Starting phenix.real_space_refine
on Wed Sep 17 13:45:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hqe_0252/09_2025/6hqe_0252.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hqe_0252/09_2025/6hqe_0252.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hqe_0252/09_2025/6hqe_0252.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hqe_0252/09_2025/6hqe_0252.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hqe_0252/09_2025/6hqe_0252.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hqe_0252/09_2025/6hqe_0252.map"
  }
  resolution = 4.4
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    5668      2.51       5
     N    1976      2.21       5
     O    1716      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s

  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: 9360
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 180
          Classifications: {'peptide': 23}
          Link IDs: {'PTRANS': 1, 'TRANS': 21}
  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: 0.85, per 1000 atoms: 0.09
  Number of scatterers: 9360
  At special positions: 0
  Unit cell: (91.08, 91.08, 92.4, 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    1716      8.00
     N    1976      7.00
     C    5668      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 504.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2392

  Finding SS restraints...
    Secondary structure from input PDB file:
      104 helices and 0 sheets defined
      78.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
    Processing helix  chain 'A' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG A  16 " --> pdb=" O   ASP A  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 7
    Processing helix  chain 'B' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG B  16 " --> pdb=" O   ASP B  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 7
    Processing helix  chain 'C' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG C  16 " --> pdb=" O   ASP C  12 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 7
    Processing helix  chain 'D' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG D  16 " --> pdb=" O   ASP D  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 7
    Processing helix  chain 'E' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG E  16 " --> pdb=" O   ASP E  12 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 7
    Processing helix  chain 'F' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG F  16 " --> pdb=" O   ASP F  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 7
    Processing helix  chain 'G' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG G  16 " --> pdb=" O   ASP G  12 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 7
    Processing helix  chain 'H' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG H  16 " --> pdb=" O   ASP H  12 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 7
    Processing helix  chain 'I' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG I  16 " --> pdb=" O   ASP I  12 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 2 through 7
    Processing helix  chain 'J' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG J  16 " --> pdb=" O   ASP J  12 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2 through 7
    Processing helix  chain 'K' and resid 12 through 23
      removed outlier: 3.590A  pdb=" N   ARG K  16 " --> pdb=" O   ASP K  12 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 2 through 7
    Processing helix  chain 'L' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG L  16 " --> pdb=" O   ASP L  12 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 2 through 7
    Processing helix  chain 'M' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG M  16 " --> pdb=" O   ASP M  12 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2 through 7
    Processing helix  chain 'N' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG N  16 " --> pdb=" O   ASP N  12 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 2 through 7
    Processing helix  chain 'O' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG O  16 " --> pdb=" O   ASP O  12 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 7
    Processing helix  chain 'P' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG P  16 " --> pdb=" O   ASP P  12 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 2 through 7
    Processing helix  chain 'Q' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG Q  16 " --> pdb=" O   ASP Q  12 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 2 through 7
    Processing helix  chain 'R' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG R  16 " --> pdb=" O   ASP R  12 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 2 through 7
    Processing helix  chain 'S' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG S  16 " --> pdb=" O   ASP S  12 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 2 through 7
    Processing helix  chain 'T' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG T  16 " --> pdb=" O   ASP T  12 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 2 through 7
    Processing helix  chain 'U' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG U  16 " --> pdb=" O   ASP U  12 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 2 through 7
    Processing helix  chain 'V' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG V  16 " --> pdb=" O   ASP V  12 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 2 through 7
    Processing helix  chain 'W' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG W  16 " --> pdb=" O   ASP W  12 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2 through 7
    Processing helix  chain 'X' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG X  16 " --> pdb=" O   ASP X  12 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 2 through 7
    Processing helix  chain 'Y' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG Y  16 " --> pdb=" O   ASP Y  12 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 2 through 7
    Processing helix  chain 'Z' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG Z  16 " --> pdb=" O   ASP Z  12 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 2 through 7
    Processing helix  chain 'a' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG a  16 " --> pdb=" O   ASP a  12 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 2 through 7
    Processing helix  chain 'b' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG b  16 " --> pdb=" O   ASP b  12 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 2 through 7
    Processing helix  chain 'c' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG c  16 " --> pdb=" O   ASP c  12 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 2 through 7
    Processing helix  chain 'd' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG d  16 " --> pdb=" O   ASP d  12 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 2 through 7
    Processing helix  chain 'e' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG e  16 " --> pdb=" O   ASP e  12 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 2 through 7
    Processing helix  chain 'f' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG f  16 " --> pdb=" O   ASP f  12 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 2 through 7
    Processing helix  chain 'g' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG g  16 " --> pdb=" O   ASP g  12 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 2 through 7
    Processing helix  chain 'h' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG h  16 " --> pdb=" O   ASP h  12 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 2 through 7
    Processing helix  chain 'i' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG i  16 " --> pdb=" O   ASP i  12 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 2 through 7
    Processing helix  chain 'j' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG j  16 " --> pdb=" O   ASP j  12 " (cutoff:3.500A)
    Processing helix  chain 'k' and resid 2 through 7
    Processing helix  chain 'k' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG k  16 " --> pdb=" O   ASP k  12 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 2 through 7
    Processing helix  chain 'l' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG l  16 " --> pdb=" O   ASP l  12 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 2 through 7
    Processing helix  chain 'm' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG m  16 " --> pdb=" O   ASP m  12 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 2 through 7
    Processing helix  chain 'n' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG n  16 " --> pdb=" O   ASP n  12 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 2 through 7
    Processing helix  chain 'o' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG o  16 " --> pdb=" O   ASP o  12 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 2 through 7
    Processing helix  chain 'p' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG p  16 " --> pdb=" O   ASP p  12 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 2 through 7
    Processing helix  chain 'q' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG q  16 " --> pdb=" O   ASP q  12 " (cutoff:3.500A)
    Processing helix  chain 'r' and resid 2 through 7
    Processing helix  chain 'r' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG r  16 " --> pdb=" O   ASP r  12 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 2 through 7
    Processing helix  chain 's' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG s  16 " --> pdb=" O   ASP s  12 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 2 through 7
    Processing helix  chain 't' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG t  16 " --> pdb=" O   ASP t  12 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 2 through 7
    Processing helix  chain 'u' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG u  16 " --> pdb=" O   ASP u  12 " (cutoff:3.500A)
    Processing helix  chain 'v' and resid 2 through 7
    Processing helix  chain 'v' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG v  16 " --> pdb=" O   ASP v  12 " (cutoff:3.500A)
    Processing helix  chain 'w' and resid 2 through 7
    Processing helix  chain 'w' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG w  16 " --> pdb=" O   ASP w  12 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 2 through 7
    Processing helix  chain 'x' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG x  16 " --> pdb=" O   ASP x  12 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 2 through 7
    Processing helix  chain 'y' and resid 12 through 23
      removed outlier: 3.591A  pdb=" N   ARG y  16 " --> pdb=" O   ASP y  12 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 2 through 7
    Processing helix  chain 'z' and resid 12 through 23
      removed outlier: 3.592A  pdb=" N   ARG z  16 " --> pdb=" O   ASP z  12 " (cutoff:3.500A)

    468 hydrogen bonds defined for protein.
