Starting phenix.real_space_refine
on Thu Sep 18 03:46:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wl1_21815/09_2025/6wl1_21815.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wl1_21815/09_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_21815/09_2025/6wl1_21815.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wl1_21815/09_2025/6wl1_21815.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wl1_21815/09_2025/6wl1_21815.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wl1_21815/09_2025/6wl1_21815.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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:
    B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W,
    X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s,
    t, u, v, w, x, y, z
  Time building chain proxies: 1.10, per 1000 atoms: 0.08
  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: 1.00
  Conformation dependent library (CDL) restraints added in 629.3 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.34
  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: 2.98

  Time building geometry restraints manager: 1.35 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'U'
  selection = chain 'V'
  selection = chain 'W'
  selection = chain 'X'
  selection = chain 'Y'
  selection = chain 'Z'
  selection = chain 'a'
  selection = chain 'b'
  selection = chain 'c'
  selection = chain 'd'
  selection = chain 'e'
  selection = chain 'f'
  selection = chain 'g'
  selection = chain 'h'
  selection = chain 'i'
  selection = chain 'j'
  selection = chain 'k'
  selection = chain 'l'
  selection = chain 'm'
  selection = chain 'n'
  selection = chain 'o'
  selection = chain 'p'
  selection = chain 'q'
  selection = chain 'r'
  selection = chain 's'
  selection = chain 't'
  selection = chain 'u'
  selection = chain 'v'
  selection = chain 'w'
  selection = chain 'x'
  selection = chain 'y'
  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:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.040
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.560
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (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
 ARG   0.008   0.003   ARG p   6 
 TYR   0.016   0.004   TYR j   8 
 HIS   0.005   0.003   HIS V  29 

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

*********************** 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  : 0.491 
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: 0.1460
  time to fit residues: 74.6406
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  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3257 r_free = 0.3257 target = 0.115852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.111205 restraints weight = 20523.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.111570 restraints weight = 17722.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.111617 restraints weight = 15980.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.111632 restraints weight = 15609.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.111632 restraints weight = 15811.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  14664  Z= 0.198
  Angle     :  0.540   4.616  19656  Z= 0.290
  Chirality :  0.037   0.102   2392
  Planarity :  0.003   0.021   2496
  Dihedral  :  3.485   8.036   1976
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.02 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.30 (0.14), residues: 1768
  helix:  2.19 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG r  10 
 TYR   0.005   0.001   TYR u   8 
 HIS   0.003   0.001   HIS u  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (14664)
  covalent geometry    : angle       0.54046 (19656)
  hydrogen bonds       : bond        0.07938 ( 1560)
  hydrogen bonds       : angle       4.87573 ( 4680)

*********************** 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
  282 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 259
  time to evaluate  : 0.592 
Fit side-chains
REVERT: C   22 GLN cc_start: 0.8309 (mt0) cc_final: 0.8050 (mt0)
REVERT: F   36 GLN cc_start: 0.8648 (mt0) cc_final: 0.8441 (mt0)
REVERT: G   31 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8552 (mm-30)
REVERT: N   22 GLN cc_start: 0.8297 (mt0) cc_final: 0.8013 (tt0)
REVERT: Q   31 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8555 (mm-30)
REVERT: h   19 LEU cc_start: 0.9352 (mt) cc_final: 0.9121 (mp)
REVERT: q   22 GLN cc_start: 0.8494 (mt0) cc_final: 0.8293 (tt0)
  outliers start: 23
  outliers final: 2
  residues processed: 275
  average time/residue: 0.1130
  time to fit residues: 46.0504
Evaluate side-chains
  208 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 206
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   22 GLN
Chi-restraints excluded: chain X residue   33 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 153 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 102 optimal weight:    0.9990
   chunk 137 optimal weight:    9.9990
   chunk 134 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
Z  22 GLN
a  22 GLN
x  36 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.119327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.113573 restraints weight = 19923.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.114049 restraints weight = 17449.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.114273 restraints weight = 15545.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.114223 restraints weight = 14730.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.114385 restraints weight = 15215.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  14664  Z= 0.137
  Angle     :  0.370   2.750  19656  Z= 0.209
  Chirality :  0.032   0.098   2392
  Planarity :  0.003   0.018   2496
  Dihedral  :  3.293   7.335   1976
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 17.53 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.84 (0.14), residues: 1768
  helix:  3.75 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG z  10 
 TYR   0.004   0.001   TYR Q   8 
 HIS   0.001   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (14664)
  covalent geometry    : angle       0.36987 (19656)
  hydrogen bonds       : bond        0.05700 ( 1560)
  hydrogen bonds       : angle       4.15668 ( 4680)

