  Angle     :  0.393   2.436  19656  Z= 0.228
  Chirality :  0.033   0.092   2392
  Planarity :  0.003   0.019   2496
  Dihedral  :  3.510   8.223   1976
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 1.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 14.20 %
    Favored  : 84.17 %
  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:  4.05 (0.15), residues: 1768
  helix:  2.65 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS S  29 
 TYR   0.009   0.002   TYR u   8 
 ARG   0.002   0.000   ARG x  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05981 ( 1560)
  hydrogen bonds       : angle       4.33572 ( 4680)
  covalent geometry    : bond        0.00242 (14664)
  covalent geometry    : angle       0.39273 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 310
  time to evaluate  : 1.487 
Fit side-chains
REVERT: E   19 LEU cc_start: 0.9447 (mt) cc_final: 0.9228 (mp)
REVERT: G   31 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8392 (mm-30)
REVERT: L   26 LEU cc_start: 0.8743 (mt) cc_final: 0.8464 (mm)
REVERT: N   22 GLN cc_start: 0.8230 (mt0) cc_final: 0.7896 (tt0)
REVERT: V   22 GLN cc_start: 0.8470 (mt0) cc_final: 0.8252 (mt0)
  outliers start: 22
  outliers final: 4
  residues processed: 328
  average time/residue: 0.2449
  time to fit residues: 119.1741
Evaluate side-chains
  232 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 228
  time to evaluate  : 1.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   33 LEU
Chi-restraints excluded: chain X residue   33 LEU
Chi-restraints excluded: chain y residue   22 GLN
Chi-restraints excluded: chain z residue   33 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 117 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 129 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
G  36 GLN
K  22 GLN
X  36 GLN
t  36 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.113307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.107205 restraints weight = 20893.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.107865 restraints weight = 16803.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.108445 restraints weight = 14302.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  14664  Z= 0.206
  Angle     :  0.525   5.233  19656  Z= 0.278
  Chirality :  0.037   0.106   2392
  Planarity :  0.003   0.021   2496
  Dihedral  :  3.259   7.300   1976
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.86 %
    Favored  : 80.25 %
  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:  5.11 (0.14), residues: 1768
  helix:  3.30 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS i  29 
 TYR   0.004   0.000   TYR l   8 
 ARG   0.004   0.000   ARG x  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07916 ( 1560)
  hydrogen bonds       : angle       4.78131 ( 4680)
  covalent geometry    : bond        0.00434 (14664)
  covalent geometry    : angle       0.52473 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 257
  time to evaluate  : 1.632 
Fit side-chains
REVERT: G   31 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8378 (mm-30)
REVERT: N   22 GLN cc_start: 0.8221 (mt0) cc_final: 0.7906 (tt0)
REVERT: d   22 GLN cc_start: 0.8140 (mt0) cc_final: 0.7916 (tt0)
  outliers start: 39
  outliers final: 14
  residues processed: 275
  average time/residue: 0.2827
  time to fit residues: 112.3741
Evaluate side-chains
  243 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 229
  time to evaluate  : 1.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain P residue   32 ILE
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain V residue   26 LEU
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain b residue   24 LYS
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain o residue   32 ILE
Chi-restraints excluded: chain r residue   26 LEU
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain t residue   36 GLN
Chi-restraints excluded: chain z residue   18 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 135 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 119 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
F  36 GLN
t  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.122915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.117890 restraints weight = 19914.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.118326 restraints weight = 17395.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.118515 restraints weight = 15469.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.3604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  14664  Z= 0.130
  Angle     :  0.344   3.047  19656  Z= 0.197
  Chirality :  0.032   0.099   2392
  Planarity :  0.002   0.015   2496
  Dihedral  :  3.236   7.356   1976
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.01 %
    Favored  : 79.51 %
  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:  6.59 (0.14), residues: 1768
  helix:  4.21 (0.08), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  29 
 TYR   0.003   0.001   TYR X   8 
 ARG   0.003   0.000   ARG z  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05318 ( 1560)
  hydrogen bonds       : angle       4.02871 ( 4680)
  covalent geometry    : bond        0.00237 (14664)
  covalent geometry    : angle       0.34417 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 307