    1404 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: 1.39

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 1716
        1.29 -     1.35: 1924
        1.35 -     1.41: 0
        1.41 -     1.48: 1602
        1.48 -     1.54: 4170
  Bond restraints: 9412
  Sorted by residual:
  bond pdb=" CG  LEU c  23 "
       pdb=" CD1 LEU c  23 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.40e+00
  bond pdb=" CG  LEU e  23 "
       pdb=" CD1 LEU e  23 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.39e+00
  bond pdb=" CG  LEU v  23 "
       pdb=" CD1 LEU v  23 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.39e+00
  bond pdb=" CG  LEU r  23 "
       pdb=" CD1 LEU r  23 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.38e+00
  bond pdb=" CG  LEU R  23 "
       pdb=" CD1 LEU R  23 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.38e+00
  ... (remaining 9407 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 11206
        1.67 -     3.34: 1222
        3.34 -     5.01: 156
        5.01 -     6.68: 0
        6.68 -     8.35: 52
  Bond angle restraints: 12636
  Sorted by residual:
  angle pdb=" CA  LEU U   4 "
        pdb=" CB  LEU U   4 "
        pdb=" CG  LEU U   4 "
      ideal   model   delta    sigma   weight residual
     116.30  124.65   -8.35 3.50e+00 8.16e-02 5.70e+00
  angle pdb=" CA  LEU E   4 "
        pdb=" CB  LEU E   4 "
        pdb=" CG  LEU E   4 "
      ideal   model   delta    sigma   weight residual
     116.30  124.65   -8.35 3.50e+00 8.16e-02 5.69e+00
  angle pdb=" CA  LEU L   4 "
        pdb=" CB  LEU L   4 "
        pdb=" CG  LEU L   4 "
      ideal   model   delta    sigma   weight residual
     116.30  124.65   -8.35 3.50e+00 8.16e-02 5.69e+00
  angle pdb=" CA  LEU p   4 "
        pdb=" CB  LEU p   4 "
        pdb=" CG  LEU p   4 "
      ideal   model   delta    sigma   weight residual
     116.30  124.64   -8.34 3.50e+00 8.16e-02 5.68e+00
  angle pdb=" CA  LEU T   4 "
        pdb=" CB  LEU T   4 "
        pdb=" CG  LEU T   4 "
      ideal   model   delta    sigma   weight residual
     116.30  124.63   -8.33 3.50e+00 8.16e-02 5.67e+00
  ... (remaining 12631 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     5.46: 4147
        5.46 -    10.93: 1157
       10.93 -    16.39: 572
       16.39 -    21.86: 208
       21.86 -    27.32: 156
  Dihedral angle restraints: 6240
    sinusoidal: 2704
      harmonic: 3536
  Sorted by residual:
  dihedral pdb=" CA  ALA o  20 "
           pdb=" C   ALA o  20 "
           pdb=" N   ARG o  21 "
           pdb=" CA  ARG o  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.99   13.01     0      5.00e+00 4.00e-02 6.77e+00
  dihedral pdb=" CA  ALA z  20 "
           pdb=" C   ALA z  20 "
           pdb=" N   ARG z  21 "
           pdb=" CA  ARG z  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.99   13.01     0      5.00e+00 4.00e-02 6.77e+00
  dihedral pdb=" CA  ALA Q  20 "
           pdb=" C   ALA Q  20 "
           pdb=" N   ARG Q  21 "
           pdb=" CA  ARG Q  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  167.00   13.00     0      5.00e+00 4.00e-02 6.76e+00
  ... (remaining 6237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 526
       0.029 -    0.059: 491
       0.059 -    0.088: 225
       0.088 -    0.118: 110
       0.118 -    0.147: 104
  Chirality restraints: 1456
  Sorted by residual:
  chirality pdb=" CA  LEU Z  23 "
            pdb=" N   LEU Z  23 "
            pdb=" C   LEU Z  23 "
            pdb=" CB  LEU Z  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" CA  LEU m  23 "
            pdb=" N   LEU m  23 "
            pdb=" C   LEU m  23 "
            pdb=" CB  LEU m  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CA  LEU g  23 "
            pdb=" N   LEU g  23 "
            pdb=" C   LEU g  23 "
            pdb=" CB  LEU g  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.33e-01
  ... (remaining 1453 not shown)

  Planarity restraints: 1716
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP o  10 "    0.039 5.00e-02 4.00e+02   5.85e-02 5.47e+00
        pdb=" N   PRO o  11 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO o  11 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO o  11 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP X  10 "   -0.039 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO X  11 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO X  11 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO X  11 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP n  10 "    0.039 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO n  11 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO n  11 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO n  11 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1713 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2964
        2.83 -     3.34: 9236
        3.34 -     3.86: 16004
        3.86 -     4.38: 18566
        4.38 -     4.90: 27403
  Nonbonded interactions: 74173
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP b  10 "
            pdb=" NE  ARG d  16 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" OD2 ASP v  10 "
            pdb=" NE  ARG x  16 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" OD2 ASP L  10 "
            pdb=" NE  ARG N  16 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" NE  ARG e  16 "
            pdb=" OD2 ASP g  10 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" NE  ARG M  16 "
            pdb=" OD2 ASP O  10 "
     model   vdw
     2.394 3.120
  ... (remaining 74168 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: 0.04
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:             0.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.490
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
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      :  0.009   0.039   9412  Z= 0.417
  Angle     :  1.254   8.355  12636  Z= 0.667
  Chirality :  0.061   0.147   1456
  Planarity :  0.011   0.058   1716
  Dihedral  :  9.670  27.320   3848
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  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: -7.05 (0.13), residues: 1092
  helix: -4.24 (0.08), residues: 988
  sheet:  None (None), residues: 0
  loop : -4.94 (0.43), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG v  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00929 ( 9412)
  covalent geometry    : angle       1.25400 (12636)
  hydrogen bonds       : bond        0.22594 (  468)
  hydrogen bonds       : angle       8.93699 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  545 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 545
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    6 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8373 (ttp-110)
REVERT: E   10 ASP cc_start: 0.8970 (t0) cc_final: 0.8706 (t0)
REVERT: F    6 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8415 (ttp-110)
REVERT: G   10 ASP cc_start: 0.9236 (t0) cc_final: 0.8943 (t0)
REVERT: K   15 VAL cc_start: 0.9481 (t) cc_final: 0.9242 (p)
REVERT: N   10 ASP cc_start: 0.9197 (t0) cc_final: 0.8935 (t0)
REVERT: P   10 ASP cc_start: 0.8947 (t0) cc_final: 0.8717 (t0)
REVERT: Q    6 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8416 (ttm110)
REVERT: S    6 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8306 (ttm-80)
REVERT: T    6 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8596 (ttm110)
REVERT: Y   10 ASP cc_start: 0.9088 (t0) cc_final: 0.8808 (t0)
REVERT: Z    6 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8509 (ttm-80)
REVERT: b   10 ASP cc_start: 0.9091 (t0) cc_final: 0.8881 (t0)
REVERT: c   15 VAL cc_start: 0.9502 (t) cc_final: 0.9168 (p)
REVERT: c   19 VAL cc_start: 0.9375 (t) cc_final: 0.9107 (t)
REVERT: c   22 ARG cc_start: 0.8568 (mmt-90) cc_final: 0.8137 (mmt-90)
REVERT: d   10 ASP cc_start: 0.9044 (t0) cc_final: 0.8794 (t0)
REVERT: f   10 ASP cc_start: 0.9147 (t0) cc_final: 0.8944 (t0)
REVERT: g   10 ASP cc_start: 0.9048 (t0) cc_final: 0.8729 (t0)
REVERT: i   10 ASP cc_start: 0.8748 (t0) cc_final: 0.8503 (t0)
REVERT: k   10 ASP cc_start: 0.9057 (t0) cc_final: 0.8788 (t0)
REVERT: l    5 GLU cc_start: 0.8968 (mp0) cc_final: 0.8660 (mp0)
REVERT: l   10 ASP cc_start: 0.9094 (t0) cc_final: 0.8872 (t0)
REVERT: n    6 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8649 (ttp-110)
REVERT: o   15 VAL cc_start: 0.9438 (t) cc_final: 0.9215 (p)
REVERT: p   10 ASP cc_start: 0.9110 (t0) cc_final: 0.8802 (t0)
REVERT: q   10 ASP cc_start: 0.9142 (t0) cc_final: 0.8909 (t0)
REVERT: u   10 ASP cc_start: 0.9032 (t0) cc_final: 0.8695 (t0)
REVERT: v   10 ASP cc_start: 0.9113 (t0) cc_final: 0.8682 (t0)