*********************** 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
  330 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 321
  time to evaluate  : 0.542 
Fit side-chains
REVERT: G   31 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8370 (mm-30)
REVERT: N   22 GLN cc_start: 0.8156 (mt0) cc_final: 0.7890 (tt0)
REVERT: d   22 GLN cc_start: 0.8136 (mt0) cc_final: 0.7901 (tt0)
REVERT: o   22 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7996 (tt0)
REVERT: t   22 GLN cc_start: 0.8226 (mt0) cc_final: 0.7963 (tt0)
REVERT: z   31 GLU cc_start: 0.8685 (tp30) cc_final: 0.8457 (tp30)
  outliers start: 9
  outliers final: 3
  residues processed: 323
  average time/residue: 0.1155
  time to fit residues: 54.5598
Evaluate side-chains
  259 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 255
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain o residue   22 GLN
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain s residue   22 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 101 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
F  36 GLN
M  36 GLN
W  36 GLN
X  36 GLN
a  22 GLN
r  36 GLN
x  36 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.119241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.114311 restraints weight = 20440.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.114700 restraints weight = 17613.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.114700 restraints weight = 15827.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.114700 restraints weight = 15827.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.114700 restraints weight = 15827.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14664  Z= 0.153
  Angle     :  0.396   3.521  19656  Z= 0.218
  Chirality :  0.034   0.104   2392
  Planarity :  0.002   0.017   2496
  Dihedral  :  3.197   7.352   1976
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 18.27 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.29 (0.14), residues: 1768
  helix:  4.03 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (14664)
  covalent geometry    : angle       0.39572 (19656)
  hydrogen bonds       : bond        0.06212 ( 1560)
  hydrogen bonds       : angle       4.26174 ( 4680)

*********************** 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
  309 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 257
  time to evaluate  : 0.620 
Fit side-chains
REVERT: G   31 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8419 (mm-30)
REVERT: d   22 GLN cc_start: 0.8055 (mt0) cc_final: 0.7810 (tt0)
REVERT: o   22 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8122 (tt0)
  outliers start: 52
  outliers final: 28
  residues processed: 284
  average time/residue: 0.1219
  time to fit residues: 51.9899
Evaluate side-chains
  272 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 243
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
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 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 Q residue   26 LEU
Chi-restraints excluded: chain S residue   18 ILE
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain f residue   32 ILE
Chi-restraints excluded: chain h residue   18 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 r residue   22 GLN
Chi-restraints excluded: chain s residue   22 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 z residue   18 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 138 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 107 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 148 optimal weight:    0.8980
   overall best weight:    1.1584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.127033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.122098 restraints weight = 19792.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.122303 restraints weight = 17013.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.122706 restraints weight = 15900.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.122772 restraints weight = 14340.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.123185 restraints weight = 13885.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.3941

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= 0.119
  Angle     :  0.320   3.026  19656  Z= 0.187
  Chirality :  0.031   0.114   2392
  Planarity :  0.002   0.012   2496
  Dihedral  :  3.258   7.261   1976
  Min Nonbonded Distance : 2.672

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 16.64 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.79 (0.14), residues: 1768
  helix:  4.34 (0.08), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  10 
 TYR   0.003   0.001   TYR D   8 
 HIS   0.002   0.000   HIS x  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (14664)
  covalent geometry    : angle       0.31997 (19656)
  hydrogen bonds       : bond        0.04710 ( 1560)
  hydrogen bonds       : angle       3.83532 ( 4680)

*********************** 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
  367 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 285
  time to evaluate  : 0.589 
Fit side-chains
REVERT: A   22 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7880 (tt0)
REVERT: B   26 LEU cc_start: 0.8478 (mt) cc_final: 0.8190 (mm)
REVERT: a   26 LEU cc_start: 0.8623 (mt) cc_final: 0.8271 (mm)
REVERT: d   22 GLN cc_start: 0.8011 (mt0) cc_final: 0.7765 (tt0)
REVERT: t   22 GLN cc_start: 0.8059 (mt0) cc_final: 0.7784 (tt0)
  outliers start: 82
  outliers final: 27
  residues processed: 343
  average time/residue: 0.1185
  time to fit residues: 61.5502
Evaluate side-chains
  267 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 239
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLN
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 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 P residue   26 LEU
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain U residue   18 ILE
Chi-restraints excluded: chain Y residue   32 ILE
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain f residue   32 ILE
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain i residue   32 ILE
Chi-restraints excluded: chain l residue   26 LEU
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 r residue   22 GLN
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain w residue   26 LEU
Chi-restraints excluded: chain x residue   22 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 75 optimal weight:    0.3980
   chunk 151 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 99 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 96 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   overall best weight:    2.0788

