Starting phenix.real_space_refine
on Wed Mar  4 11:01:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rb9_4789/03_2026/6rb9_4789.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rb9_4789/03_2026/6rb9_4789.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rb9_4789/03_2026/6rb9_4789.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rb9_4789/03_2026/6rb9_4789.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rb9_4789/03_2026/6rb9_4789.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rb9_4789/03_2026/6rb9_4789.map"
  }
  resolution = 3.2
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    8414      2.51       5
     N    2212      2.21       5
     O    2730      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13391
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1913
          Classifications: {'peptide': 248}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 9, 'TRANS': 238}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 1.52, per 1000 atoms: 0.11
  Number of scatterers: 13391
  At special positions: 0
  Unit cell: (129.47, 129.47, 114.49, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O    2730      8.00
     N    2212      7.00
     C    8414      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 553.6 milliseconds
  

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3262

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 0 sheets defined
      22.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 38
      removed outlier: 3.768A  pdb=" N   LYS A  26 " --> pdb=" O   THR A  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 38
      removed outlier: 3.768A  pdb=" N   LYS B  26 " --> pdb=" O   THR B  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 38
      removed outlier: 3.768A  pdb=" N   LYS C  26 " --> pdb=" O   THR C  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 38
      removed outlier: 3.768A  pdb=" N   LYS D  26 " --> pdb=" O   THR D  22 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 38
      removed outlier: 3.768A  pdb=" N   LYS E  26 " --> pdb=" O   THR E  22 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 20 through 38
      removed outlier: 3.768A  pdb=" N   LYS F  26 " --> pdb=" O   THR F  22 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 20 through 38
      removed outlier: 3.768A  pdb=" N   LYS G  26 " --> pdb=" O   THR G  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 40
      removed outlier: 4.444A  pdb=" N   LEU A  23 " --> pdb=" O   ASN A  19 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS A  26 " --> pdb=" O   THR A  22 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   MET A  39 " --> pdb=" O   TYR A  35 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   GLU A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 5.863A  pdb=" N   ALA A  48 " --> pdb=" O   ASN A  45 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   TYR A  49 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   PHE A  50 " --> pdb=" O   MET A  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 50'
    Processing helix  chain 'A' and resid 222 through 224
      No H-bonds generated for 'chain 'A' and resid 222 through 224'
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 5.470A  pdb=" N   LEU A 230 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 40
      removed outlier: 4.444A  pdb=" N   LEU B  23 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS B  26 " --> pdb=" O   THR B  22 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   MET B  39 " --> pdb=" O   TYR B  35 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   GLU B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 50
      removed outlier: 5.863A  pdb=" N   ALA B  48 " --> pdb=" O   ASN B  45 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   TYR B  49 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   PHE B  50 " --> pdb=" O   MET B  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 45 through 50'
    Processing helix  chain 'B' and resid 222 through 224
      No H-bonds generated for 'chain 'B' and resid 222 through 224'
    Processing helix  chain 'B' and resid 226 through 230
      removed outlier: 5.470A  pdb=" N   LEU B 230 " --> pdb=" O   LYS B 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 40
      removed outlier: 4.444A  pdb=" N   LEU C  23 " --> pdb=" O   ASN C  19 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS C  26 " --> pdb=" O   THR C  22 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   MET C  39 " --> pdb=" O   TYR C  35 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU C  40 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 50
      removed outlier: 5.863A  pdb=" N   ALA C  48 " --> pdb=" O   ASN C  45 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   TYR C  49 " --> pdb=" O   ALA C  46 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   PHE C  50 " --> pdb=" O   MET C  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 50'
    Processing helix  chain 'C' and resid 222 through 224
      No H-bonds generated for 'chain 'C' and resid 222 through 224'
    Processing helix  chain 'C' and resid 226 through 230
      removed outlier: 5.471A  pdb=" N   LEU C 230 " --> pdb=" O   LYS C 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 40
      removed outlier: 4.443A  pdb=" N   LEU D  23 " --> pdb=" O   ASN D  19 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS D  26 " --> pdb=" O   THR D  22 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   MET D  39 " --> pdb=" O   TYR D  35 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU D  40 " --> pdb=" O   LEU D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 50
      removed outlier: 5.863A  pdb=" N   ALA D  48 " --> pdb=" O   ASN D  45 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   TYR D  49 " --> pdb=" O   ALA D  46 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   PHE D  50 " --> pdb=" O   MET D  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 50'
    Processing helix  chain 'D' and resid 222 through 224
      No H-bonds generated for 'chain 'D' and resid 222 through 224'
    Processing helix  chain 'D' and resid 226 through 230
      removed outlier: 5.470A  pdb=" N   LEU D 230 " --> pdb=" O   LYS D 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 19 through 40
      removed outlier: 4.444A  pdb=" N   LEU E  23 " --> pdb=" O   ASN E  19 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS E  26 " --> pdb=" O   THR E  22 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   MET E  39 " --> pdb=" O   TYR E  35 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU E  40 " --> pdb=" O   LEU E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 50
      removed outlier: 5.862A  pdb=" N   ALA E  48 " --> pdb=" O   ASN E  45 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   TYR E  49 " --> pdb=" O   ALA E  46 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   PHE E  50 " --> pdb=" O   MET E  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 45 through 50'
    Processing helix  chain 'E' and resid 222 through 224
      No H-bonds generated for 'chain 'E' and resid 222 through 224'
    Processing helix  chain 'E' and resid 226 through 230
      removed outlier: 5.471A  pdb=" N   LEU E 230 " --> pdb=" O   LYS E 227 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 19 through 40
      removed outlier: 4.444A  pdb=" N   LEU F  23 " --> pdb=" O   ASN F  19 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS F  26 " --> pdb=" O   THR F  22 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   MET F  39 " --> pdb=" O   TYR F  35 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU F  40 " --> pdb=" O   LEU F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 50
      removed outlier: 5.862A  pdb=" N   ALA F  48 " --> pdb=" O   ASN F  45 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   TYR F  49 " --> pdb=" O   ALA F  46 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   PHE F  50 " --> pdb=" O   MET F  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 45 through 50'
    Processing helix  chain 'F' and resid 222 through 224
      No H-bonds generated for 'chain 'F' and resid 222 through 224'
    Processing helix  chain 'F' and resid 226 through 230
      removed outlier: 5.470A  pdb=" N   LEU F 230 " --> pdb=" O   LYS F 227 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 19 through 40
      removed outlier: 4.444A  pdb=" N   LEU G  23 " --> pdb=" O   ASN G  19 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS G  26 " --> pdb=" O   THR G  22 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   MET G  39 " --> pdb=" O   TYR G  35 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLU G  40 " --> pdb=" O   LEU G  36 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 50
      removed outlier: 5.863A  pdb=" N   ALA G  48 " --> pdb=" O   ASN G  45 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   TYR G  49 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   PHE G  50 " --> pdb=" O   MET G  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 50'
    Processing helix  chain 'G' and resid 222 through 224
      No H-bonds generated for 'chain 'G' and resid 222 through 224'
    Processing helix  chain 'G' and resid 226 through 230
      removed outlier: 5.470A  pdb=" N   LEU G 230 " --> pdb=" O   LYS G 227 " (cutoff:3.500A)