REVERT: x   10 ASP cc_start: 0.9008 (t0) cc_final: 0.8775 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 545
  average time/residue: 0.1736
  time to fit residues: 115.7419
Evaluate side-chains
  396 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 396
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   overall best weight:    3.6788

-------------------------------------------------------------------------------
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 = 0.3166 r_free = 0.3166 target = 0.090195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.082419 restraints weight = 19355.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.084615 restraints weight = 10290.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.086102 restraints weight = 6182.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.087124 restraints weight = 4042.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.087825 restraints weight = 2800.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.4695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9412  Z= 0.145
  Angle     :  0.586   5.133  12636  Z= 0.317
  Chirality :  0.041   0.120   1456
  Planarity :  0.010   0.055   1716
  Dihedral  :  4.310  11.873   1404
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  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: -2.90 (0.26), residues: 1092
  helix: -1.91 (0.16), residues: 988
  sheet:  None (None), residues: 0
  loop :  0.87 (0.99), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG V   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9412)
  covalent geometry    : angle       0.58581 (12636)
  hydrogen bonds       : bond        0.04293 (  468)
  hydrogen bonds       : angle       7.11011 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  540 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 540
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 ARG cc_start: 0.8714 (ttp-110) cc_final: 0.8454 (ttm110)
REVERT: E    5 GLU cc_start: 0.9112 (mp0) cc_final: 0.8861 (mm-30)
REVERT: E   10 ASP cc_start: 0.9098 (t0) cc_final: 0.8654 (t0)
REVERT: E   21 ARG cc_start: 0.9181 (mmm-85) cc_final: 0.8941 (mmm-85)
REVERT: F   10 ASP cc_start: 0.9099 (t0) cc_final: 0.8826 (t0)
REVERT: G   21 ARG cc_start: 0.9079 (mmm-85) cc_final: 0.8816 (mmm-85)
REVERT: H   21 ARG cc_start: 0.8953 (mmm-85) cc_final: 0.8473 (mmm-85)
REVERT: I   21 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8800 (mmm-85)
REVERT: K   10 ASP cc_start: 0.9386 (t0) cc_final: 0.9018 (t0)
REVERT: K   22 ARG cc_start: 0.9031 (tpp-160) cc_final: 0.8630 (tpp-160)
REVERT: N   10 ASP cc_start: 0.9205 (t0) cc_final: 0.8775 (t0)
REVERT: N   21 ARG cc_start: 0.8938 (mmm-85) cc_final: 0.8726 (mmm-85)
REVERT: O   10 ASP cc_start: 0.9251 (t0) cc_final: 0.8777 (t0)
REVERT: S   12 ASP cc_start: 0.7805 (t0) cc_final: 0.7560 (t0)
REVERT: V    5 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8741 (mm-30)
REVERT: W   21 ARG cc_start: 0.8948 (mmm-85) cc_final: 0.8542 (mmm-85)
REVERT: Y   10 ASP cc_start: 0.9224 (t0) cc_final: 0.8836 (t0)
REVERT: Z   23 LEU cc_start: 0.8510 (mm) cc_final: 0.7653 (pp)
REVERT: b   10 ASP cc_start: 0.9138 (t0) cc_final: 0.8582 (t0)
REVERT: c   12 ASP cc_start: 0.8365 (t70) cc_final: 0.7756 (t70)
REVERT: d   10 ASP cc_start: 0.9229 (t0) cc_final: 0.9010 (t0)
REVERT: f   10 ASP cc_start: 0.9133 (t0) cc_final: 0.8916 (t0)
REVERT: f   21 ARG cc_start: 0.8867 (mmm-85) cc_final: 0.8628 (mmm-85)
REVERT: g   10 ASP cc_start: 0.9083 (t0) cc_final: 0.8525 (t0)
REVERT: i    5 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8702 (mm-30)
REVERT: i   10 ASP cc_start: 0.9069 (t0) cc_final: 0.8529 (t0)
REVERT: j    6 ARG cc_start: 0.8894 (ttm110) cc_final: 0.8665 (ttm110)
REVERT: j   10 ASP cc_start: 0.9180 (t0) cc_final: 0.8815 (t0)
REVERT: k   10 ASP cc_start: 0.9247 (t0) cc_final: 0.8843 (t0)
REVERT: l    6 ARG cc_start: 0.8894 (ttm110) cc_final: 0.8665 (ttm110)
REVERT: m   21 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8620 (mmm-85)
REVERT: o    5 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8986 (mm-30)
REVERT: p   10 ASP cc_start: 0.9238 (t0) cc_final: 0.8757 (t0)
REVERT: q   10 ASP cc_start: 0.9123 (t0) cc_final: 0.8719 (t0)
REVERT: s   19 VAL cc_start: 0.9581 (t) cc_final: 0.9367 (t)
REVERT: u   10 ASP cc_start: 0.9149 (t0) cc_final: 0.8574 (t0)
REVERT: v   12 ASP cc_start: 0.7762 (t70) cc_final: 0.7512 (t70)
REVERT: w   12 ASP cc_start: 0.8033 (t70) cc_final: 0.7828 (t70)
REVERT: x   10 ASP cc_start: 0.9098 (t0) cc_final: 0.8710 (t0)
REVERT: y    5 GLU cc_start: 0.8900 (mp0) cc_final: 0.8659 (mm-30)
REVERT: y   22 ARG cc_start: 0.9176 (tpp80) cc_final: 0.8685 (ttm110)
REVERT: z    5 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8878 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 540
  average time/residue: 0.1804
  time to fit residues: 118.5936
Evaluate side-chains
  503 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 503
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 80 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 96 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0970
   chunk 85 optimal weight:    8.9990
   overall best weight:    5.6186

-------------------------------------------------------------------------------
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 = 0.3068 r_free = 0.3068 target = 0.084223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.076195 restraints weight = 20207.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.078286 restraints weight = 10884.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.079753 restraints weight = 6646.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.080784 restraints weight = 4435.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.081519 restraints weight = 3150.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.5359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9412  Z= 0.188
  Angle     :  0.671   8.904  12636  Z= 0.339
  Chirality :  0.042   0.123   1456
  Planarity :  0.009   0.048   1716
  Dihedral  :  3.970  11.870   1404
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  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: -1.48 (0.25), residues: 1092
  helix: -0.77 (0.16), residues: 936
  sheet:  None (None), residues: 0
  loop : -1.08 (0.67), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 9412)
  covalent geometry    : angle       0.67145 (12636)
  hydrogen bonds       : bond        0.03956 (  468)
  hydrogen bonds       : angle       7.14878 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  547 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 547
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   12 ASP cc_start: 0.7905 (t70) cc_final: 0.7685 (t70)
REVERT: B    6 ARG cc_start: 0.8774 (ttp-110) cc_final: 0.8518 (ttm110)
REVERT: B   10 ASP cc_start: 0.9247 (t0) cc_final: 0.9014 (t0)
REVERT: C   12 ASP cc_start: 0.7946 (t0) cc_final: 0.7696 (t0)
REVERT: E   10 ASP cc_start: 0.9088 (t0) cc_final: 0.8619 (t0)
REVERT: F   10 ASP cc_start: 0.9191 (t0) cc_final: 0.8853 (t0)
REVERT: F   19 VAL cc_start: 0.9483 (t) cc_final: 0.9264 (t)
REVERT: G    5 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8764 (mm-30)
REVERT: G   10 ASP cc_start: 0.9218 (t0) cc_final: 0.8840 (t0)
REVERT: G   21 ARG cc_start: 0.9175 (mmm-85) cc_final: 0.8944 (mmm-85)
REVERT: H   21 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8665 (mmm-85)
REVERT: J    5 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8713 (mm-30)
REVERT: J    6 ARG cc_start: 0.8776 (ttm110) cc_final: 0.8314 (ttm110)
REVERT: J   12 ASP cc_start: 0.7922 (t0) cc_final: 0.7709 (t0)
REVERT: J   21 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8574 (mmm-85)
REVERT: K    5 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8788 (mm-30)
REVERT: K   10 ASP cc_start: 0.9288 (t0) cc_final: 0.8932 (t0)
REVERT: K   22 ARG cc_start: 0.8972 (tpp-160) cc_final: 0.8688 (tpp-160)
REVERT: L    6 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8435 (ttm110)
REVERT: M   10 ASP cc_start: 0.9167 (t0) cc_final: 0.8810 (t0)
REVERT: N    6 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8339 (ttm110)
REVERT: N   10 ASP cc_start: 0.9180 (t0) cc_final: 0.8792 (t0)
REVERT: O   10 ASP cc_start: 0.9287 (t0) cc_final: 0.8760 (t0)
REVERT: S   22 ARG cc_start: 0.9209 (tpp80) cc_final: 0.8852 (ttm-80)
REVERT: V    5 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8681 (mm-30)
REVERT: W   21 ARG cc_start: 0.9029 (mmm-85) cc_final: 0.8643 (mmm-85)
REVERT: Y   10 ASP cc_start: 0.9217 (t0) cc_final: 0.8843 (t0)
REVERT: Z   10 ASP cc_start: 0.9222 (t0) cc_final: 0.8860 (t0)
REVERT: Z   21 ARG cc_start: 0.9012 (mmm-85) cc_final: 0.8795 (mmm-85)
REVERT: b   10 ASP cc_start: 0.9160 (t0) cc_final: 0.8635 (t0)