-------------------------------------------------------------------------------
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
a  36 GLN
c  36 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.121920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.116760 restraints weight = 20154.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.117258 restraints weight = 17192.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.117717 restraints weight = 15018.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.117802 restraints weight = 13343.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.117802 restraints weight = 12875.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.4103

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= 0.140
  Angle     :  0.368   3.677  19656  Z= 0.205
  Chirality :  0.033   0.106   2392
  Planarity :  0.002   0.011   2496
  Dihedral  :  3.202   7.792   1976
  Min Nonbonded Distance : 2.674

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 16.72 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.70 (0.14), residues: 1768
  helix:  4.29 (0.08), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (14664)
  covalent geometry    : angle       0.36832 (19656)
  hydrogen bonds       : bond        0.05568 ( 1560)
  hydrogen bonds       : angle       4.01652 ( 4680)

*********************** 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
  315 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 241
  time to evaluate  : 0.599 
Fit side-chains
REVERT: d   22 GLN cc_start: 0.8106 (mt0) cc_final: 0.7880 (tt0)
  outliers start: 74
  outliers final: 49
  residues processed: 276
  average time/residue: 0.1210
  time to fit residues: 50.5296
Evaluate side-chains
  283 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 234
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
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 E residue   18 ILE
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 P residue   26 LEU
Chi-restraints excluded: chain Q residue    3 GLU
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain S residue   18 ILE
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 U residue   32 ILE
Chi-restraints excluded: chain X residue   32 ILE
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 c residue   22 GLN
Chi-restraints excluded: chain f residue   32 ILE
Chi-restraints excluded: chain h residue   18 ILE
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   26 LEU
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain s residue   22 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 x residue   32 ILE
Chi-restraints excluded: chain y residue   18 ILE
Chi-restraints excluded: chain z residue   32 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 129 optimal weight:    5.9990
   chunk 155 optimal weight:    7.9990
   chunk 128 optimal weight:    4.9990
   chunk 140 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 137 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 99 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.3209 r_free = 0.3209 target = 0.113381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.108351 restraints weight = 20656.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.108562 restraints weight = 17946.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.108943 restraints weight = 16749.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.109276 restraints weight = 15185.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.109321 restraints weight = 13931.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.4027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14664  Z= 0.196
  Angle     :  0.475   4.664  19656  Z= 0.255
  Chirality :  0.035   0.127   2392
  Planarity :  0.002   0.013   2496
  Dihedral  :  3.208   8.454   1976
  Min Nonbonded Distance : 2.656

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 16.20 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.16 (0.14), residues: 1768
  helix:  3.95 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG r  10 
 TYR   0.006   0.001   TYR l   8 
 HIS   0.003   0.001   HIS x  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (14664)
  covalent geometry    : angle       0.47513 (19656)
  hydrogen bonds       : bond        0.07265 ( 1560)
  hydrogen bonds       : angle       4.51873 ( 4680)

*********************** 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
  298 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 218
  time to evaluate  : 0.601 
Fit side-chains
REVERT: R   19 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9305 (mm)
REVERT: d   22 GLN cc_start: 0.8057 (mt0) cc_final: 0.7780 (tt0)
REVERT: o   22 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8097 (tt0)
REVERT: z   31 GLU cc_start: 0.8825 (tp30) cc_final: 0.8597 (tp30)
  outliers start: 80
  outliers final: 52
  residues processed: 264
  average time/residue: 0.1148
  time to fit residues: 46.8513
Evaluate side-chains
  264 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 210
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain E residue   18 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   18 ILE
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain N residue   32 ILE
Chi-restraints excluded: chain P residue   26 LEU
Chi-restraints excluded: chain Q residue   26 LEU
Chi-restraints excluded: chain R residue   19 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 W residue   26 LEU
Chi-restraints excluded: chain X residue   32 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   32 ILE
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain e residue   18 ILE
Chi-restraints excluded: chain g residue   26 LEU
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain i residue   18 ILE
Chi-restraints excluded: chain j residue   32 ILE
Chi-restraints excluded: chain k residue   18 ILE
Chi-restraints excluded: chain l residue   26 LEU
Chi-restraints excluded: chain m 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   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   26 LEU
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain u residue   19 LEU
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain x residue   22 GLN
Chi-restraints excluded: chain x residue   32 ILE
Chi-restraints excluded: chain y residue   18 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 70 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    3.1988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.115720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.110573 restraints weight = 20592.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.110920 restraints weight = 17737.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.111346 restraints weight = 16021.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.111346 restraints weight = 14470.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.111346 restraints weight = 14470.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  14664  Z= 0.176
  Angle     :  0.438   4.190  19656  Z= 0.237
  Chirality :  0.034   0.105   2392
  Planarity :  0.002   0.011   2496
  Dihedral  :  3.225   8.933   1976
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 16.49 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.27 (0.14), residues: 1768
  helix:  4.01 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG r  10 
 TYR   0.004   0.001   TYR b   8 
 HIS   0.003   0.001   HIS x  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (14664)
  covalent geometry    : angle       0.43793 (19656)
  hydrogen bonds       : bond        0.06708 ( 1560)
  hydrogen bonds       : angle       4.37167 ( 4680)