  time to evaluate  : 1.530 
Fit side-chains
REVERT: A   22 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7969 (tt0)
REVERT: G   31 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8340 (mm-30)
REVERT: i   22 GLN cc_start: 0.8301 (mt0) cc_final: 0.8051 (tt0)
REVERT: i   31 GLU cc_start: 0.9150 (tp30) cc_final: 0.8852 (tp30)
REVERT: m   22 GLN cc_start: 0.8496 (mt0) cc_final: 0.8213 (tt0)
  outliers start: 20
  outliers final: 13
  residues processed: 315
  average time/residue: 0.2588
  time to fit residues: 119.7338
Evaluate side-chains
  277 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 263
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain G residue   26 LEU
Chi-restraints excluded: chain P residue   32 ILE
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain a residue   22 GLN
Chi-restraints excluded: chain b residue   24 LYS
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain f residue   32 ILE
Chi-restraints excluded: chain o residue   24 LYS
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain w residue   26 LEU
Chi-restraints excluded: chain z residue   18 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 129 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 139 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 49 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 92 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
K  22 GLN
K  36 GLN
M  36 GLN
c  36 GLN
z  36 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.116896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.111963 restraints weight = 20604.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.112246 restraints weight = 17764.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.112246 restraints weight = 16170.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14664  Z= 0.166
  Angle     :  0.416   4.102  19656  Z= 0.228
  Chirality :  0.034   0.104   2392
  Planarity :  0.002   0.012   2496
  Dihedral  :  3.178   7.619   1976
  Min Nonbonded Distance : 2.680

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  8.21 %
    Allowed  : 15.46 %
    Favored  : 76.33 %
  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:  6.36 (0.14), residues: 1768
  helix:  4.08 (0.08), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS d  29 
 TYR   0.004   0.001   TYR l   8 
 ARG   0.003   0.000   ARG t  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06585 ( 1560)
  hydrogen bonds       : angle       4.34899 ( 4680)
  covalent geometry    : bond        0.00331 (14664)
  covalent geometry    : angle       0.41621 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 111
    poor density    : 250
  time to evaluate  : 1.490 
Fit side-chains
REVERT: A   22 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.8010 (tt0)
REVERT: G   31 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8342 (mm-30)
REVERT: i   22 GLN cc_start: 0.8356 (mt0) cc_final: 0.8130 (tt0)
REVERT: m   22 GLN cc_start: 0.8524 (mt0) cc_final: 0.8184 (tt0)
REVERT: o   22 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8065 (tt0)
  outliers start: 111
  outliers final: 41
  residues processed: 328
  average time/residue: 0.2240
  time to fit residues: 112.2820
Evaluate side-chains
  284 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 241
  time to evaluate  : 1.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain L residue   26 LEU
Chi-restraints excluded: chain M residue   26 LEU
Chi-restraints excluded: chain N residue   32 ILE
Chi-restraints excluded: chain P residue   22 GLN
Chi-restraints excluded: chain P residue   32 ILE
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain S residue   18 ILE
Chi-restraints excluded: chain T residue   26 LEU
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain U residue   32 ILE
Chi-restraints excluded: chain V residue   26 LEU
Chi-restraints excluded: chain W residue   26 LEU
Chi-restraints excluded: chain Y residue   32 ILE
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain b residue   24 LYS
Chi-restraints excluded: chain b residue   26 LEU
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain g residue   26 LEU
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain m residue   32 ILE
Chi-restraints excluded: chain n residue   32 ILE
Chi-restraints excluded: chain o residue   18 ILE
Chi-restraints excluded: chain o residue   22 GLN
Chi-restraints excluded: chain o residue   26 LEU
Chi-restraints excluded: chain o residue   32 ILE
Chi-restraints excluded: chain p residue   32 ILE
Chi-restraints excluded: chain q residue   18 ILE
Chi-restraints excluded: chain q residue   22 GLN
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain r residue   26 LEU
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain u residue   18 ILE
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain w residue   26 LEU
Chi-restraints excluded: chain x residue   22 GLN
Chi-restraints excluded: chain z residue   18 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 152 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
H  22 GLN