    203 hydrogen bonds defined for protein.
    588 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: 1.53

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 4251
        1.33 -     1.45: 1713
        1.45 -     1.56: 7609
        1.56 -     1.68: 0
        1.68 -     1.80: 63
  Bond restraints: 13636
  Sorted by residual:
  bond pdb=" CB  VAL F 192 "
       pdb=" CG1 VAL F 192 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.18e+00
  bond pdb=" CB  VAL C 192 "
       pdb=" CG1 VAL C 192 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.16e+00
  bond pdb=" CB  VAL E 192 "
       pdb=" CG1 VAL E 192 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.15e+00
  bond pdb=" CB  VAL D 192 "
       pdb=" CG1 VAL D 192 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.14e+00
  bond pdb=" CB  VAL B 192 "
       pdb=" CG1 VAL B 192 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.13e+00
  ... (remaining 13631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 17368
        1.54 -     3.08: 1075
        3.08 -     4.62: 88
        4.62 -     6.16: 26
        6.16 -     7.70: 14
  Bond angle restraints: 18571
  Sorted by residual:
  angle pdb=" N   LYS E  41 "
        pdb=" CA  LYS E  41 "
        pdb=" C   LYS E  41 "
      ideal   model   delta    sigma   weight residual
     112.72  108.61    4.11 1.28e+00 6.10e-01 1.03e+01
  angle pdb=" N   LYS A  41 "
        pdb=" CA  LYS A  41 "
        pdb=" C   LYS A  41 "
      ideal   model   delta    sigma   weight residual
     112.72  108.62    4.10 1.28e+00 6.10e-01 1.02e+01
  angle pdb=" N   LYS F  41 "
        pdb=" CA  LYS F  41 "
        pdb=" C   LYS F  41 "
      ideal   model   delta    sigma   weight residual
     112.72  108.63    4.09 1.28e+00 6.10e-01 1.02e+01
  angle pdb=" N   LYS C  41 "
        pdb=" CA  LYS C  41 "
        pdb=" C   LYS C  41 "
      ideal   model   delta    sigma   weight residual
     112.72  108.64    4.08 1.28e+00 6.10e-01 1.02e+01
  angle pdb=" N   LYS D  41 "
        pdb=" CA  LYS D  41 "
        pdb=" C   LYS D  41 "
      ideal   model   delta    sigma   weight residual
     112.72  108.64    4.08 1.28e+00 6.10e-01 1.02e+01
  ... (remaining 18566 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.25: 6566
       11.25 -    22.50: 1051
       22.50 -    33.75: 419
       33.75 -    44.99: 91
       44.99 -    56.24: 42
  Dihedral angle restraints: 8169
    sinusoidal: 3073
      harmonic: 5096
  Sorted by residual:
  dihedral pdb=" CA  ASN G  19 "
           pdb=" C   ASN G  19 "
           pdb=" N   VAL G  20 "
           pdb=" CA  VAL G  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.24   20.76     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  ASN C  19 "
           pdb=" C   ASN C  19 "
           pdb=" N   VAL C  20 "
           pdb=" CA  VAL C  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.26   20.74     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  ASN B  19 "
           pdb=" C   ASN B  19 "
           pdb=" N   VAL B  20 "
           pdb=" CA  VAL B  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.26   20.74     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 8166 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 927
       0.029 -    0.058: 708
       0.058 -    0.086: 285
       0.086 -    0.115: 185
       0.115 -    0.144: 51
  Chirality restraints: 2156
  Sorted by residual:
  chirality pdb=" CA  VAL E 164 "
            pdb=" N   VAL E 164 "
            pdb=" C   VAL E 164 "
            pdb=" CB  VAL E 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  VAL C 164 "
            pdb=" N   VAL C 164 "
            pdb=" C   VAL C 164 "
            pdb=" CB  VAL C 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  VAL F 164 "
            pdb=" N   VAL F 164 "
            pdb=" C   VAL F 164 "
            pdb=" CB  VAL F 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 2153 not shown)

  Planarity restraints: 2415
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 171 "    0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO C 172 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO C 172 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 172 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 171 "   -0.029 5.00e-02 4.00e+02   4.45e-02 3.16e+00
        pdb=" N   PRO A 172 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 172 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 172 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 171 "    0.029 5.00e-02 4.00e+02   4.44e-02 3.16e+00
        pdb=" N   PRO D 172 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO D 172 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 172 "    0.025 5.00e-02 4.00e+02
  ... (remaining 2412 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 196
        2.62 -     3.19: 12496
        3.19 -     3.76: 20246
        3.76 -     4.33: 29230
        4.33 -     4.90: 49372
  Nonbonded interactions: 111540
  Sorted by model distance:
  nonbonded pdb=" CE  LYS F 130 "
            pdb=" OE1 GLU G 137 "
     model   vdw
     2.049 3.440
  nonbonded pdb=" CE  LYS D 130 "
            pdb=" OE1 GLU E 137 "
     model   vdw
     2.049 3.440
  nonbonded pdb=" CE  LYS B 130 "
            pdb=" OE1 GLU C 137 "
     model   vdw
     2.050 3.440
  nonbonded pdb=" OE1 GLU A 137 "
            pdb=" CE  LYS G 130 "
     model   vdw
     2.050 3.440
  nonbonded pdb=" CE  LYS C 130 "
            pdb=" OE1 GLU D 137 "
     model   vdw
     2.050 3.440
  ... (remaining 111535 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.290
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
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      :  0.010   0.059  13636  Z= 0.416
  Angle     :  0.824   7.702  18571  Z= 0.463
  Chirality :  0.051   0.144   2156
  Planarity :  0.005   0.045   2415
  Dihedral  : 13.721  56.242   4907
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.85 %
    Favored  : 84.15 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.46 %
    Favored  : 86.12 %
  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 are not related in a simple way.
  whole: -5.55 (0.15), residues: 1722
  helix: -1.81 (0.32), residues: 140
  sheet: -3.54 (0.18), residues: 595
  loop : -4.22 (0.14), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F  38 
 TYR   0.018   0.003   TYR G  84 
 PHE   0.028   0.003   PHE G 135 
 TRP   0.004   0.002   TRP E 203 
 HIS   0.004   0.002   HIS G 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00976 (13636)
  covalent geometry    : angle       0.82375 (18571)
  hydrogen bonds       : bond        0.19211 (  105)
  hydrogen bonds       : angle       8.19573 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 276
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8309 (mttp)
REVERT: A  205 GLU cc_start: 0.8130 (pp20) cc_final: 0.7344 (pt0)
REVERT: B   68 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8344 (mttp)
REVERT: B   77 MET cc_start: 0.8922 (mmt) cc_final: 0.8193 (mmt)
REVERT: B   82 ASP cc_start: 0.8086 (m-30) cc_final: 0.7873 (m-30)
REVERT: B  205 GLU cc_start: 0.8088 (pp20) cc_final: 0.7523 (pp20)
REVERT: C   68 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8376 (mttp)
REVERT: C   77 MET cc_start: 0.8948 (mmt) cc_final: 0.8382 (mmt)
REVERT: C   81 GLU cc_start: 0.7578 (pm20) cc_final: 0.7227 (pm20)
REVERT: C  205 GLU cc_start: 0.8196 (pp20) cc_final: 0.7911 (pp20)
REVERT: D   21 ASP cc_start: 0.7753 (m-30) cc_final: 0.7470 (m-30)
REVERT: D   68 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8483 (mttp)
REVERT: D  205 GLU cc_start: 0.8197 (pp20) cc_final: 0.7516 (pt0)
REVERT: E   68 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8327 (mttp)
REVERT: E   81 GLU cc_start: 0.7707 (pm20) cc_final: 0.7469 (pm20)
REVERT: E  205 GLU cc_start: 0.8090 (pp20) cc_final: 0.7495 (pt0)
REVERT: F   25 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7767 (mm-30)
REVERT: F   68 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8278 (mttp)
REVERT: F  205 GLU cc_start: 0.8085 (pp20) cc_final: 0.7742 (pp20)
REVERT: G   39 MET cc_start: 0.4813 (mmm) cc_final: 0.4607 (mmp)
REVERT: G   68 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8356 (mttp)
REVERT: G  205 GLU cc_start: 0.8049 (pp20) cc_final: 0.7607 (pp20)
  outliers start: 21
  outliers final: 13
  residues processed: 297
  average time/residue: 0.0847
  time to fit residues: 40.2079
Evaluate side-chains
  176 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  171 VAL
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  171 VAL
Chi-restraints excluded: chain F residue   25 GLU
Chi-restraints excluded: chain F residue  155 THR
Chi-restraints excluded: chain F residue  171 VAL
Chi-restraints excluded: chain G residue  155 THR
Chi-restraints excluded: chain G residue  171 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    0.6980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 191 ASN
A 226 ASN
A 243 ASN
B 136 ASN
B 191 ASN
B 226 ASN
B 243 ASN
C 136 ASN
C 191 ASN
C 226 ASN
C 243 ASN
D 136 ASN
D 191 ASN
D 226 ASN
D 243 ASN
E 136 ASN
E 191 ASN
E 226 ASN
E 243 ASN
F 136 ASN
F 191 ASN
F 226 ASN
F 243 ASN
G 136 ASN
G 191 ASN
G 226 ASN
G 243 ASN