*********************** 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
  288 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 223
  time to evaluate  : 0.557 
Fit side-chains
REVERT: d   22 GLN cc_start: 0.8040 (mt0) cc_final: 0.7765 (tt0)
REVERT: z   31 GLU cc_start: 0.8864 (tp30) cc_final: 0.8609 (tp30)
  outliers start: 65
  outliers final: 55
  residues processed: 261
  average time/residue: 0.1158
  time to fit residues: 46.7231
Evaluate side-chains
  277 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 222
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain D residue   26 LEU
Chi-restraints excluded: chain E residue   18 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 J residue   26 LEU
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain L residue   22 GLN
Chi-restraints excluded: chain N 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 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   18 ILE
Chi-restraints excluded: chain Z residue   26 LEU
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain a residue   32 ILE
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain e residue   18 ILE
Chi-restraints excluded: chain g residue   26 LEU
Chi-restraints excluded: chain h residue   18 ILE
Chi-restraints excluded: chain i residue   18 ILE
Chi-restraints excluded: chain j residue   32 ILE
Chi-restraints excluded: chain k residue   18 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   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   26 LEU
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain t residue   22 GLN
Chi-restraints excluded: chain u residue   18 ILE
Chi-restraints excluded: chain u residue   19 LEU
Chi-restraints excluded: chain x residue   22 GLN
Chi-restraints excluded: chain x residue   32 ILE
Chi-restraints excluded: chain y residue   18 ILE
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 144 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 133 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 107 optimal weight:    6.9990
   chunk 109 optimal weight:    8.9990
   overall best weight:    4.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.111196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.106122 restraints weight = 21124.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.106500 restraints weight = 18461.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.106547 restraints weight = 16590.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.106547 restraints weight = 16238.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.106547 restraints weight = 16238.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14664  Z= 0.224
  Angle     :  0.529   5.271  19656  Z= 0.278
  Chirality :  0.037   0.126   2392
  Planarity :  0.002   0.015   2496
  Dihedral  :  3.259   8.795   1976
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 16.49 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.80 (0.14), residues: 1768
  helix:  3.73 (0.09), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG z  10 
 TYR   0.006   0.001   TYR l   8 
 HIS   0.004   0.001   HIS x  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 (14664)
  covalent geometry    : angle       0.52878 (19656)
  hydrogen bonds       : bond        0.07782 ( 1560)
  hydrogen bonds       : angle       4.71775 ( 4680)

*********************** 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
  274 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 207
  time to evaluate  : 0.737 
Fit side-chains
REVERT: d   22 GLN cc_start: 0.8029 (mt0) cc_final: 0.7768 (tt0)
REVERT: z   31 GLU cc_start: 0.8869 (tp30) cc_final: 0.8628 (tp30)
  outliers start: 67
  outliers final: 52
  residues processed: 251
  average time/residue: 0.1127
  time to fit residues: 44.0583
Evaluate side-chains
  259 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 207
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain E residue   18 ILE
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain G residue   26 LEU
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain K residue   18 ILE
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain L residue   18 ILE
Chi-restraints excluded: chain O residue   26 LEU
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 W residue   26 LEU
Chi-restraints excluded: chain Y residue   18 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   18 ILE
Chi-restraints excluded: chain a residue   32 ILE
Chi-restraints excluded: chain c residue   22 GLN
Chi-restraints excluded: chain c residue   26 LEU
Chi-restraints excluded: chain e residue   18 ILE
Chi-restraints excluded: chain g residue   26 LEU
Chi-restraints excluded: chain h residue   18 ILE
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 k residue   18 ILE
Chi-restraints excluded: chain l residue   26 LEU
Chi-restraints excluded: chain m residue   32 ILE
Chi-restraints excluded: chain o residue   18 ILE
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 q residue   26 LEU
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain s residue   22 GLN
Chi-restraints excluded: chain t residue   22 GLN
Chi-restraints excluded: chain u residue   18 ILE
Chi-restraints excluded: chain u residue   19 LEU
Chi-restraints excluded: chain x residue   22 GLN
Chi-restraints excluded: chain x residue   32 ILE
Chi-restraints excluded: chain y residue   18 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 121 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0050
   chunk 55 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 84 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.7798