r  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.125445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.120311 restraints weight = 19855.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.120599 restraints weight = 17097.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.121029 restraints weight = 15760.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14664  Z= 0.124
  Angle     :  0.340   2.872  19656  Z= 0.192
  Chirality :  0.032   0.105   2392
  Planarity :  0.002   0.012   2496
  Dihedral  :  3.225   7.591   1976
  Min Nonbonded Distance : 2.682

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 16.64 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  6.86 (0.14), residues: 1768
  helix:  4.38 (0.08), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS d  29 
 TYR   0.002   0.000   TYR D   8 
 ARG   0.002   0.000   ARG r  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05019 ( 1560)
  hydrogen bonds       : angle       3.86670 ( 4680)
  covalent geometry    : bond        0.00222 (14664)
  covalent geometry    : angle       0.33973 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 260
  time to evaluate  : 1.672 
Fit side-chains
REVERT: a   26 LEU cc_start: 0.8541 (mt) cc_final: 0.8267 (mm)
REVERT: i   22 GLN cc_start: 0.8291 (mt0) cc_final: 0.8088 (tt0)
REVERT: i   31 GLU cc_start: 0.9127 (tp30) cc_final: 0.8874 (tp30)
REVERT: m   22 GLN cc_start: 0.8429 (mt0) cc_final: 0.8195 (tt0)
  outliers start: 64
  outliers final: 44
  residues processed: 293
  average time/residue: 0.2432
  time to fit residues: 107.2507
Evaluate side-chains
  284 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 240
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain G residue   26 LEU
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain L residue   26 LEU
Chi-restraints excluded: chain N residue   32 ILE
Chi-restraints excluded: chain P residue   26 LEU
Chi-restraints excluded: chain P residue   32 ILE
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain S residue   32 ILE
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain V residue   26 LEU
Chi-restraints excluded: chain W residue   26 LEU
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain b residue   24 LYS
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain f residue   32 ILE
Chi-restraints excluded: chain g residue   26 LEU
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain h residue   22 GLN
Chi-restraints excluded: chain j residue   32 ILE
Chi-restraints excluded: chain l residue   26 LEU
Chi-restraints excluded: chain m residue   32 ILE
Chi-restraints excluded: chain n residue   32 ILE
Chi-restraints excluded: chain o residue   18 ILE
Chi-restraints excluded: chain o residue   26 LEU
Chi-restraints excluded: chain o residue   32 ILE
Chi-restraints excluded: chain q residue   18 ILE
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain r residue   26 LEU
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain t residue   36 GLN
Chi-restraints excluded: chain u residue   19 LEU
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain w residue   26 LEU
Chi-restraints excluded: chain x residue   22 GLN
Chi-restraints excluded: chain z residue   18 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 150 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 127 optimal weight:    9.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
k  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.123415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.118354 restraints weight = 20135.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.118616 restraints weight = 17270.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.119098 restraints weight = 15945.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.4275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14664  Z= 0.132
  Angle     :  0.362   3.735  19656  Z= 0.201
  Chirality :  0.032   0.104   2392
  Planarity :  0.001   0.010   2496
  Dihedral  :  3.209   7.679   1976
  Min Nonbonded Distance : 2.677

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 16.27 %
    Favored  : 78.25 %
  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:  6.76 (0.14), residues: 1768
  helix:  4.32 (0.08), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS d  29 
 TYR   0.002   0.000   TYR l   8 
 ARG   0.002   0.000   ARG r  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05255 ( 1560)
  hydrogen bonds       : angle       3.91982 ( 4680)
  covalent geometry    : bond        0.00251 (14664)
  covalent geometry    : angle       0.36211 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 240
  time to evaluate  : 1.669 
Fit side-chains
REVERT: i   22 GLN cc_start: 0.8338 (mt0) cc_final: 0.8136 (tt0)
REVERT: i   31 GLU cc_start: 0.9114 (tp30) cc_final: 0.8876 (tp30)
REVERT: m   22 GLN cc_start: 0.8487 (mt0) cc_final: 0.8262 (tt0)
  outliers start: 74
  outliers final: 58
  residues processed: 272
  average time/residue: 0.2615
  time to fit residues: 107.9156
Evaluate side-chains
  292 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 234
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain G residue   26 LEU
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain K residue   32 ILE
Chi-restraints excluded: chain L residue   26 LEU
Chi-restraints excluded: chain N residue   32 ILE
Chi-restraints excluded: chain O residue   32 ILE
Chi-restraints excluded: chain P residue   26 LEU