REVERT: d   10 ASP cc_start: 0.9269 (t0) cc_final: 0.8969 (t0)
REVERT: f   10 ASP cc_start: 0.9211 (t0) cc_final: 0.8895 (t0)
REVERT: g   10 ASP cc_start: 0.9045 (t0) cc_final: 0.8507 (t0)
REVERT: g   21 ARG cc_start: 0.9043 (mmm-85) cc_final: 0.8712 (tmm-80)
REVERT: i   10 ASP cc_start: 0.9068 (t0) cc_final: 0.8553 (t0)
REVERT: j   10 ASP cc_start: 0.9155 (t0) cc_final: 0.8716 (t0)
REVERT: k   10 ASP cc_start: 0.9229 (t0) cc_final: 0.8775 (t0)
REVERT: l    6 ARG cc_start: 0.8916 (ttm110) cc_final: 0.8647 (ttm110)
REVERT: m   21 ARG cc_start: 0.8994 (mmm-85) cc_final: 0.8747 (mmm-85)
REVERT: n   21 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8504 (mmm-85)
REVERT: o   10 ASP cc_start: 0.9322 (t0) cc_final: 0.8782 (t0)
REVERT: p   10 ASP cc_start: 0.9223 (t0) cc_final: 0.8693 (t0)
REVERT: q   10 ASP cc_start: 0.9138 (t0) cc_final: 0.8669 (t0)
REVERT: q   22 ARG cc_start: 0.9052 (tpp-160) cc_final: 0.8806 (tpp80)
REVERT: s   12 ASP cc_start: 0.7816 (t70) cc_final: 0.7555 (t70)
REVERT: s   19 VAL cc_start: 0.9607 (t) cc_final: 0.9380 (t)
REVERT: t   12 ASP cc_start: 0.8037 (t0) cc_final: 0.7547 (t0)
REVERT: u   10 ASP cc_start: 0.9285 (t0) cc_final: 0.8818 (t0)
REVERT: u   15 VAL cc_start: 0.9394 (p) cc_final: 0.9118 (p)
REVERT: v    6 ARG cc_start: 0.8748 (ttm-80) cc_final: 0.8419 (ttm-80)
REVERT: v   10 ASP cc_start: 0.9214 (t0) cc_final: 0.8814 (t0)
REVERT: w   12 ASP cc_start: 0.8194 (t70) cc_final: 0.7875 (t0)
REVERT: x    6 ARG cc_start: 0.8860 (ttm-80) cc_final: 0.8553 (ttm110)
REVERT: x   10 ASP cc_start: 0.9089 (t0) cc_final: 0.8669 (t0)
REVERT: y    5 GLU cc_start: 0.9035 (mp0) cc_final: 0.8777 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 547
  average time/residue: 0.1751
  time to fit residues: 116.7952
Evaluate side-chains
  515 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 515
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 22 optimal weight:    0.2980
   chunk 67 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9990
   chunk 103 optimal weight:    9.9990
   chunk 96 optimal weight:    8.9990
   chunk 42 optimal weight:    9.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    5.0588

-------------------------------------------------------------------------------
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 = 0.3101 r_free = 0.3101 target = 0.086556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.078963 restraints weight = 20294.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.080992 restraints weight = 10949.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.082375 restraints weight = 6709.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.083333 restraints weight = 4470.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.084030 restraints weight = 3172.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.5695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9412  Z= 0.172
  Angle     :  0.658   7.142  12636  Z= 0.334
  Chirality :  0.041   0.131   1456
  Planarity :  0.009   0.047   1716
  Dihedral  :  3.881  12.092   1404
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  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: -0.48 (0.25), residues: 1092
  helix: -0.04 (0.16), residues: 936
  sheet:  None (None), residues: 0
  loop : -1.19 (0.66), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG M   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 9412)
  covalent geometry    : angle       0.65834 (12636)
  hydrogen bonds       : bond        0.03578 (  468)
  hydrogen bonds       : angle       6.96018 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  551 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 551
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A    5 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8779 (mm-30)
REVERT: B    6 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.8477 (ttm110)
REVERT: B   10 ASP cc_start: 0.9327 (t0) cc_final: 0.9117 (t0)
REVERT: C    5 GLU cc_start: 0.9041 (mp0) cc_final: 0.8568 (mp0)
REVERT: E   10 ASP cc_start: 0.9174 (t0) cc_final: 0.8630 (t0)
REVERT: E   21 ARG cc_start: 0.9058 (mmm-85) cc_final: 0.8847 (mmm-85)
REVERT: F   10 ASP cc_start: 0.9201 (t0) cc_final: 0.8870 (t0)
REVERT: F   19 VAL cc_start: 0.9485 (t) cc_final: 0.9247 (t)
REVERT: G   10 ASP cc_start: 0.9221 (t0) cc_final: 0.8899 (t0)
REVERT: G   21 ARG cc_start: 0.9121 (mmm-85) cc_final: 0.8889 (mmm-85)
REVERT: H   21 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8654 (mmm-85)
REVERT: K    5 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8705 (mm-30)
REVERT: K   10 ASP cc_start: 0.9321 (t0) cc_final: 0.8975 (t0)
REVERT: M   10 ASP cc_start: 0.9180 (t0) cc_final: 0.8787 (t0)
REVERT: N    6 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8339 (ttm110)
REVERT: N   10 ASP cc_start: 0.9145 (t0) cc_final: 0.8767 (t0)
REVERT: O   10 ASP cc_start: 0.9202 (t0) cc_final: 0.8763 (t0)
REVERT: Q    6 ARG cc_start: 0.8670 (ttm110) cc_final: 0.8285 (ttm110)
REVERT: Q   12 ASP cc_start: 0.8379 (t0) cc_final: 0.8166 (t0)
REVERT: S    6 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8337 (ttm-80)
REVERT: S   22 ARG cc_start: 0.9142 (tpp80) cc_final: 0.8888 (ttm-80)
REVERT: U   12 ASP cc_start: 0.7875 (t70) cc_final: 0.7618 (t0)
REVERT: V    5 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8586 (mm-30)
REVERT: W   21 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8581 (mmm-85)
REVERT: Y   10 ASP cc_start: 0.9236 (t0) cc_final: 0.8847 (t0)
REVERT: Z   10 ASP cc_start: 0.9267 (t0) cc_final: 0.8891 (t0)
REVERT: Z   21 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8782 (mmm-85)
REVERT: b   10 ASP cc_start: 0.9103 (t0) cc_final: 0.8632 (t0)
REVERT: c   12 ASP cc_start: 0.8560 (t70) cc_final: 0.8297 (t70)
REVERT: d   10 ASP cc_start: 0.9275 (t0) cc_final: 0.8991 (t0)
REVERT: f   10 ASP cc_start: 0.9191 (t0) cc_final: 0.8979 (t0)
REVERT: g   10 ASP cc_start: 0.9248 (t0) cc_final: 0.8760 (t0)
REVERT: i    6 ARG cc_start: 0.8665 (ttm110) cc_final: 0.8418 (ttm110)
REVERT: i   10 ASP cc_start: 0.9135 (t0) cc_final: 0.8606 (t0)
REVERT: j   10 ASP cc_start: 0.9128 (t0) cc_final: 0.8736 (t0)
REVERT: k   10 ASP cc_start: 0.9308 (t0) cc_final: 0.8843 (t0)
REVERT: l    6 ARG cc_start: 0.8832 (ttm110) cc_final: 0.8595 (ttm110)
REVERT: m    5 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8698 (mm-30)
REVERT: n   21 ARG cc_start: 0.9020 (mmm-85) cc_final: 0.8619 (mmm-85)
REVERT: o   10 ASP cc_start: 0.9371 (t0) cc_final: 0.8864 (t0)
REVERT: p    5 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8644 (mm-30)
REVERT: p   10 ASP cc_start: 0.9251 (t0) cc_final: 0.8726 (t0)
REVERT: q   10 ASP cc_start: 0.9109 (t0) cc_final: 0.8647 (t0)
REVERT: r   23 LEU cc_start: 0.8284 (mm) cc_final: 0.7726 (pp)
REVERT: s   10 ASP cc_start: 0.9358 (t0) cc_final: 0.8863 (t0)
REVERT: t   12 ASP cc_start: 0.7917 (t0) cc_final: 0.7589 (t0)
REVERT: u   10 ASP cc_start: 0.9274 (t0) cc_final: 0.8823 (t0)
REVERT: v    6 ARG cc_start: 0.8713 (ttm-80) cc_final: 0.8331 (ttm-80)
REVERT: v   10 ASP cc_start: 0.9293 (t0) cc_final: 0.8828 (t0)
REVERT: w   12 ASP cc_start: 0.8154 (t70) cc_final: 0.7881 (t0)
REVERT: x    6 ARG cc_start: 0.8748 (ttm-80) cc_final: 0.8535 (ttm110)
REVERT: x   10 ASP cc_start: 0.9120 (t0) cc_final: 0.8820 (t0)
REVERT: y    5 GLU cc_start: 0.8923 (mp0) cc_final: 0.8660 (mm-30)
REVERT: z    6 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8592 (ttm110)
  outliers start: 0
  outliers final: 0
  residues processed: 551
  average time/residue: 0.1748
  time to fit residues: 117.6475
Evaluate side-chains
  518 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 518
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 34 optimal weight:   20.0000
   chunk 32 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   overall best weight:    1.8184

-------------------------------------------------------------------------------
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 = 0.3180 r_free = 0.3180 target = 0.091391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.083318 restraints weight = 19423.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.085652 restraints weight = 9819.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.087223 restraints weight = 5680.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.088296 restraints weight = 3608.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.089048 restraints weight = 2450.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.5982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9412  Z= 0.122
  Angle     :  0.618   5.167  12636  Z= 0.320
  Chirality :  0.039   0.124   1456
  Planarity :  0.008   0.045   1716
  Dihedral  :  3.636  11.088   1404