Total number of N/Q/H flips: 28

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.126615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.095841 restraints weight = 17601.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.94
r_work: 0.3106 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13636  Z= 0.196
  Angle     :  0.647   6.232  18571  Z= 0.334
  Chirality :  0.046   0.137   2156
  Planarity :  0.005   0.041   2415
  Dihedral  :  5.955  64.003   1878
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.92 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 18.21 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.91 (0.17), residues: 1722
  helix:  0.88 (0.42), residues: 140
  sheet: -3.24 (0.16), residues: 784
  loop : -4.01 (0.16), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  28 
 TYR   0.017   0.002   TYR F 244 
 PHE   0.018   0.002   PHE F 135 
 TRP   0.001   0.001   TRP G 203 
 HIS   0.002   0.001   HIS D 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (13636)
  covalent geometry    : angle       0.64746 (18571)
  hydrogen bonds       : bond        0.02708 (  105)
  hydrogen bonds       : angle       2.21327 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 174
  time to evaluate  : 0.491 
Fit side-chains
REVERT: A   64 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8781 (mp)
REVERT: A   68 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8363 (mttp)
REVERT: A  205 GLU cc_start: 0.8192 (pp20) cc_final: 0.7825 (pp20)
REVERT: C   64 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8807 (mp)
REVERT: C   68 LYS cc_start: 0.9107 (mtpt) cc_final: 0.8425 (mttp)
REVERT: C   81 GLU cc_start: 0.7923 (pm20) cc_final: 0.7548 (pm20)
REVERT: C  130 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8116 (mtpp)
REVERT: C  205 GLU cc_start: 0.8239 (pp20) cc_final: 0.7838 (pt0)
REVERT: D   68 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8474 (mttp)
REVERT: D  130 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8277 (mttm)
REVERT: D  205 GLU cc_start: 0.8276 (pp20) cc_final: 0.7440 (pp20)
REVERT: E   68 LYS cc_start: 0.9066 (mtpt) cc_final: 0.8395 (mttp)
REVERT: E   81 GLU cc_start: 0.8156 (pm20) cc_final: 0.7840 (pm20)
REVERT: E  130 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8087 (mtpp)
REVERT: E  205 GLU cc_start: 0.8222 (pp20) cc_final: 0.7713 (pt0)
REVERT: E  250 ASP cc_start: 0.8959 (m-30) cc_final: 0.8710 (m-30)
REVERT: F   68 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8307 (mttp)
REVERT: F  205 GLU cc_start: 0.8139 (pp20) cc_final: 0.7211 (pp20)
REVERT: G   39 MET cc_start: 0.4808 (mmm) cc_final: 0.4545 (mmp)
REVERT: G   68 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8417 (mttp)
REVERT: G  130 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8111 (mttm)
REVERT: G  205 GLU cc_start: 0.8239 (pp20) cc_final: 0.7502 (pp20)
  outliers start: 64
  outliers final: 43
  residues processed: 231
  average time/residue: 0.0854
  time to fit residues: 31.2219
Evaluate side-chains
  214 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 169
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  171 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  128 THR
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  171 VAL
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  128 THR
Chi-restraints excluded: chain F residue  151 THR
Chi-restraints excluded: chain F residue  155 THR
Chi-restraints excluded: chain F residue  171 VAL
Chi-restraints excluded: chain F residue  188 VAL
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  128 THR
Chi-restraints excluded: chain G residue  155 THR
Chi-restraints excluded: chain G residue  171 VAL
Chi-restraints excluded: chain G residue  188 VAL
Chi-restraints excluded: chain G residue  225 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 141 optimal weight:    6.9990
   chunk 148 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0060
   chunk 130 optimal weight:    4.9990
   chunk 123 optimal weight:    0.0020
   chunk 78 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 140 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.9008