Chi-restraints excluded: chain P residue   32 ILE
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain S residue   18 ILE
Chi-restraints excluded: chain T residue   26 LEU
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain V residue   26 LEU
Chi-restraints excluded: chain W residue   26 LEU
Chi-restraints excluded: chain Y residue   18 ILE
Chi-restraints excluded: chain Y residue   32 ILE
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain a residue   32 ILE
Chi-restraints excluded: chain b residue   24 LYS
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain f residue   32 ILE
Chi-restraints excluded: chain g residue   26 LEU
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain h residue   22 GLN
Chi-restraints excluded: chain j residue   32 ILE
Chi-restraints excluded: chain l residue   26 LEU
Chi-restraints excluded: chain m residue   32 ILE
Chi-restraints excluded: chain n residue   32 ILE
Chi-restraints excluded: chain o residue   18 ILE
Chi-restraints excluded: chain o residue   26 LEU
Chi-restraints excluded: chain o residue   32 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   26 LEU
Chi-restraints excluded: chain p residue   32 ILE
Chi-restraints excluded: chain q residue   18 ILE
Chi-restraints excluded: chain q residue   22 GLN
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain r residue   26 LEU
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain t residue   22 GLN
Chi-restraints excluded: chain t residue   24 LYS
Chi-restraints excluded: chain t residue   36 GLN
Chi-restraints excluded: chain u residue   18 ILE
Chi-restraints excluded: chain u residue   19 LEU
Chi-restraints excluded: chain u residue   26 LEU
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain w residue   26 LEU
Chi-restraints excluded: chain x residue   22 GLN
Chi-restraints excluded: chain z residue   18 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 148 optimal weight:    7.9990
   chunk 144 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 111 optimal weight:    2.9990
   chunk 138 optimal weight:    3.9990
   chunk 136 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 103 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.116502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.111396 restraints weight = 20494.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.111729 restraints weight = 17594.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.112155 restraints weight = 15963.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14664  Z= 0.169
  Angle     :  0.433   3.689  19656  Z= 0.233
  Chirality :  0.034   0.106   2392
  Planarity :  0.002   0.011   2496
  Dihedral  :  3.186   8.251   1976
  Min Nonbonded Distance : 2.669

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 16.27 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  6.45 (0.14), residues: 1768
  helix:  4.13 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS d  29 
 TYR   0.005   0.001   TYR l   8 
 ARG   0.003   0.000   ARG z  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06573 ( 1560)
  hydrogen bonds       : angle       4.29300 ( 4680)
  covalent geometry    : bond        0.00346 (14664)
  covalent geometry    : angle       0.43331 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 233
  time to evaluate  : 1.483 
Fit side-chains
REVERT: P   31 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8379 (mm-30)
REVERT: i   22 GLN cc_start: 0.8337 (mt0) cc_final: 0.8107 (tt0)
  outliers start: 72
  outliers final: 60
  residues processed: 268
  average time/residue: 0.2336
  time to fit residues: 94.8678
Evaluate side-chains
  287 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 227
  time to evaluate  : 1.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain G residue   26 LEU
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain L residue   22 GLN
Chi-restraints excluded: chain L residue   26 LEU
Chi-restraints excluded: chain N residue   32 ILE
Chi-restraints excluded: chain O residue   32 ILE
Chi-restraints excluded: chain P residue   22 GLN
Chi-restraints excluded: chain P residue   26 LEU
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain S residue   18 ILE
Chi-restraints excluded: chain T residue   26 LEU
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain V residue   26 LEU
Chi-restraints excluded: chain W residue   26 LEU
Chi-restraints excluded: chain X residue   18 ILE
Chi-restraints excluded: chain Y residue   18 ILE
Chi-restraints excluded: chain Y residue   32 ILE
Chi-restraints excluded: chain Z residue   18 ILE
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain a residue   32 ILE
Chi-restraints excluded: chain b residue   24 LYS
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain f residue   32 ILE
Chi-restraints excluded: chain g residue   26 LEU
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain h residue   22 GLN
Chi-restraints excluded: chain j residue   32 ILE
Chi-restraints excluded: chain m residue   32 ILE
Chi-restraints excluded: chain n residue   32 ILE
Chi-restraints excluded: chain o residue   18 ILE
Chi-restraints excluded: chain o residue   26 LEU
Chi-restraints excluded: chain o residue   32 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   26 LEU