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  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:  0.43 (0.26), residues: 1092
  helix:  0.61 (0.16), residues: 936
  sheet:  None (None), residues: 0
  loop : -1.08 (0.67), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9412)
  covalent geometry    : angle       0.61796 (12636)
  hydrogen bonds       : bond        0.02750 (  468)
  hydrogen bonds       : angle       6.09794 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  549 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 549
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ASP cc_start: 0.7734 (t70) cc_final: 0.7527 (t70)
REVERT: B    6 ARG cc_start: 0.8798 (ttp-110) cc_final: 0.8530 (ttm110)
REVERT: B   10 ASP cc_start: 0.9288 (t0) cc_final: 0.9007 (t0)
REVERT: B   15 VAL cc_start: 0.9295 (p) cc_final: 0.9048 (p)
REVERT: C   12 ASP cc_start: 0.7984 (t0) cc_final: 0.7754 (t0)
REVERT: E   10 ASP cc_start: 0.9198 (t0) cc_final: 0.8559 (t0)
REVERT: F   10 ASP cc_start: 0.9148 (t0) cc_final: 0.8797 (t0)
REVERT: G   10 ASP cc_start: 0.9211 (t0) cc_final: 0.8782 (t0)
REVERT: G   22 ARG cc_start: 0.9090 (tpp80) cc_final: 0.8643 (tpp-160)
REVERT: H   21 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8741 (mmm-85)
REVERT: I    5 GLU cc_start: 0.9098 (mp0) cc_final: 0.8747 (mm-30)
REVERT: J    6 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8362 (ttm110)
REVERT: K    5 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8799 (mm-30)
REVERT: K   10 ASP cc_start: 0.9321 (t0) cc_final: 0.8877 (t0)
REVERT: M   10 ASP cc_start: 0.9125 (t0) cc_final: 0.8623 (t0)
REVERT: N   10 ASP cc_start: 0.9162 (t0) cc_final: 0.8798 (t0)
REVERT: O   10 ASP cc_start: 0.9246 (t0) cc_final: 0.8675 (t0)
REVERT: P   23 LEU cc_start: 0.8274 (mt) cc_final: 0.8040 (mt)
REVERT: Q    6 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8398 (ttm110)
REVERT: S    6 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8373 (ttm-80)
REVERT: W   21 ARG cc_start: 0.9128 (mmm-85) cc_final: 0.8875 (mmm-85)
REVERT: X   23 LEU cc_start: 0.8289 (mm) cc_final: 0.7267 (pp)
REVERT: Y   10 ASP cc_start: 0.9270 (t0) cc_final: 0.8848 (t0)
REVERT: Z   10 ASP cc_start: 0.9197 (t0) cc_final: 0.8742 (t0)
REVERT: Z   21 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8717 (mmm-85)
REVERT: Z   23 LEU cc_start: 0.8651 (mm) cc_final: 0.8442 (mt)
REVERT: b    6 ARG cc_start: 0.8839 (ttm110) cc_final: 0.8635 (ttm110)
REVERT: b   10 ASP cc_start: 0.9065 (t0) cc_final: 0.8512 (t0)
REVERT: d   10 ASP cc_start: 0.9311 (t0) cc_final: 0.8980 (t0)
REVERT: f   10 ASP cc_start: 0.9134 (t0) cc_final: 0.8909 (t0)
REVERT: f   23 LEU cc_start: 0.8145 (mm) cc_final: 0.7763 (pp)
REVERT: g   10 ASP cc_start: 0.9240 (t0) cc_final: 0.8701 (t0)
REVERT: h   12 ASP cc_start: 0.8196 (t70) cc_final: 0.7901 (t70)
REVERT: j   10 ASP cc_start: 0.9152 (t0) cc_final: 0.8637 (t0)
REVERT: k   10 ASP cc_start: 0.9332 (t0) cc_final: 0.8809 (t0)
REVERT: l    6 ARG cc_start: 0.8954 (ttm110) cc_final: 0.8737 (ttm110)
REVERT: l   21 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7934 (tpp80)
REVERT: l   23 LEU cc_start: 0.7944 (mm) cc_final: 0.6972 (pp)
REVERT: m   10 ASP cc_start: 0.9363 (t0) cc_final: 0.8931 (t0)
REVERT: n    5 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9078 (mm-30)
REVERT: n   21 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8711 (mmm-85)
REVERT: n   23 LEU cc_start: 0.8255 (mm) cc_final: 0.7384 (pp)
REVERT: o   10 ASP cc_start: 0.9327 (t0) cc_final: 0.8761 (t0)
REVERT: p    5 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8677 (mm-30)
REVERT: p   10 ASP cc_start: 0.9140 (t0) cc_final: 0.8564 (t0)
REVERT: p   23 LEU cc_start: 0.8222 (mm) cc_final: 0.7469 (pp)
REVERT: q   10 ASP cc_start: 0.9051 (t0) cc_final: 0.8519 (t0)
REVERT: r   10 ASP cc_start: 0.9233 (t0) cc_final: 0.8832 (t0)
REVERT: r   23 LEU cc_start: 0.8100 (mm) cc_final: 0.7518 (pp)
REVERT: t   12 ASP cc_start: 0.7995 (t0) cc_final: 0.7584 (t0)
REVERT: u   10 ASP cc_start: 0.9399 (t0) cc_final: 0.8825 (t0)
REVERT: v    6 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8348 (ttm-80)
REVERT: v   10 ASP cc_start: 0.9181 (t0) cc_final: 0.8706 (t0)
REVERT: w    5 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8483 (mm-30)
REVERT: w   12 ASP cc_start: 0.8195 (t70) cc_final: 0.7823 (t70)
REVERT: x   10 ASP cc_start: 0.9145 (t0) cc_final: 0.8697 (t0)
REVERT: y    5 GLU cc_start: 0.8983 (mp0) cc_final: 0.8780 (mm-30)
REVERT: y   22 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8558 (ttm110)
REVERT: z    5 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8658 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 549
  average time/residue: 0.1781
  time to fit residues: 119.3860
Evaluate side-chains
  515 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 515
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 74 optimal weight:   20.0000
   chunk 103 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 89 optimal weight:    7.9990
   chunk 30 optimal weight:    8.9990
   chunk 19 optimal weight:    7.9990
   chunk 98 optimal weight:    0.0770
   chunk 40 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    1.3542

-------------------------------------------------------------------------------
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 = 0.3234 r_free = 0.3234 target = 0.094286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.086557 restraints weight = 19381.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.088826 restraints weight = 9811.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.090391 restraints weight = 5674.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.091408 restraints weight = 3579.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.092126 restraints weight = 2423.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.6213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9412  Z= 0.124
  Angle     :  0.638   4.826  12636  Z= 0.329
  Chirality :  0.039   0.139   1456
  Planarity :  0.008   0.049   1716
  Dihedral  :  3.573  10.445   1404
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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:  0.87 (0.26), residues: 1092
  helix:  0.89 (0.17), residues: 936
  sheet:  None (None), residues: 0
  loop : -0.89 (0.68), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG m   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9412)
  covalent geometry    : angle       0.63808 (12636)
  hydrogen bonds       : bond        0.02513 (  468)
  hydrogen bonds       : angle       5.81999 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  537 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 537
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 ASP cc_start: 0.9277 (t0) cc_final: 0.8951 (t0)
REVERT: C    6 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8382 (ttm-80)
REVERT: E   10 ASP cc_start: 0.9237 (t0) cc_final: 0.8609 (t0)
REVERT: F   10 ASP cc_start: 0.9207 (t0) cc_final: 0.8868 (t0)
REVERT: G   10 ASP cc_start: 0.9175 (t0) cc_final: 0.8772 (t0)
REVERT: G   22 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8621 (tpp-160)
REVERT: H   21 ARG cc_start: 0.8956 (mmm-85) cc_final: 0.8696 (mmm-85)
REVERT: I    5 GLU cc_start: 0.9036 (mp0) cc_final: 0.8716 (mm-30)
REVERT: I   21 ARG cc_start: 0.9318 (mmm-85) cc_final: 0.8966 (mmm-85)
REVERT: J    6 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8344 (ttm110)
REVERT: K    5 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8691 (mm-30)
REVERT: K   10 ASP cc_start: 0.9270 (t0) cc_final: 0.8909 (t0)
REVERT: L   22 ARG cc_start: 0.8955 (tpp-160) cc_final: 0.8637 (tpp-160)
REVERT: N   10 ASP cc_start: 0.9195 (t0) cc_final: 0.8810 (t0)
REVERT: O   10 ASP cc_start: 0.9247 (t0) cc_final: 0.8729 (t0)
REVERT: S    6 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8287 (ttm-80)
REVERT: V   12 ASP cc_start: 0.7870 (t0) cc_final: 0.7617 (t0)
REVERT: W   21 ARG cc_start: 0.9023 (mmm-85) cc_final: 0.8791 (mmm-85)
REVERT: X    5 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8685 (mm-30)
REVERT: Y   10 ASP cc_start: 0.9279 (t0) cc_final: 0.8879 (t0)
REVERT: Z   10 ASP cc_start: 0.9180 (t0) cc_final: 0.8852 (t0)
REVERT: Z   23 LEU cc_start: 0.8536 (mm) cc_final: 0.8311 (mt)
REVERT: b    6 ARG cc_start: 0.8782 (ttm110) cc_final: 0.8533 (ttm110)
REVERT: b   10 ASP cc_start: 0.9069 (t0) cc_final: 0.8515 (t0)
REVERT: c   12 ASP cc_start: 0.8692 (t70) cc_final: 0.8430 (t0)
REVERT: d   10 ASP cc_start: 0.9292 (t0) cc_final: 0.8965 (t0)
REVERT: d   23 LEU cc_start: 0.8315 (mm) cc_final: 0.7691 (pp)
REVERT: f   10 ASP cc_start: 0.9092 (t0) cc_final: 0.8773 (t0)
REVERT: f   23 LEU cc_start: 0.8077 (mm) cc_final: 0.7533 (pp)
REVERT: g   10 ASP cc_start: 0.9142 (t0) cc_final: 0.8666 (t0)