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.131307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.100426 restraints weight = 17245.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.81
r_work: 0.3202 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  13636  Z= 0.130
  Angle     :  0.571   6.219  18571  Z= 0.296
  Chirality :  0.044   0.135   2156
  Planarity :  0.004   0.040   2415
  Dihedral  :  5.241  30.058   1875
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 17.67 %
    Favored  : 77.52 %
  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 are not related in a simple way.
  whole: -4.42 (0.19), residues: 1722
  helix:  1.75 (0.47), residues: 140
  sheet: -2.92 (0.17), residues: 784
  loop : -3.79 (0.17), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  38 
 TYR   0.015   0.002   TYR F 244 
 PHE   0.018   0.002   PHE A 135 
 TRP   0.002   0.001   TRP E 203 
 HIS   0.002   0.001   HIS G 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (13636)
  covalent geometry    : angle       0.57103 (18571)
  hydrogen bonds       : bond        0.02315 (  105)
  hydrogen bonds       : angle       1.83191 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 201
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A   64 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8471 (mp)
REVERT: A   68 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8185 (mttp)
REVERT: A  205 GLU cc_start: 0.8048 (pp20) cc_final: 0.7461 (pt0)
REVERT: A  230 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7260 (pp)
REVERT: B  154 ASN cc_start: 0.8452 (p0) cc_final: 0.8213 (p0)
REVERT: B  230 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7552 (pp)
REVERT: C   64 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8565 (mp)
REVERT: C   68 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8085 (mttp)
REVERT: C   81 GLU cc_start: 0.7885 (pm20) cc_final: 0.7410 (pm20)
REVERT: C  130 LYS cc_start: 0.8470 (mtmm) cc_final: 0.7965 (mtpp)
REVERT: C  154 ASN cc_start: 0.8473 (p0) cc_final: 0.8259 (p0)
REVERT: C  205 GLU cc_start: 0.8055 (pp20) cc_final: 0.7756 (pt0)
REVERT: C  230 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7282 (pp)
REVERT: D   68 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8265 (mttp)
REVERT: D  130 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8048 (mttm)
REVERT: D  187 ASN cc_start: 0.8286 (p0) cc_final: 0.7777 (p0)
REVERT: D  205 GLU cc_start: 0.8128 (pp20) cc_final: 0.7125 (pp20)
REVERT: D  230 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7301 (pp)
REVERT: E   68 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8162 (mttp)
REVERT: E   81 GLU cc_start: 0.8153 (pm20) cc_final: 0.7781 (pm20)
REVERT: E  130 LYS cc_start: 0.8616 (mtmm) cc_final: 0.8376 (mtmm)
REVERT: E  154 ASN cc_start: 0.8568 (p0) cc_final: 0.8313 (p0)
REVERT: E  205 GLU cc_start: 0.8099 (pp20) cc_final: 0.7549 (pt0)
REVERT: E  236 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7962 (pt)
REVERT: F   68 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8089 (mttp)
REVERT: F   77 MET cc_start: 0.9244 (mmt) cc_final: 0.8532 (mmt)
REVERT: F   81 GLU cc_start: 0.8295 (pm20) cc_final: 0.8047 (pm20)
REVERT: F  187 ASN cc_start: 0.8384 (p0) cc_final: 0.8001 (p0)
REVERT: F  205 GLU cc_start: 0.8010 (pp20) cc_final: 0.7512 (pt0)
REVERT: G   68 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8225 (mttp)
REVERT: G  130 LYS cc_start: 0.8554 (mtmm) cc_final: 0.7948 (mtpp)
REVERT: G  154 ASN cc_start: 0.8642 (p0) cc_final: 0.8360 (p0)
REVERT: G  205 GLU cc_start: 0.8080 (pp20) cc_final: 0.7823 (pt0)
  outliers start: 71
  outliers final: 51
  residues processed: 265
  average time/residue: 0.0871
  time to fit residues: 36.8016
Evaluate side-chains
  232 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 174
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  236 ILE
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  171 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  236 ILE
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  128 THR
Chi-restraints excluded: chain E residue  171 VAL
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  230 LEU
Chi-restraints excluded: chain E residue  236 ILE
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  128 THR
Chi-restraints excluded: chain F residue  151 THR
Chi-restraints excluded: chain F residue  171 VAL
Chi-restraints excluded: chain F residue  188 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  236 ILE
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  128 THR
Chi-restraints excluded: chain G residue  171 VAL
Chi-restraints excluded: chain G residue  188 VAL
Chi-restraints excluded: chain G residue  225 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 166 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 148 optimal weight:    6.9990
   chunk 134 optimal weight:    6.9990
   chunk 45 optimal weight:    0.2980
   chunk 147 optimal weight:    0.0020
   chunk 32 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 160 optimal weight:    5.9990
   overall best weight:    1.4594