Chi-restraints excluded: chain p residue   32 ILE
Chi-restraints excluded: chain q residue   18 ILE
Chi-restraints excluded: chain q residue   22 GLN
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain r residue   26 LEU
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain t residue   22 GLN
Chi-restraints excluded: chain t residue   36 GLN
Chi-restraints excluded: chain u residue   18 ILE
Chi-restraints excluded: chain u residue   19 LEU
Chi-restraints excluded: chain u residue   26 LEU
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain w residue   26 LEU
Chi-restraints excluded: chain x residue   22 GLN
Chi-restraints excluded: chain y residue   26 LEU
Chi-restraints excluded: chain z residue   18 ILE
Chi-restraints excluded: chain z residue   32 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 112 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 139 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 126 optimal weight:    1.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    2.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.118497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.113363 restraints weight = 20289.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.113801 restraints weight = 17406.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.114206 restraints weight = 15389.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14664  Z= 0.156
  Angle     :  0.408   3.878  19656  Z= 0.222
  Chirality :  0.033   0.123   2392
  Planarity :  0.002   0.010   2496
  Dihedral  :  3.198   8.277   1976
  Min Nonbonded Distance : 2.672

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 15.61 %
    Favored  : 78.99 %
  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:  6.52 (0.14), residues: 1768
  helix:  4.17 (0.08), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS Q  29 
 TYR   0.004   0.001   TYR l   8 
 ARG   0.002   0.000   ARG z  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06150 ( 1560)
  hydrogen bonds       : angle       4.18419 ( 4680)
  covalent geometry    : bond        0.00315 (14664)
  covalent geometry    : angle       0.40836 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 229
  time to evaluate  : 1.569 
Fit side-chains
REVERT: i   22 GLN cc_start: 0.8293 (mt0) cc_final: 0.8084 (tt0)
  outliers start: 73
  outliers final: 61
  residues processed: 263
  average time/residue: 0.2307
  time to fit residues: 92.7624
Evaluate side-chains
  290 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 229
  time to evaluate  : 1.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain G residue   26 LEU
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain L residue   26 LEU
Chi-restraints excluded: chain N residue   32 ILE
Chi-restraints excluded: chain O residue   32 ILE
Chi-restraints excluded: chain P residue   22 GLN
Chi-restraints excluded: chain P residue   26 LEU
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain S residue   18 ILE
Chi-restraints excluded: chain T residue   26 LEU
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain U residue   32 ILE
Chi-restraints excluded: chain V residue   26 LEU
Chi-restraints excluded: chain W residue   26 LEU
Chi-restraints excluded: chain X residue   18 ILE
Chi-restraints excluded: chain Y residue   18 ILE
Chi-restraints excluded: chain Y residue   32 ILE
Chi-restraints excluded: chain Z residue   26 LEU
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain a residue   22 GLN
Chi-restraints excluded: chain a residue   32 ILE
Chi-restraints excluded: chain b residue   24 LYS
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain f residue   32 ILE
Chi-restraints excluded: chain f residue   36 GLN
Chi-restraints excluded: chain g residue   26 LEU
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain h residue   22 GLN
Chi-restraints excluded: chain j residue   32 ILE
Chi-restraints excluded: chain m residue   32 ILE
Chi-restraints excluded: chain n residue   32 ILE
Chi-restraints excluded: chain o residue   18 ILE
Chi-restraints excluded: chain o residue   26 LEU
Chi-restraints excluded: chain o residue   32 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   26 LEU
Chi-restraints excluded: chain p residue   32 ILE
Chi-restraints excluded: chain q residue   18 ILE
Chi-restraints excluded: chain q residue   22 GLN
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain r residue   26 LEU
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain t residue   22 GLN
Chi-restraints excluded: chain t residue   36 GLN
Chi-restraints excluded: chain u residue   18 ILE
Chi-restraints excluded: chain u residue   19 LEU
Chi-restraints excluded: chain u residue   26 LEU
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain w residue   26 LEU
Chi-restraints excluded: chain x residue   22 GLN
Chi-restraints excluded: chain z residue   18 ILE
Chi-restraints excluded: chain z residue   32 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 153 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 103 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    3.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.114856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.109726 restraints weight = 20579.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.110127 restraints weight = 17703.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.110239 restraints weight = 15859.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14664  Z= 0.183