REVERT: g   13 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7456 (ttm170)
REVERT: h   23 LEU cc_start: 0.7818 (mt) cc_final: 0.7509 (tt)
REVERT: j   10 ASP cc_start: 0.9197 (t0) cc_final: 0.8789 (t0)
REVERT: k   10 ASP cc_start: 0.9356 (t0) cc_final: 0.8846 (t0)
REVERT: l   12 ASP cc_start: 0.7862 (t70) cc_final: 0.7399 (t70)
REVERT: m   10 ASP cc_start: 0.9344 (t0) cc_final: 0.8959 (t0)
REVERT: n    5 GLU cc_start: 0.9247 (mm-30) cc_final: 0.9031 (mm-30)
REVERT: n   21 ARG cc_start: 0.8821 (mmm-85) cc_final: 0.8588 (mmm-85)
REVERT: o   10 ASP cc_start: 0.9364 (t0) cc_final: 0.8891 (t0)
REVERT: p   10 ASP cc_start: 0.9137 (t0) cc_final: 0.8637 (t0)
REVERT: p   23 LEU cc_start: 0.7925 (mm) cc_final: 0.7161 (pp)
REVERT: q   10 ASP cc_start: 0.9070 (t0) cc_final: 0.8619 (t0)
REVERT: r   10 ASP cc_start: 0.9271 (t0) cc_final: 0.8960 (t0)
REVERT: t   12 ASP cc_start: 0.7454 (t0) cc_final: 0.7201 (t0)
REVERT: u   10 ASP cc_start: 0.9416 (t0) cc_final: 0.8859 (t0)
REVERT: v    5 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8799 (mm-30)
REVERT: v    6 ARG cc_start: 0.8745 (ttm-80) cc_final: 0.8385 (ttm-80)
REVERT: v   10 ASP cc_start: 0.9176 (t0) cc_final: 0.8788 (t0)
REVERT: w    5 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8467 (mm-30)
REVERT: w   12 ASP cc_start: 0.7980 (t70) cc_final: 0.7646 (t0)
REVERT: w   22 ARG cc_start: 0.9049 (tpp80) cc_final: 0.8691 (tpp-160)
REVERT: x   10 ASP cc_start: 0.9121 (t0) cc_final: 0.8699 (t0)
REVERT: y    5 GLU cc_start: 0.8933 (mp0) cc_final: 0.8724 (mm-30)
REVERT: y   22 ARG cc_start: 0.8932 (tpp80) cc_final: 0.8477 (ttm110)
REVERT: z   12 ASP cc_start: 0.7941 (t70) cc_final: 0.7722 (t0)
REVERT: z   15 VAL cc_start: 0.8826 (p) cc_final: 0.8621 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 537
  average time/residue: 0.1828
  time to fit residues: 118.8863
Evaluate side-chains
  510 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 510
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 72 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   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 = 0.3157 r_free = 0.3157 target = 0.089738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.081852 restraints weight = 19953.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.084073 restraints weight = 10356.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.085582 restraints weight = 6158.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.086614 restraints weight = 3980.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.087330 restraints weight = 2739.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.6319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9412  Z= 0.153
  Angle     :  0.685   9.021  12636  Z= 0.348
  Chirality :  0.040   0.224   1456
  Planarity :  0.009   0.056   1716
  Dihedral  :  3.691  10.937   1404
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 16.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  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:  1.03 (0.26), residues: 1092
  helix:  1.00 (0.16), residues: 936
  sheet:  None (None), residues: 0
  loop : -0.86 (0.68), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG m   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 9412)
  covalent geometry    : angle       0.68458 (12636)
  hydrogen bonds       : bond        0.03077 (  468)
  hydrogen bonds       : angle       6.38201 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  518 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 518
  time to evaluate  : 0.284 
Fit side-chains
REVERT: B   10 ASP cc_start: 0.9310 (t0) cc_final: 0.9044 (t0)
REVERT: C    6 ARG cc_start: 0.8523 (ttp-110) cc_final: 0.8244 (ttm-80)
REVERT: E   10 ASP cc_start: 0.9213 (t0) cc_final: 0.8680 (t0)
REVERT: F   10 ASP cc_start: 0.9249 (t0) cc_final: 0.8928 (t0)
REVERT: G    5 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8643 (mm-30)
REVERT: G   10 ASP cc_start: 0.9221 (t0) cc_final: 0.8815 (t0)
REVERT: G   22 ARG cc_start: 0.9001 (tpp80) cc_final: 0.8159 (tpp-160)
REVERT: I    5 GLU cc_start: 0.9005 (mp0) cc_final: 0.8567 (mm-30)
REVERT: I   21 ARG cc_start: 0.9318 (mmm-85) cc_final: 0.9027 (mmm-85)
REVERT: K    5 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8626 (mm-30)
REVERT: K   10 ASP cc_start: 0.9266 (t0) cc_final: 0.9005 (t0)
REVERT: L   10 ASP cc_start: 0.9162 (t0) cc_final: 0.8937 (t0)
REVERT: L   21 ARG cc_start: 0.9071 (mmm-85) cc_final: 0.8797 (mmm-85)
REVERT: L   22 ARG cc_start: 0.8838 (tpp-160) cc_final: 0.8549 (tpp-160)
REVERT: M    6 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8444 (ttm110)
REVERT: M   10 ASP cc_start: 0.9205 (t0) cc_final: 0.8751 (t0)
REVERT: N   10 ASP cc_start: 0.9210 (t0) cc_final: 0.8933 (t0)
REVERT: O   10 ASP cc_start: 0.9254 (t0) cc_final: 0.8772 (t0)
REVERT: P   12 ASP cc_start: 0.8170 (t0) cc_final: 0.7868 (t0)
REVERT: T    6 ARG cc_start: 0.8897 (ttp-110) cc_final: 0.8683 (ttm110)
REVERT: V   10 ASP cc_start: 0.9339 (t0) cc_final: 0.8880 (t0)
REVERT: W    5 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8546 (mm-30)
REVERT: W   21 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8677 (mmm-85)
REVERT: W   22 ARG cc_start: 0.8990 (tpp-160) cc_final: 0.8778 (ttm-80)
REVERT: X    5 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8617 (mm-30)
REVERT: X   10 ASP cc_start: 0.9091 (t0) cc_final: 0.8865 (t0)
REVERT: Y   10 ASP cc_start: 0.9290 (t0) cc_final: 0.9009 (t0)
REVERT: Z   10 ASP cc_start: 0.9206 (t0) cc_final: 0.8854 (t0)
REVERT: b   10 ASP cc_start: 0.9059 (t0) cc_final: 0.8564 (t0)
REVERT: c   12 ASP cc_start: 0.8388 (t70) cc_final: 0.8152 (t0)
REVERT: d   10 ASP cc_start: 0.9291 (t0) cc_final: 0.9030 (t0)
REVERT: d   23 LEU cc_start: 0.8457 (mm) cc_final: 0.8250 (mt)
REVERT: g   10 ASP cc_start: 0.9271 (t0) cc_final: 0.8733 (t0)
REVERT: i   10 ASP cc_start: 0.9208 (t0) cc_final: 0.8685 (t0)
REVERT: j   10 ASP cc_start: 0.9166 (t0) cc_final: 0.8789 (t0)
REVERT: k   10 ASP cc_start: 0.9380 (t0) cc_final: 0.8968 (t0)
REVERT: l   10 ASP cc_start: 0.9314 (t0) cc_final: 0.8969 (t0)
REVERT: m   10 ASP cc_start: 0.9387 (t0) cc_final: 0.9043 (t0)
REVERT: n    5 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8957 (mm-30)
REVERT: n   21 ARG cc_start: 0.9020 (mmm-85) cc_final: 0.8751 (mmm-85)
REVERT: o   10 ASP cc_start: 0.9314 (t0) cc_final: 0.8901 (t0)
REVERT: p   10 ASP cc_start: 0.9133 (t0) cc_final: 0.8649 (t0)
REVERT: q   10 ASP cc_start: 0.9171 (t0) cc_final: 0.8671 (t0)
REVERT: r   10 ASP cc_start: 0.9233 (t0) cc_final: 0.9023 (t0)
REVERT: t   12 ASP cc_start: 0.7631 (t0) cc_final: 0.7373 (t0)
REVERT: u   10 ASP cc_start: 0.9424 (t0) cc_final: 0.9068 (t0)
REVERT: v    6 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8445 (ttm-80)
REVERT: v   10 ASP cc_start: 0.9324 (t0) cc_final: 0.8829 (t0)
REVERT: w    5 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8483 (mm-30)
REVERT: w   12 ASP cc_start: 0.8022 (t70) cc_final: 0.7705 (t0)
REVERT: w   21 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8650 (tmm-80)
REVERT: x   10 ASP cc_start: 0.9095 (t0) cc_final: 0.8794 (t0)
REVERT: y    5 GLU cc_start: 0.8892 (mp0) cc_final: 0.8671 (mm-30)
REVERT: y   22 ARG cc_start: 0.9123 (tpp80) cc_final: 0.8642 (ttm110)
REVERT: z   12 ASP cc_start: 0.8339 (t70) cc_final: 0.7677 (t70)
REVERT: z   15 VAL cc_start: 0.9019 (p) cc_final: 0.8640 (m)
REVERT: z   21 ARG cc_start: 0.8933 (mmm-85) cc_final: 0.8635 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 518
  average time/residue: 0.1792
  time to fit residues: 112.9892
Evaluate side-chains
  498 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 498
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    0.2980
   chunk 46 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 36 optimal weight:   20.0000
   chunk 87 optimal weight:    0.9980
   chunk 58 optimal weight:   20.0000
   chunk 84 optimal weight:    2.9990
   chunk 92 optimal weight:   10.0000
   overall best weight:    2.2586

-------------------------------------------------------------------------------
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 = 0.3223 r_free = 0.3223 target = 0.093478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.085759 restraints weight = 19387.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.087954 restraints weight = 10112.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.089464 restraints weight = 6018.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.090510 restraints weight = 3867.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.091222 restraints weight = 2644.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.6457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9412  Z= 0.137
  Angle     :  0.693   8.791  12636  Z= 0.355