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
D 154 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.139059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.108231 restraints weight = 16701.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.86
r_work: 0.3194 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13636  Z= 0.163
  Angle     :  0.572   5.557  18571  Z= 0.298
  Chirality :  0.045   0.136   2156
  Planarity :  0.004   0.046   2415
  Dihedral  :  5.010  29.241   1870
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 17.26 %
    Favored  : 76.03 %
  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 are not related in a simple way.
  whole: -4.16 (0.19), residues: 1722
  helix:  2.31 (0.47), residues: 133
  sheet: -2.79 (0.17), residues: 784
  loop : -3.60 (0.18), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 257 
 TYR   0.015   0.002   TYR E  84 
 PHE   0.019   0.002   PHE D 135 
 TRP   0.002   0.001   TRP D 203 
 HIS   0.002   0.001   HIS D 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (13636)
  covalent geometry    : angle       0.57168 (18571)
  hydrogen bonds       : bond        0.02293 (  105)
  hydrogen bonds       : angle       1.83307 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 99
    poor density    : 184
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A   47 MET cc_start: 0.4134 (mmm) cc_final: 0.3467 (mmp)
REVERT: A   64 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8724 (mp)
REVERT: A   68 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8303 (mttp)
REVERT: A  205 GLU cc_start: 0.8221 (pp20) cc_final: 0.7557 (pt0)
REVERT: A  230 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7629 (pp)
REVERT: B   23 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7387 (mm)
REVERT: B  154 ASN cc_start: 0.8567 (p0) cc_final: 0.8279 (p0)
REVERT: B  230 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7833 (pp)
REVERT: C   64 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8763 (mp)
REVERT: C   68 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8268 (mttp)
REVERT: C   81 GLU cc_start: 0.7864 (pm20) cc_final: 0.7497 (pm20)
REVERT: C  154 ASN cc_start: 0.8560 (p0) cc_final: 0.8304 (p0)
REVERT: C  205 GLU cc_start: 0.8179 (pp20) cc_final: 0.7783 (pt0)
REVERT: C  230 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7573 (pp)
REVERT: D   68 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8420 (mttp)
REVERT: D  178 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8332 (tt0)
REVERT: D  187 ASN cc_start: 0.8464 (p0) cc_final: 0.7959 (p0)
REVERT: D  205 GLU cc_start: 0.8310 (pp20) cc_final: 0.7317 (pp20)
REVERT: D  230 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7453 (pp)
REVERT: E   68 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8308 (mttp)
REVERT: E   81 GLU cc_start: 0.8117 (pm20) cc_final: 0.7822 (pm20)
REVERT: E  130 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8563 (mtmm)
REVERT: E  154 ASN cc_start: 0.8646 (p0) cc_final: 0.8359 (p0)
REVERT: E  205 GLU cc_start: 0.8211 (pp20) cc_final: 0.7635 (pt0)
REVERT: F   68 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8247 (mttp)
REVERT: F  187 ASN cc_start: 0.8628 (p0) cc_final: 0.8277 (p0)
REVERT: F  205 GLU cc_start: 0.8203 (pp20) cc_final: 0.7619 (pt0)
REVERT: G   47 MET cc_start: 0.3945 (mmp) cc_final: 0.3237 (mmm)
REVERT: G   68 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8399 (mttp)
REVERT: G  130 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8075 (mtpp)
REVERT: G  154 ASN cc_start: 0.8641 (p0) cc_final: 0.8321 (p0)
REVERT: G  205 GLU cc_start: 0.8217 (pp20) cc_final: 0.7426 (pp20)
  outliers start: 99
  outliers final: 76
  residues processed: 274
  average time/residue: 0.0785
  time to fit residues: 34.8431
Evaluate side-chains
  259 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 176
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  236 ILE
Chi-restraints excluded: chain C residue  248 MET
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  171 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  236 ILE
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  128 THR
Chi-restraints excluded: chain E residue  171 VAL
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  230 LEU
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  128 THR
Chi-restraints excluded: chain F residue  151 THR
Chi-restraints excluded: chain F residue  155 THR
Chi-restraints excluded: chain F residue  171 VAL
Chi-restraints excluded: chain F residue  188 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain F residue  229 ASP
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  236 ILE
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   31 THR
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  128 THR
Chi-restraints excluded: chain G residue  155 THR
Chi-restraints excluded: chain G residue  171 VAL
Chi-restraints excluded: chain G residue  188 VAL
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain G residue  225 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 135 optimal weight:    1.9990
   chunk 96 optimal weight:   10.0000
   chunk 162 optimal weight:    1.9990
   chunk 152 optimal weight:    0.3980
   chunk 121 optimal weight:    3.9990
   chunk 116 optimal weight:    7.9990
   chunk 139 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
D 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.128467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.096513 restraints weight = 17512.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.94
r_work: 0.3144 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  13636  Z= 0.261
  Angle     :  0.659   7.424  18571  Z= 0.337
  Chirality :  0.047   0.146   2156
  Planarity :  0.004   0.043   2415
  Dihedral  :  5.404  37.821   1870
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.54 %
    Favored  : 87.46 %
  Rotamer:
    Outliers :  7.92 %
    Allowed  : 18.55 %
    Favored  : 73.53 %
  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 are not related in a simple way.
  whole: -4.10 (0.19), residues: 1722
  helix:  2.47 (0.47), residues: 133
  sheet: -2.78 (0.18), residues: 784
  loop : -3.55 (0.18), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 257 
 TYR   0.017   0.002   TYR F  84 
 PHE   0.022   0.002   PHE F 135 
 TRP   0.003   0.001   TRP D 203 
 HIS   0.003   0.001   HIS D 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00640 (13636)
  covalent geometry    : angle       0.65893 (18571)
  hydrogen bonds       : bond        0.02433 (  105)
  hydrogen bonds       : angle       2.09788 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 117
    poor density    : 151
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A   64 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8784 (mp)
REVERT: A   68 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8399 (mttp)
REVERT: A  205 GLU cc_start: 0.8370 (pp20) cc_final: 0.7936 (pp20)
REVERT: A  230 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7574 (pp)
REVERT: B   23 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7458 (mm)
REVERT: B  154 ASN cc_start: 0.8611 (p0) cc_final: 0.8351 (p0)
REVERT: B  230 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7885 (pp)
REVERT: C   68 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8376 (mttp)
REVERT: C   81 GLU cc_start: 0.8044 (pm20) cc_final: 0.7617 (pm20)
REVERT: C  230 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7608 (pp)
REVERT: D   64 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8618 (mm)
REVERT: D   68 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8458 (mttp)
REVERT: D  154 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8444 (p0)
REVERT: D  205 GLU cc_start: 0.8282 (pp20) cc_final: 0.7355 (pp20)
REVERT: D  230 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7585 (pp)
REVERT: E   68 LYS cc_start: 0.9010 (mtpt) cc_final: 0.8296 (mttp)
REVERT: E  126 GLN cc_start: 0.8957 (tt0) cc_final: 0.8749 (tt0)
REVERT: E  178 GLU cc_start: 0.8552 (tt0) cc_final: 0.8300 (tt0)
REVERT: E  205 GLU cc_start: 0.8280 (pp20) cc_final: 0.7554 (pp20)
REVERT: F   68 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8264 (mttp)
REVERT: G   47 MET cc_start: 0.3980 (OUTLIER) cc_final: 0.3277 (mmm)
REVERT: G   68 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8367 (mttp)
REVERT: G  130 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8064 (mttm)
REVERT: G  154 ASN cc_start: 0.8605 (p0) cc_final: 0.8281 (p0)
REVERT: G  205 GLU cc_start: 0.8305 (pp20) cc_final: 0.7476 (pp20)
  outliers start: 117
  outliers final: 94
  residues processed: 258
  average time/residue: 0.0801
  time to fit residues: 33.6071
Evaluate side-chains
  255 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 103
    poor density    : 152
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   31 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  236 ILE
Chi-restraints excluded: chain C residue  248 MET
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   31 THR
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain D residue   70 GLU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  171 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  236 ILE
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   31 THR
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  128 THR
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  171 VAL
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  194 LEU
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  230 LEU
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  128 THR
Chi-restraints excluded: chain F residue  151 THR
Chi-restraints excluded: chain F residue  155 THR
Chi-restraints excluded: chain F residue  171 VAL
Chi-restraints excluded: chain F residue  188 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  236 ILE
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   31 THR
Chi-restraints excluded: chain G residue   47 MET
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  128 THR
Chi-restraints excluded: chain G residue  155 THR
Chi-restraints excluded: chain G residue  171 VAL
Chi-restraints excluded: chain G residue  188 VAL
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain G residue  225 VAL
Chi-restraints excluded: chain G residue  230 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0000
   chunk 146 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.129787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.098348 restraints weight = 17378.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.83
r_work: 0.3165 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13636  Z= 0.173
  Angle     :  0.592   7.817  18571  Z= 0.304
  Chirality :  0.045   0.136   2156
  Planarity :  0.004   0.040   2415
  Dihedral  :  5.166  34.743   1870
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  7.38 %
    Allowed  : 20.11 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.97 (0.19), residues: 1722
  helix:  2.56 (0.48), residues: 133
  sheet: -2.65 (0.18), residues: 784
  loop : -3.52 (0.18), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 257 
 TYR   0.017   0.002   TYR F 244 
 PHE   0.018   0.002   PHE A 135 
 TRP   0.002   0.001   TRP D 203 
 HIS   0.002   0.001   HIS F 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (13636)
  covalent geometry    : angle       0.59173 (18571)
  hydrogen bonds       : bond        0.02203 (  105)
  hydrogen bonds       : angle       1.89878 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 109
    poor density    : 161
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A   64 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8444 (mp)
REVERT: A   68 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8182 (mttp)
REVERT: A  205 GLU cc_start: 0.8114 (pp20) cc_final: 0.7503 (pt0)
REVERT: A  230 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7192 (pp)
REVERT: B   23 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7053 (mm)
REVERT: B  154 ASN cc_start: 0.8488 (p0) cc_final: 0.8235 (p0)
REVERT: B  230 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7411 (pp)
REVERT: C   68 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8097 (mttp)
REVERT: C   81 GLU cc_start: 0.7933 (pm20) cc_final: 0.7464 (pm20)
REVERT: C  154 ASN cc_start: 0.8493 (p0) cc_final: 0.8271 (p0)
REVERT: C  230 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7189 (pp)
REVERT: D   64 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8314 (mm)
REVERT: D   68 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8247 (mttp)
REVERT: D  205 GLU cc_start: 0.7992 (pp20) cc_final: 0.6965 (pp20)
REVERT: D  230 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7120 (pp)
REVERT: E   68 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8118 (mttp)
REVERT: E  154 ASN cc_start: 0.8594 (p0) cc_final: 0.8322 (p0)
REVERT: E  178 GLU cc_start: 0.8625 (tt0) cc_final: 0.8352 (tt0)
REVERT: E  205 GLU cc_start: 0.8121 (pp20) cc_final: 0.6995 (pp20)
REVERT: E  236 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7923 (pt)
REVERT: F   68 LYS cc_start: 0.8907 (mtpt) cc_final: 0.8075 (mttp)
REVERT: F  187 ASN cc_start: 0.8304 (p0) cc_final: 0.7976 (p0)
REVERT: G   68 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8220 (mttp)
REVERT: G  130 LYS cc_start: 0.8549 (mtmm) cc_final: 0.7848 (mttm)
REVERT: G  154 ASN cc_start: 0.8534 (p0) cc_final: 0.8204 (p0)
REVERT: G  205 GLU cc_start: 0.8113 (pp20) cc_final: 0.7203 (pp20)
  outliers start: 109
  outliers final: 89
  residues processed: 260
  average time/residue: 0.0807
  time to fit residues: 34.3268
Evaluate side-chains
  249 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 97
    poor density    : 152
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   31 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  236 ILE
Chi-restraints excluded: chain C residue  248 MET
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   31 THR
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  171 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  236 ILE
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   31 THR
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  128 THR
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  171 VAL
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  194 LEU
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  230 LEU
Chi-restraints excluded: chain E residue  236 ILE
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  128 THR
Chi-restraints excluded: chain F residue  151 THR
Chi-restraints excluded: chain F residue  155 THR
Chi-restraints excluded: chain F residue  171 VAL
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  188 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  236 ILE
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   31 THR
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  128 THR
Chi-restraints excluded: chain G residue  155 THR
Chi-restraints excluded: chain G residue  171 VAL
Chi-restraints excluded: chain G residue  188 VAL
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain G residue  225 VAL
Chi-restraints excluded: chain G residue  230 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 135 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 165 optimal weight:    8.9990
   chunk 150 optimal weight:    2.9990
   chunk 159 optimal weight:    0.0770
   chunk 109 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 56 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    1.4544