  Angle     :  0.460   4.402  19656  Z= 0.245
  Chirality :  0.035   0.116   2392
  Planarity :  0.002   0.012   2496
  Dihedral  :  3.205   8.569   1976
  Min Nonbonded Distance : 2.662

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 15.98 %
    Favored  : 79.07 %
  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:  6.27 (0.14), residues: 1768
  helix:  4.02 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS j  29 
 TYR   0.005   0.001   TYR l   8 
 ARG   0.003   0.001   ARG t  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06934 ( 1560)
  hydrogen bonds       : angle       4.41973 ( 4680)
  covalent geometry    : bond        0.00385 (14664)
  covalent geometry    : angle       0.46021 (19656)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 219
  time to evaluate  : 1.702 
Fit side-chains
REVERT: P   31 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8383 (mm-30)
REVERT: i   22 GLN cc_start: 0.8325 (mt0) cc_final: 0.8101 (tt0)
  outliers start: 67
  outliers final: 58
  residues processed: 259
  average time/residue: 0.2319
  time to fit residues: 92.0267
Evaluate side-chains
  278 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 220
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain C residue   24 LYS
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain I residue   32 ILE
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain L residue   26 LEU
Chi-restraints excluded: chain O residue   32 ILE
Chi-restraints excluded: chain P residue   22 GLN
Chi-restraints excluded: chain P residue   26 LEU
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain S residue   18 ILE
Chi-restraints excluded: chain T residue   26 LEU
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain V residue   26 LEU
Chi-restraints excluded: chain W residue   26 LEU
Chi-restraints excluded: chain X residue   18 ILE
Chi-restraints excluded: chain Y residue   18 ILE
Chi-restraints excluded: chain Y residue   32 ILE
Chi-restraints excluded: chain Z residue   18 ILE
Chi-restraints excluded: chain Z residue   26 LEU
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain a residue   22 GLN
Chi-restraints excluded: chain a residue   32 ILE
Chi-restraints excluded: chain b residue   24 LYS
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain f residue   36 GLN
Chi-restraints excluded: chain g residue   26 LEU
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain h residue   22 GLN
Chi-restraints excluded: chain h residue   32 ILE
Chi-restraints excluded: chain i residue   18 ILE
Chi-restraints excluded: chain j residue   32 ILE
Chi-restraints excluded: chain m residue   32 ILE
Chi-restraints excluded: chain n residue   32 ILE
Chi-restraints excluded: chain o residue   18 ILE
Chi-restraints excluded: chain o residue   26 LEU
Chi-restraints excluded: chain o residue   32 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   26 LEU
Chi-restraints excluded: chain p residue   32 ILE
Chi-restraints excluded: chain q residue   18 ILE
Chi-restraints excluded: chain q residue   22 GLN
Chi-restraints excluded: chain r residue   26 LEU
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain t residue   22 GLN
Chi-restraints excluded: chain t residue   36 GLN
Chi-restraints excluded: chain u residue   18 ILE
Chi-restraints excluded: chain u residue   19 LEU
Chi-restraints excluded: chain u residue   26 LEU
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain x residue   22 GLN
Chi-restraints excluded: chain z residue   18 ILE
Chi-restraints excluded: chain z residue   32 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 110 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 137 optimal weight:    0.9980
   chunk 115 optimal weight:    0.7980
   chunk 128 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.128509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.123308 restraints weight = 19728.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.123743 restraints weight = 16634.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.123875 restraints weight = 14745.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.4642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  14664  Z= 0.115
  Angle     :  0.336   3.896  19656  Z= 0.190
  Chirality :  0.031   0.128   2392
  Planarity :  0.001   0.008   2496
  Dihedral  :  3.307   7.867   1976
  Min Nonbonded Distance : 2.670

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.75 %
    Favored  : 78.92 %
  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:  6.87 (0.14), residues: 1768
  helix:  4.38 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  29 
 TYR   0.002   0.000   TYR D   8 
 ARG   0.001   0.000   ARG r  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04332 ( 1560)
  hydrogen bonds       : angle       3.69009 ( 4680)
  covalent geometry    : bond        0.00210 (14664)
  covalent geometry    : angle       0.33575 (19656)

===============================================================================
Job complete
usr+sys time: 3759.39 seconds
wall clock time: 66 minutes 8.11 seconds (3968.11 seconds total)