  Chirality :  0.039   0.120   1456
  Planarity :  0.009   0.059   1716
  Dihedral  :  3.611  11.704   1404
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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:  1.30 (0.27), residues: 1092
  helix:  1.20 (0.17), residues: 936
  sheet:  None (None), residues: 0
  loop : -0.84 (0.67), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG m   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9412)
  covalent geometry    : angle       0.69287 (12636)
  hydrogen bonds       : bond        0.02597 (  468)
  hydrogen bonds       : angle       5.96689 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  521 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 521
  time to evaluate  : 0.413 
Fit side-chains
REVERT: B   10 ASP cc_start: 0.9289 (t0) cc_final: 0.9009 (t0)
REVERT: C    5 GLU cc_start: 0.9049 (mp0) cc_final: 0.8559 (mp0)
REVERT: C    6 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.8189 (ttm-80)
REVERT: E   10 ASP cc_start: 0.9200 (t0) cc_final: 0.8655 (t0)
REVERT: F   10 ASP cc_start: 0.9261 (t0) cc_final: 0.8984 (t0)
REVERT: G   10 ASP cc_start: 0.9192 (t0) cc_final: 0.8783 (t0)
REVERT: I    5 GLU cc_start: 0.9040 (mp0) cc_final: 0.8614 (mm-30)
REVERT: I   21 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.8982 (mmm-85)
REVERT: K    5 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8597 (mm-30)
REVERT: K   10 ASP cc_start: 0.9279 (t0) cc_final: 0.8944 (t0)
REVERT: L   10 ASP cc_start: 0.9151 (t0) cc_final: 0.8836 (t0)
REVERT: M   10 ASP cc_start: 0.9199 (t0) cc_final: 0.8725 (t0)
REVERT: N   10 ASP cc_start: 0.9228 (t0) cc_final: 0.8954 (t0)
REVERT: O   10 ASP cc_start: 0.9204 (t0) cc_final: 0.8730 (t0)
REVERT: W    5 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8569 (mm-30)
REVERT: W   21 ARG cc_start: 0.8917 (mmm-85) cc_final: 0.8608 (mmm-85)
REVERT: X    5 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8565 (mm-30)
REVERT: X   10 ASP cc_start: 0.9099 (t0) cc_final: 0.8886 (t0)
REVERT: Y   10 ASP cc_start: 0.9281 (t0) cc_final: 0.8940 (t0)
REVERT: Z   10 ASP cc_start: 0.9175 (t0) cc_final: 0.8830 (t0)
REVERT: Z   23 LEU cc_start: 0.7906 (mt) cc_final: 0.7604 (mt)
REVERT: b   10 ASP cc_start: 0.9044 (t0) cc_final: 0.8532 (t0)
REVERT: c   12 ASP cc_start: 0.8457 (t70) cc_final: 0.8201 (t0)
REVERT: d   10 ASP cc_start: 0.9295 (t0) cc_final: 0.9015 (t0)
REVERT: d   23 LEU cc_start: 0.8293 (mm) cc_final: 0.8080 (mt)
REVERT: e   10 ASP cc_start: 0.9283 (t0) cc_final: 0.8993 (t0)
REVERT: f   23 LEU cc_start: 0.8204 (mm) cc_final: 0.7510 (pp)
REVERT: g   10 ASP cc_start: 0.9238 (t0) cc_final: 0.8704 (t0)
REVERT: h   12 ASP cc_start: 0.8102 (t70) cc_final: 0.7897 (t70)
REVERT: i   10 ASP cc_start: 0.9193 (t0) cc_final: 0.8673 (t0)
REVERT: j   10 ASP cc_start: 0.9174 (t0) cc_final: 0.8796 (t0)
REVERT: k   10 ASP cc_start: 0.9366 (t0) cc_final: 0.8988 (t0)
REVERT: l   10 ASP cc_start: 0.9284 (t0) cc_final: 0.8987 (t0)
REVERT: m   10 ASP cc_start: 0.9360 (t0) cc_final: 0.8971 (t0)
REVERT: n    5 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8936 (mm-30)
REVERT: n   21 ARG cc_start: 0.8942 (mmm-85) cc_final: 0.8702 (mmm-85)
REVERT: o   10 ASP cc_start: 0.9322 (t0) cc_final: 0.8913 (t0)
REVERT: p   10 ASP cc_start: 0.9099 (t0) cc_final: 0.8649 (t0)
REVERT: q   10 ASP cc_start: 0.9136 (t0) cc_final: 0.8707 (t0)
REVERT: r   10 ASP cc_start: 0.9229 (t0) cc_final: 0.8971 (t0)
REVERT: t    6 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8434 (ttm-80)
REVERT: t   12 ASP cc_start: 0.7552 (t0) cc_final: 0.7257 (t0)
REVERT: u   10 ASP cc_start: 0.9422 (t0) cc_final: 0.9055 (t0)
REVERT: v    6 ARG cc_start: 0.8742 (ttm-80) cc_final: 0.8422 (ttm-80)
REVERT: v   10 ASP cc_start: 0.9284 (t0) cc_final: 0.8846 (t0)
REVERT: w    5 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8424 (mm-30)
REVERT: w   12 ASP cc_start: 0.7965 (t70) cc_final: 0.7668 (t0)
REVERT: w   22 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8388 (ttm170)
REVERT: x   10 ASP cc_start: 0.9105 (t0) cc_final: 0.8775 (t0)
REVERT: y    5 GLU cc_start: 0.8861 (mp0) cc_final: 0.8643 (mm-30)
REVERT: y   22 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8543 (ttm110)
REVERT: z   12 ASP cc_start: 0.8274 (t70) cc_final: 0.7624 (t70)
REVERT: z   15 VAL cc_start: 0.8935 (p) cc_final: 0.8587 (m)
REVERT: z   21 ARG cc_start: 0.8875 (mmm-85) cc_final: 0.8599 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 521
  average time/residue: 0.1850
  time to fit residues: 116.7831
Evaluate side-chains
  498 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 498
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 84 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 85 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.3170 r_free = 0.3170 target = 0.089960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.081433 restraints weight = 20235.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.083780 restraints weight = 10433.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.085414 restraints weight = 6183.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.086510 restraints weight = 4024.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.087277 restraints weight = 2815.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.6494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9412  Z= 0.178
  Angle     :  0.750   8.546  12636  Z= 0.382
  Chirality :  0.041   0.125   1456
  Planarity :  0.009   0.069   1716
  Dihedral  :  3.851  11.642   1404
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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:  1.31 (0.26), residues: 1092
  helix:  1.22 (0.17), residues: 936
  sheet:  None (None), residues: 0
  loop : -0.95 (0.66), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG m   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 9412)
  covalent geometry    : angle       0.75026 (12636)
  hydrogen bonds       : bond        0.03226 (  468)
  hydrogen bonds       : angle       6.64053 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  514 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 514
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A   12 ASP cc_start: 0.7743 (t70) cc_final: 0.7512 (t0)
REVERT: B   10 ASP cc_start: 0.9296 (t0) cc_final: 0.8999 (t0)
REVERT: C    5 GLU cc_start: 0.9102 (mp0) cc_final: 0.8553 (mp0)
REVERT: C    6 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8293 (ttm-80)
REVERT: D    2 GLU cc_start: 0.8491 (mp0) cc_final: 0.8275 (mp0)
REVERT: E   10 ASP cc_start: 0.9256 (t0) cc_final: 0.8706 (t0)
REVERT: F   10 ASP cc_start: 0.9297 (t0) cc_final: 0.8983 (t0)
REVERT: F   12 ASP cc_start: 0.7720 (t70) cc_final: 0.7449 (t70)
REVERT: G   10 ASP cc_start: 0.9251 (t0) cc_final: 0.8795 (t0)
REVERT: I   21 ARG cc_start: 0.9431 (mmm-85) cc_final: 0.9048 (mmm-85)
REVERT: K    5 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8758 (mm-30)
REVERT: K   10 ASP cc_start: 0.9310 (t0) cc_final: 0.8956 (t0)
REVERT: L   10 ASP cc_start: 0.9077 (t0) cc_final: 0.8814 (t0)
REVERT: M    6 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8486 (ttm110)
REVERT: M   10 ASP cc_start: 0.9202 (t0) cc_final: 0.8723 (t0)
REVERT: N   10 ASP cc_start: 0.9221 (t0) cc_final: 0.8948 (t0)
REVERT: O   10 ASP cc_start: 0.9323 (t0) cc_final: 0.8814 (t0)
REVERT: P   12 ASP cc_start: 0.7987 (t70) cc_final: 0.7628 (t0)
REVERT: Q   10 ASP cc_start: 0.8770 (t0) cc_final: 0.8525 (t0)
REVERT: Q   14 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8962 (tp30)
REVERT: T   10 ASP cc_start: 0.9169 (t0) cc_final: 0.8839 (t0)
REVERT: V   10 ASP cc_start: 0.9351 (t0) cc_final: 0.8845 (t0)
REVERT: W    5 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8635 (mm-30)
REVERT: W   21 ARG cc_start: 0.9046 (mmm-85) cc_final: 0.8825 (mmm-85)
REVERT: X   10 ASP cc_start: 0.9169 (t0) cc_final: 0.8927 (t0)
REVERT: Y   10 ASP cc_start: 0.9250 (t0) cc_final: 0.8959 (t0)
REVERT: Z   10 ASP cc_start: 0.9245 (t0) cc_final: 0.8888 (t0)
REVERT: b   10 ASP cc_start: 0.9046 (t0) cc_final: 0.8500 (t0)
REVERT: c   12 ASP cc_start: 0.8593 (t70) cc_final: 0.8308 (t0)
REVERT: d   10 ASP cc_start: 0.9325 (t0) cc_final: 0.9013 (t0)
REVERT: e   10 ASP cc_start: 0.9327 (t0) cc_final: 0.9032 (t0)
REVERT: g   10 ASP cc_start: 0.9241 (t0) cc_final: 0.8687 (t0)
REVERT: h   12 ASP cc_start: 0.8162 (t70) cc_final: 0.7901 (t70)
REVERT: i   10 ASP cc_start: 0.9202 (t0) cc_final: 0.8657 (t0)
REVERT: j   10 ASP cc_start: 0.9230 (t0) cc_final: 0.8811 (t0)
REVERT: k   10 ASP cc_start: 0.9376 (t0) cc_final: 0.8958 (t0)
REVERT: m   10 ASP cc_start: 0.9431 (t0) cc_final: 0.9020 (t0)
REVERT: n    5 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9044 (mm-30)