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.138126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.107017 restraints weight = 16806.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.86
r_work: 0.3215 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13636  Z= 0.165
  Angle     :  0.592   8.193  18571  Z= 0.302
  Chirality :  0.045   0.137   2156
  Planarity :  0.004   0.040   2415
  Dihedral  :  5.036  35.347   1870
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  7.45 %
    Allowed  : 20.18 %
    Favored  : 72.38 %
  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 are not related in a simple way.
  whole: -3.91 (0.19), residues: 1722
  helix:  2.53 (0.47), residues: 133
  sheet: -2.68 (0.18), residues: 805
  loop : -3.39 (0.18), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  38 
 TYR   0.016   0.002   TYR F 244 
 PHE   0.019   0.002   PHE E 135 
 TRP   0.002   0.001   TRP B 203 
 HIS   0.002   0.001   HIS D 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (13636)
  covalent geometry    : angle       0.59236 (18571)
  hydrogen bonds       : bond        0.02293 (  105)
  hydrogen bonds       : angle       1.90144 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 110
    poor density    : 160
  time to evaluate  : 0.507 
Fit side-chains
REVERT: A   64 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8741 (mp)
REVERT: A   68 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8366 (mttp)
REVERT: A  205 GLU cc_start: 0.8273 (pp20) cc_final: 0.7616 (pt0)
REVERT: A  230 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7626 (pp)
REVERT: B   23 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7466 (mm)
REVERT: B  154 ASN cc_start: 0.8556 (p0) cc_final: 0.8290 (p0)
REVERT: B  230 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7757 (pp)
REVERT: C   68 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8278 (mttp)
REVERT: C   81 GLU cc_start: 0.7901 (pm20) cc_final: 0.7574 (pm20)
REVERT: C  154 ASN cc_start: 0.8581 (p0) cc_final: 0.8321 (p0)
REVERT: C  230 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7549 (pp)
REVERT: D   64 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8625 (mm)
REVERT: D   68 LYS cc_start: 0.9077 (mtpt) cc_final: 0.8450 (mttp)
REVERT: D  187 ASN cc_start: 0.8581 (p0) cc_final: 0.8094 (p0)
REVERT: D  230 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7481 (pp)
REVERT: E   68 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8347 (mttp)
REVERT: E  154 ASN cc_start: 0.8647 (p0) cc_final: 0.8361 (p0)
REVERT: E  178 GLU cc_start: 0.8447 (tt0) cc_final: 0.8219 (tt0)
REVERT: E  205 GLU cc_start: 0.8257 (pp20) cc_final: 0.7509 (pp20)
REVERT: E  236 ILE cc_start: 0.8394 (pt) cc_final: 0.8142 (pt)
REVERT: F   68 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8293 (mttp)
REVERT: F  187 ASN cc_start: 0.8572 (p0) cc_final: 0.8188 (p0)
REVERT: G   47 MET cc_start: 0.4055 (mmm) cc_final: 0.3385 (mmm)
REVERT: G   68 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8407 (mttp)
REVERT: G  130 LYS cc_start: 0.8725 (mtmm) cc_final: 0.7981 (mttm)
REVERT: G  154 ASN cc_start: 0.8604 (p0) cc_final: 0.8235 (p0)
  outliers start: 110
  outliers final: 94
  residues processed: 262
  average time/residue: 0.0817
  time to fit residues: 34.9821
Evaluate side-chains
  257 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 156
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   31 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  236 ILE
Chi-restraints excluded: chain C residue  248 MET
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   31 THR
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  171 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  236 ILE
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   31 THR
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  128 THR
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  171 VAL
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  194 LEU
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  230 LEU
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  128 THR
Chi-restraints excluded: chain F residue  151 THR
Chi-restraints excluded: chain F residue  155 THR
Chi-restraints excluded: chain F residue  171 VAL
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  188 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  236 ILE
Chi-restraints excluded: chain G residue   20 VAL
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   31 THR
Chi-restraints excluded: chain G residue  106 THR
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  128 THR
Chi-restraints excluded: chain G residue  155 THR
Chi-restraints excluded: chain G residue  171 VAL
Chi-restraints excluded: chain G residue  188 VAL
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain G residue  225 VAL
Chi-restraints excluded: chain G residue  236 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 159 optimal weight:    0.0060
   chunk 23 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 87 optimal weight:    0.3980
   chunk 107 optimal weight:    3.9990
   chunk 143 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 64 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.6600