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.129777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.124662 restraints weight = 19750.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.124968 restraints weight = 17016.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.125227 restraints weight = 15282.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.125548 restraints weight = 14011.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.125674 restraints weight = 13331.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.4714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  14664  Z= 0.114
  Angle     :  0.341   4.438  19656  Z= 0.194
  Chirality :  0.031   0.180   2392
  Planarity :  0.002   0.007   2496
  Dihedral  :  3.353   7.942   1976
  Min Nonbonded Distance : 2.679

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.71 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.86 (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
 ARG   0.001   0.000   ARG w  10 
 TYR   0.002   0.000   TYR D   8 
 HIS   0.002   0.000   HIS h  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (14664)
  covalent geometry    : angle       0.34132 (19656)
  hydrogen bonds       : bond        0.04204 ( 1560)
  hydrogen bonds       : angle       3.68312 ( 4680)

********************** 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
  315 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 281
  time to evaluate  : 0.594 
Fit side-chains
REVERT: J   22 GLN cc_start: 0.8181 (mt0) cc_final: 0.7666 (tt0)
REVERT: R   22 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7799 (tt0)
REVERT: d   22 GLN cc_start: 0.7948 (mt0) cc_final: 0.7717 (tt0)
REVERT: i   31 GLU cc_start: 0.9085 (tp30) cc_final: 0.8854 (tp30)
REVERT: q   26 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7868 (mm)
  outliers start: 34
  outliers final: 24
  residues processed: 294
  average time/residue: 0.1215
  time to fit residues: 53.8829
Evaluate side-chains
  268 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 242
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 LEU
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain K residue   26 LEU
Chi-restraints excluded: chain N residue   32 ILE
Chi-restraints excluded: chain O residue   26 LEU
Chi-restraints excluded: chain P residue   26 LEU
Chi-restraints excluded: chain R residue   22 GLN
Chi-restraints excluded: chain T residue   32 ILE
Chi-restraints excluded: chain W residue   26 LEU
Chi-restraints excluded: chain Z residue   32 ILE
Chi-restraints excluded: chain a residue   32 ILE
Chi-restraints excluded: chain c residue   26 LEU
Chi-restraints excluded: chain h 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   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   26 LEU
Chi-restraints excluded: chain r residue   22 GLN
Chi-restraints excluded: chain u residue   26 LEU
Chi-restraints excluded: chain y residue   18 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 117 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 124 optimal weight:    1.9990
   chunk 46 optimal weight:    9.9990
   chunk 115 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0270
   chunk 152 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    1.6042

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

Flipped N/Q/H residues before XYZ refinement:
F  36 GLN
W  36 GLN
d  36 GLN
e  36 GLN
j  36 GLN
k  36 GLN
m  36 GLN
z  36 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.124383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.119212 restraints weight = 19907.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.119615 restraints weight = 17051.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.120075 restraints weight = 15138.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.120382 restraints weight = 13427.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.120524 restraints weight = 12368.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.4594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14664  Z= 0.129
  Angle     :  0.378   4.405  19656  Z= 0.206
  Chirality :  0.032   0.106   2392
  Planarity :  0.002   0.008   2496
  Dihedral  :  3.255   7.718   1976
  Min Nonbonded Distance : 2.684

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.45 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.71 (0.14), residues: 1768
  helix:  4.29 (0.08), residues: 1768
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG t  10 
 TYR   0.002   0.000   TYR b   8 
 HIS   0.002   0.000   HIS Q  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (14664)
  covalent geometry    : angle       0.37790 (19656)
  hydrogen bonds       : bond        0.04932 ( 1560)
  hydrogen bonds       : angle       3.84651 ( 4680)

===============================================================================
Job complete
usr+sys time: 1890.97 seconds
wall clock time: 33 minutes 42.47 seconds (2022.47 seconds total)