REVERT: n   10 ASP cc_start: 0.9285 (t0) cc_final: 0.8977 (t0)
REVERT: n   21 ARG cc_start: 0.9116 (mmm-85) cc_final: 0.8788 (mmm-85)
REVERT: o   10 ASP cc_start: 0.9358 (t0) cc_final: 0.9057 (t0)
REVERT: p   10 ASP cc_start: 0.9264 (t0) cc_final: 0.8631 (t0)
REVERT: q   10 ASP cc_start: 0.9173 (t0) cc_final: 0.8688 (t0)
REVERT: r   10 ASP cc_start: 0.9198 (t0) cc_final: 0.8947 (t0)
REVERT: s   10 ASP cc_start: 0.9335 (t0) cc_final: 0.8982 (t0)
REVERT: s   15 VAL cc_start: 0.9271 (p) cc_final: 0.9044 (p)
REVERT: t    6 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8491 (ttm110)
REVERT: t   12 ASP cc_start: 0.7756 (t0) cc_final: 0.7389 (t0)
REVERT: u   10 ASP cc_start: 0.9409 (t0) cc_final: 0.9041 (t0)
REVERT: v   10 ASP cc_start: 0.9356 (t0) cc_final: 0.8843 (t0)
REVERT: w    5 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8585 (mm-30)
REVERT: w   12 ASP cc_start: 0.8117 (t70) cc_final: 0.7740 (t0)
REVERT: x   10 ASP cc_start: 0.9151 (t0) cc_final: 0.8826 (t0)
REVERT: y    5 GLU cc_start: 0.8995 (mp0) cc_final: 0.8780 (mm-30)
REVERT: y   22 ARG cc_start: 0.9023 (tpp80) cc_final: 0.8464 (ttm110)
REVERT: z   12 ASP cc_start: 0.8333 (t70) cc_final: 0.7629 (t70)
REVERT: z   15 VAL cc_start: 0.9043 (p) cc_final: 0.8613 (m)
REVERT: z   21 ARG cc_start: 0.9027 (mmm-85) cc_final: 0.8753 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 514
  average time/residue: 0.1795
  time to fit residues: 112.3560
Evaluate side-chains
  495 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 495
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0000
   chunk 27 optimal weight:    8.9990
   chunk 61 optimal weight:    0.6980
   chunk 81 optimal weight:    6.9990
   chunk 76 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0570
   chunk 85 optimal weight:    6.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    2.1506

-------------------------------------------------------------------------------
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 = 0.3175 r_free = 0.3175 target = 0.092104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.084630 restraints weight = 19779.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.086730 restraints weight = 10455.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.088180 restraints weight = 6311.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.089186 restraints weight = 4069.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.089892 restraints weight = 2782.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.6649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9412  Z= 0.146
  Angle     :  0.741   8.104  12636  Z= 0.379
  Chirality :  0.040   0.128   1456
  Planarity :  0.009   0.064   1716
  Dihedral  :  3.758  12.593   1404
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  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:  1.50 (0.27), residues: 1092
  helix:  1.34 (0.17), residues: 936
  sheet:  None (None), residues: 0
  loop : -0.84 (0.67), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG w   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9412)
  covalent geometry    : angle       0.74139 (12636)
  hydrogen bonds       : bond        0.02617 (  468)
  hydrogen bonds       : angle       6.16210 ( 1404)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  503 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 503
  time to evaluate  : 0.392 
Fit side-chains
REVERT: B   10 ASP cc_start: 0.9277 (t0) cc_final: 0.8986 (t0)
REVERT: C    5 GLU cc_start: 0.9016 (mp0) cc_final: 0.8614 (mp0)
REVERT: C    6 ARG cc_start: 0.8518 (ttp-110) cc_final: 0.8190 (ttp-110)
REVERT: D    2 GLU cc_start: 0.8345 (mp0) cc_final: 0.8136 (mp0)
REVERT: E    6 ARG cc_start: 0.8699 (ttm110) cc_final: 0.8459 (ttm-80)
REVERT: E   10 ASP cc_start: 0.9210 (t0) cc_final: 0.8708 (t0)
REVERT: F   10 ASP cc_start: 0.9242 (t0) cc_final: 0.8956 (t0)
REVERT: G   10 ASP cc_start: 0.9160 (t0) cc_final: 0.8835 (t0)
REVERT: I    5 GLU cc_start: 0.8920 (mp0) cc_final: 0.8561 (mm-30)
REVERT: I   21 ARG cc_start: 0.9349 (mmm-85) cc_final: 0.9015 (mmm-85)
REVERT: K    5 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8668 (mm-30)
REVERT: K   10 ASP cc_start: 0.9312 (t0) cc_final: 0.9014 (t0)
REVERT: L   10 ASP cc_start: 0.9090 (t0) cc_final: 0.8784 (t0)
REVERT: M   10 ASP cc_start: 0.9165 (t0) cc_final: 0.8707 (t0)
REVERT: N   10 ASP cc_start: 0.9169 (t0) cc_final: 0.8936 (t0)
REVERT: O   10 ASP cc_start: 0.9194 (t0) cc_final: 0.8743 (t0)
REVERT: P   12 ASP cc_start: 0.7729 (t70) cc_final: 0.7487 (t0)
REVERT: V   10 ASP cc_start: 0.9280 (t0) cc_final: 0.8825 (t0)
REVERT: W    5 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8589 (mm-30)
REVERT: W   21 ARG cc_start: 0.8934 (mmm-85) cc_final: 0.8449 (mmm-85)
REVERT: Y   10 ASP cc_start: 0.9314 (t0) cc_final: 0.9001 (t0)
REVERT: Z   10 ASP cc_start: 0.9150 (t0) cc_final: 0.8818 (t0)
REVERT: b   10 ASP cc_start: 0.9014 (t0) cc_final: 0.8547 (t0)
REVERT: b   23 LEU cc_start: 0.8705 (mm) cc_final: 0.7989 (pp)
REVERT: c   12 ASP cc_start: 0.8331 (t70) cc_final: 0.8116 (t0)
REVERT: d   10 ASP cc_start: 0.9287 (t0) cc_final: 0.8891 (t0)
REVERT: g   10 ASP cc_start: 0.9258 (t0) cc_final: 0.8907 (t0)
REVERT: h   12 ASP cc_start: 0.8141 (t70) cc_final: 0.7905 (t70)
REVERT: i   10 ASP cc_start: 0.9196 (t0) cc_final: 0.8642 (t0)
REVERT: j   10 ASP cc_start: 0.9182 (t0) cc_final: 0.8785 (t0)
REVERT: k   10 ASP cc_start: 0.9358 (t0) cc_final: 0.8976 (t0)
REVERT: m   10 ASP cc_start: 0.9349 (t0) cc_final: 0.8748 (t0)
REVERT: n   12 ASP cc_start: 0.7161 (t0) cc_final: 0.6778 (t0)
REVERT: n   21 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8574 (mmm-85)
REVERT: o   10 ASP cc_start: 0.9273 (t0) cc_final: 0.8927 (t0)
REVERT: p   10 ASP cc_start: 0.9230 (t0) cc_final: 0.8702 (t0)
REVERT: q   10 ASP cc_start: 0.9158 (t0) cc_final: 0.8773 (t0)
REVERT: r   10 ASP cc_start: 0.9160 (t0) cc_final: 0.8928 (t0)
REVERT: r   23 LEU cc_start: 0.7744 (mt) cc_final: 0.7520 (tt)
REVERT: t    6 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8463 (ttm110)
REVERT: u   10 ASP cc_start: 0.9411 (t0) cc_final: 0.9055 (t0)
REVERT: v    6 ARG cc_start: 0.8793 (ttm-80) cc_final: 0.8431 (ttm-80)
REVERT: v   10 ASP cc_start: 0.9281 (t0) cc_final: 0.8864 (t0)
REVERT: w    5 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: w   12 ASP cc_start: 0.8018 (t70) cc_final: 0.7669 (t0)
REVERT: w   22 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8769 (ttm110)
REVERT: x   10 ASP cc_start: 0.9052 (t0) cc_final: 0.8794 (t0)
REVERT: y    5 GLU cc_start: 0.8903 (mp0) cc_final: 0.8667 (mm-30)
REVERT: y   22 ARG cc_start: 0.9059 (tpp80) cc_final: 0.8629 (ttm110)
REVERT: z   12 ASP cc_start: 0.8032 (t70) cc_final: 0.7407 (t70)
REVERT: z   15 VAL cc_start: 0.8872 (p) cc_final: 0.8454 (m)
REVERT: z   21 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.8631 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 503
  average time/residue: 0.1818
  time to fit residues: 111.1213
Evaluate side-chains
  487 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 487
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0010
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    1.7392

-------------------------------------------------------------------------------
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 = 0.3221 r_free = 0.3221 target = 0.094456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.086859 restraints weight = 19349.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.089059 restraints weight = 10159.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.090528 restraints weight = 6015.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.091540 restraints weight = 3870.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.092247 restraints weight = 2645.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.6731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9412  Z= 0.142
  Angle     :  0.742   7.901  12636  Z= 0.379
  Chirality :  0.039   0.118   1456
  Planarity :  0.009   0.064   1716
  Dihedral  :  3.677  11.326   1404
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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:  1.60 (0.27), residues: 1092
  helix:  1.40 (0.17), residues: 936
  sheet:  None (None), residues: 0
  loop : -0.72 (0.68), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG m   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9412)
  covalent geometry    : angle       0.74244 (12636)
  hydrogen bonds       : bond        0.02360 (  468)
  hydrogen bonds       : angle       5.95862 ( 1404)

===============================================================================
Job complete
usr+sys time: 2052.49 seconds
wall clock time: 35 minutes 49.55 seconds (2149.55 seconds total)