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

Flipped N/Q/H residues before XYZ refinement:
E 174 ASN
G 174 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.142528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.111191 restraints weight = 16380.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.85
r_work: 0.3273 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13636  Z= 0.115
  Angle     :  0.549   6.584  18571  Z= 0.285
  Chirality :  0.043   0.131   2156
  Planarity :  0.004   0.040   2415
  Dihedral  :  4.671  30.242   1870
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 21.73 %
    Favored  : 71.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.75 (0.19), residues: 1722
  helix:  2.42 (0.48), residues: 133
  sheet: -2.48 (0.18), residues: 805
  loop : -3.34 (0.19), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  38 
 TYR   0.016   0.001   TYR F 244 
 PHE   0.017   0.002   PHE E 135 
 TRP   0.001   0.000   TRP E 203 
 HIS   0.001   0.001   HIS G 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13636)
  covalent geometry    : angle       0.54892 (18571)
  hydrogen bonds       : bond        0.02187 (  105)
  hydrogen bonds       : angle       1.74429 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 183
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   64 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8713 (mp)
REVERT: A   68 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8329 (mttp)
REVERT: A  154 ASN cc_start: 0.8425 (p0) cc_final: 0.7826 (p0)
REVERT: B   23 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7351 (mm)
REVERT: B   77 MET cc_start: 0.9215 (mmt) cc_final: 0.8724 (mmt)
REVERT: B  154 ASN cc_start: 0.8472 (p0) cc_final: 0.8219 (p0)
REVERT: B  230 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7696 (pp)
REVERT: C   68 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8235 (mttp)
REVERT: C   81 GLU cc_start: 0.7797 (pm20) cc_final: 0.7514 (pm20)
REVERT: C  154 ASN cc_start: 0.8489 (p0) cc_final: 0.8228 (p0)
REVERT: C  230 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7476 (pp)
REVERT: D   68 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8423 (mttp)
REVERT: D  187 ASN cc_start: 0.8415 (p0) cc_final: 0.7800 (p0)
REVERT: D  205 GLU cc_start: 0.8239 (pp20) cc_final: 0.7230 (pp20)
REVERT: D  230 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7419 (pp)
REVERT: E   68 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8313 (mttp)
REVERT: E  154 ASN cc_start: 0.8541 (p0) cc_final: 0.8250 (p0)
REVERT: E  205 GLU cc_start: 0.8268 (pp20) cc_final: 0.7519 (pp20)
REVERT: E  236 ILE cc_start: 0.8349 (pt) cc_final: 0.8057 (pt)
REVERT: F   68 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8298 (mttp)
REVERT: F  178 GLU cc_start: 0.8463 (tt0) cc_final: 0.8191 (tt0)
REVERT: F  187 ASN cc_start: 0.8467 (p0) cc_final: 0.8022 (p0)
REVERT: F  205 GLU cc_start: 0.8297 (pp20) cc_final: 0.7674 (pt0)
REVERT: G   68 LYS cc_start: 0.9008 (mtpt) cc_final: 0.8371 (mttp)
REVERT: G  130 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8090 (mttm)
REVERT: G  154 ASN cc_start: 0.8576 (p0) cc_final: 0.8236 (p0)
  outliers start: 93
  outliers final: 78
  residues processed: 270
  average time/residue: 0.0831
  time to fit residues: 36.3173
Evaluate side-chains
  263 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 180
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  171 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  171 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  236 ILE
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   31 THR
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  128 THR
Chi-restraints excluded: chain E residue  171 VAL
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  192 VAL
Chi-restraints excluded: chain E residue  194 LEU
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  230 LEU
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  128 THR
Chi-restraints excluded: chain F residue  151 THR
Chi-restraints excluded: chain F residue  155 THR
Chi-restraints excluded: chain F residue  171 VAL
Chi-restraints excluded: chain F residue  186 VAL
Chi-restraints excluded: chain F residue  188 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  236 ILE
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   31 THR
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  128 THR
Chi-restraints excluded: chain G residue  171 VAL
Chi-restraints excluded: chain G residue  188 VAL
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain G residue  225 VAL
Chi-restraints excluded: chain G residue  236 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 164 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0870
   chunk 77 optimal weight:    6.9990
   chunk 99 optimal weight:    0.4980
   chunk 72 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 141 optimal weight:    0.0040
   chunk 44 optimal weight:    0.0470
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.3068

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

Flipped N/Q/H residues before XYZ refinement:
B 119 HIS
D 174 ASN
G 174 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.142147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.117220 restraints weight = 16898.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.54
r_work: 0.3302 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  13636  Z= 0.102
  Angle     :  0.542   9.226  18571  Z= 0.280
  Chirality :  0.043   0.169   2156
  Planarity :  0.004   0.040   2415
  Dihedral  :  4.369  24.943   1870
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 23.02 %
    Favored  : 71.63 %
  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 are not related in a simple way.
  whole: -3.54 (0.20), residues: 1722
  helix:  2.35 (0.48), residues: 133
  sheet: -2.27 (0.18), residues: 805
  loop : -3.25 (0.19), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 214 
 TYR   0.016   0.001   TYR A 209 
 PHE   0.017   0.001   PHE E 135 
 TRP   0.013   0.002   TRP E 203 
 HIS   0.002   0.000   HIS C 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (13636)
  covalent geometry    : angle       0.54193 (18571)
  hydrogen bonds       : bond        0.02136 (  105)
  hydrogen bonds       : angle       1.63043 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 201
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A   64 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8733 (mp)
REVERT: A   68 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8365 (mttp)
REVERT: A  154 ASN cc_start: 0.8044 (p0) cc_final: 0.7465 (p0)
REVERT: A  203 TRP cc_start: 0.8117 (p90) cc_final: 0.7843 (p90)
REVERT: A  229 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7330 (t0)
REVERT: B   23 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7438 (mm)
REVERT: B   77 MET cc_start: 0.9008 (mmt) cc_final: 0.8544 (mmt)
REVERT: B  154 ASN cc_start: 0.8282 (p0) cc_final: 0.8034 (p0)
REVERT: B  203 TRP cc_start: 0.8006 (p90) cc_final: 0.7806 (p90)
REVERT: B  205 GLU cc_start: 0.8320 (pp20) cc_final: 0.7563 (pp20)
REVERT: B  230 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7939 (pp)
REVERT: C   23 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7655 (mt)
REVERT: C   68 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8287 (mttp)
REVERT: C  154 ASN cc_start: 0.8211 (p0) cc_final: 0.7950 (p0)
REVERT: C  178 GLU cc_start: 0.8052 (tt0) cc_final: 0.7817 (tt0)
REVERT: C  230 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7600 (pp)
REVERT: D   68 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8438 (mttp)
REVERT: D  187 ASN cc_start: 0.8373 (p0) cc_final: 0.7735 (p0)
REVERT: D  230 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7660 (pp)
REVERT: E   68 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8352 (mttp)
REVERT: E  154 ASN cc_start: 0.8311 (p0) cc_final: 0.8005 (p0)
REVERT: E  203 TRP cc_start: 0.8072 (p90) cc_final: 0.7791 (p90)
REVERT: F   68 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8227 (mttp)
REVERT: F   77 MET cc_start: 0.8915 (mmt) cc_final: 0.8335 (mmt)
REVERT: F  187 ASN cc_start: 0.8357 (p0) cc_final: 0.7946 (p0)
REVERT: F  203 TRP cc_start: 0.7995 (p90) cc_final: 0.7640 (p90)
REVERT: G   68 LYS cc_start: 0.8889 (mtpt) cc_final: 0.8473 (mttp)
REVERT: G  130 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8162 (mttm)
REVERT: G  154 ASN cc_start: 0.8282 (p0) cc_final: 0.7944 (p0)
REVERT: G  178 GLU cc_start: 0.8000 (tt0) cc_final: 0.7774 (tt0)
  outliers start: 79
  outliers final: 65
  residues processed: 274
  average time/residue: 0.0891
  time to fit residues: 38.6130
Evaluate side-chains
  259 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 187
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   31 THR
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  236 ILE
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   31 THR
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  128 THR
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  194 LEU
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  230 LEU
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  128 THR
Chi-restraints excluded: chain F residue  151 THR
Chi-restraints excluded: chain F residue  155 THR
Chi-restraints excluded: chain F residue  188 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  236 ILE
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  128 THR
Chi-restraints excluded: chain G residue  171 VAL
Chi-restraints excluded: chain G residue  188 VAL
Chi-restraints excluded: chain G residue  192 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 147 optimal weight:    5.9990
   chunk 151 optimal weight:    0.8980
   chunk 154 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 138 optimal weight:    0.1980
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    0.4980
   chunk 58 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.140928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.115186 restraints weight = 16821.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.47
r_work: 0.3322 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13636  Z= 0.127
  Angle     :  0.571   9.454  18571  Z= 0.293
  Chirality :  0.043   0.137   2156
  Planarity :  0.004   0.041   2415
  Dihedral  :  4.337  17.948   1864
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 22.82 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.40 (0.20), residues: 1722
  helix:  2.44 (0.48), residues: 133
  sheet: -2.13 (0.18), residues: 805
  loop : -3.22 (0.19), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 257 
 TYR   0.016   0.001   TYR A 209 
 PHE   0.017   0.002   PHE E 135 
 TRP   0.012   0.002   TRP G 203 
 HIS   0.002   0.001   HIS D 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (13636)
  covalent geometry    : angle       0.57138 (18571)
  hydrogen bonds       : bond        0.02109 (  105)
  hydrogen bonds       : angle       1.69135 (  588)

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

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

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3444 Ramachandran restraints generated.
    1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 193
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A   64 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8751 (mp)
REVERT: A   68 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8422 (mttp)
REVERT: A  154 ASN cc_start: 0.8041 (p0) cc_final: 0.7422 (p0)
REVERT: A  203 TRP cc_start: 0.8161 (p90) cc_final: 0.7879 (p90)
REVERT: B   23 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7450 (mm)
REVERT: B   77 MET cc_start: 0.9021 (mmt) cc_final: 0.8594 (mmt)
REVERT: B  154 ASN cc_start: 0.8251 (p0) cc_final: 0.8002 (p0)
REVERT: B  205 GLU cc_start: 0.8345 (pp20) cc_final: 0.7634 (pp20)
REVERT: B  230 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7999 (pp)
REVERT: C   68 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8336 (mttp)
REVERT: C  154 ASN cc_start: 0.8209 (p0) cc_final: 0.7927 (p0)
REVERT: C  230 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7700 (pp)
REVERT: D   64 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8657 (mm)
REVERT: D   68 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8484 (mttp)
REVERT: D  187 ASN cc_start: 0.8430 (p0) cc_final: 0.7811 (p0)
REVERT: D  203 TRP cc_start: 0.8057 (p90) cc_final: 0.7811 (p90)
REVERT: D  230 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7753 (pp)
REVERT: E   68 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8419 (mttp)
REVERT: E  154 ASN cc_start: 0.8317 (p0) cc_final: 0.7983 (p0)
REVERT: F   68 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8245 (mttp)
REVERT: F  187 ASN cc_start: 0.8418 (p0) cc_final: 0.7990 (p0)
REVERT: G   68 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8504 (mttp)
REVERT: G  130 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8210 (mttm)
REVERT: G  154 ASN cc_start: 0.8292 (p0) cc_final: 0.7947 (p0)
REVERT: G  203 TRP cc_start: 0.7963 (p90) cc_final: 0.7590 (p90)
  outliers start: 81
  outliers final: 72
  residues processed: 269
  average time/residue: 0.0856
  time to fit residues: 37.0039
Evaluate side-chains
  265 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 187
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  236 ILE
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   31 THR
Chi-restraints excluded: chain C residue  116 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  130 LYS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  192 VAL
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   31 THR
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  155 THR
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  192 VAL
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  230 LEU
Chi-restraints excluded: chain D residue  236 ILE
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   31 THR
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  128 THR
Chi-restraints excluded: chain E residue  188 VAL
Chi-restraints excluded: chain E residue  194 LEU
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  225 VAL
Chi-restraints excluded: chain E residue  230 LEU
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   64 ILE
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain F residue  128 THR
Chi-restraints excluded: chain F residue  151 THR
Chi-restraints excluded: chain F residue  155 THR
Chi-restraints excluded: chain F residue  188 VAL
Chi-restraints excluded: chain F residue  192 VAL
Chi-restraints excluded: chain F residue  225 VAL
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  236 ILE
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   31 THR
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  128 THR
Chi-restraints excluded: chain G residue  171 VAL
Chi-restraints excluded: chain G residue  188 VAL
Chi-restraints excluded: chain G residue  192 VAL
Chi-restraints excluded: chain G residue  236 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 27 optimal weight:    0.1980
   chunk 115 optimal weight:    0.6980
   chunk 118 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0170
   chunk 132 optimal weight:    0.9990
   chunk 51 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0010
   chunk 103 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0030
   overall best weight:    0.1234

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
C 174 ASN
F 174 ASN
G 174 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.144400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.120018 restraints weight = 16695.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.42
r_work: 0.3392 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13636  Z= 0.107
  Angle     :  0.551   7.941  18571  Z= 0.288
  Chirality :  0.043   0.166   2156
  Planarity :  0.004   0.041   2415
  Dihedral  :  4.094  18.197   1864
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 26.00 %
    Favored  : 71.09 %
  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 are not related in a simple way.
  whole: -3.14 (0.20), residues: 1722
  helix:  2.21 (0.48), residues: 133
  sheet: -1.90 (0.19), residues: 777
  loop : -3.02 (0.19), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 257 
 TYR   0.020   0.001   TYR A 209 
 PHE   0.016   0.001   PHE E 135 
 TRP   0.011   0.002   TRP F 203 
 HIS   0.001   0.000   HIS D 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (13636)
  covalent geometry    : angle       0.55095 (18571)
  hydrogen bonds       : bond        0.02104 (  105)
  hydrogen bonds       : angle       1.53037 (  588)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3159.93 seconds
wall clock time: 54 minutes 58.76 seconds (3298.76 seconds total)