Starting phenix.real_space_refine
on Thu Mar  5 01:31:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zxp_15013/03_2026/7zxp_15013.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxp_15013/03_2026/7zxp_15013.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxp_15013/03_2026/7zxp_15013.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxp_15013/03_2026/7zxp_15013.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxp_15013/03_2026/7zxp_15013.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxp_15013/03_2026/7zxp_15013.map"
  }
  resolution = 2.39
  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=   0.002
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     168      5.16       5
     C   12192      2.51       5
     N    3060      2.21       5
     O    3000      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 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: 18420
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1535
          Classifications: {'peptide': 191}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L
  Time building chain proxies: 1.73, per 1000 atoms: 0.09
  Number of scatterers: 18420
  At special positions: 0
  Unit cell: (106.602, 98.754, 164.154, 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     168     16.00
     O    3000      8.00
     N    3060      7.00
     C   12192      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=36, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  53 " - pdb=" SG  CYS C 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  53 " - pdb=" SG  CYS E 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  53 " - pdb=" SG  CYS F 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  53 " - pdb=" SG  CYS G 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  53 " - pdb=" SG  CYS H 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  53 " - pdb=" SG  CYS I 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  53 " - pdb=" SG  CYS J 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  53 " - pdb=" SG  CYS K 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  53 " - pdb=" SG  CYS L 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  60 " - pdb=" SG  CYS E 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  60 " - pdb=" SG  CYS F 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  60 " - pdb=" SG  CYS G 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  60 " - pdb=" SG  CYS H 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  60 " - pdb=" SG  CYS I 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  60 " - pdb=" SG  CYS J 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  60 " - pdb=" SG  CYS K 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  60 " - pdb=" SG  CYS L 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  64 " - pdb=" SG  CYS D 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  64 " - pdb=" SG  CYS E 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  64 " - pdb=" SG  CYS F 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  64 " - pdb=" SG  CYS G 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  64 " - pdb=" SG  CYS H 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  64 " - pdb=" SG  CYS I 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  64 " - pdb=" SG  CYS J 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  64 " - pdb=" SG  CYS K 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  64 " - pdb=" SG  CYS L 168 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.36
  Conformation dependent library (CDL) restraints added in 710.3 milliseconds
  

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4416

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 12 sheets defined
      74.9% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 43
      removed outlier: 3.736A  pdb=" N   GLU A  41 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER A  42 " --> pdb=" O   VAL A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 72 through 107
      Proline residue:  A  87  - end of helix
    Processing helix  chain 'A' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR A 134 " --> pdb=" O   THR A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 220
    Processing helix  chain 'B' and resid 21 through 43
      removed outlier: 3.735A  pdb=" N   GLU B  41 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER B  42 " --> pdb=" O   VAL B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 72 through 107
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR B 134 " --> pdb=" O   THR B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 220
    Processing helix  chain 'C' and resid 21 through 43
      removed outlier: 3.736A  pdb=" N   GLU C  41 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER C  42 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 72 through 107
      Proline residue:  C  87  - end of helix
    Processing helix  chain 'C' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP C 133 " --> pdb=" O   GLY C 129 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR C 134 " --> pdb=" O   THR C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 220
    Processing helix  chain 'D' and resid 21 through 43
      removed outlier: 3.736A  pdb=" N   GLU D  41 " --> pdb=" O   VAL D  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER D  42 " --> pdb=" O   VAL D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'D' and resid 72 through 107
      Proline residue:  D  87  - end of helix
    Processing helix  chain 'D' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP D 133 " --> pdb=" O   GLY D 129 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR D 134 " --> pdb=" O   THR D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 183 through 220
    Processing helix  chain 'E' and resid 21 through 43
      removed outlier: 3.736A  pdb=" N   GLU E  41 " --> pdb=" O   VAL E  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER E  42 " --> pdb=" O   VAL E  38 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 59 through 69
    Processing helix  chain 'E' and resid 72 through 107
      Proline residue:  E  87  - end of helix
    Processing helix  chain 'E' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP E 133 " --> pdb=" O   GLY E 129 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR E 134 " --> pdb=" O   THR E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 183 through 220
    Processing helix  chain 'F' and resid 21 through 43
      removed outlier: 3.736A  pdb=" N   GLU F  41 " --> pdb=" O   VAL F  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER F  42 " --> pdb=" O   VAL F  38 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 59 through 69
    Processing helix  chain 'F' and resid 72 through 107
      Proline residue:  F  87  - end of helix
    Processing helix  chain 'F' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP F 133 " --> pdb=" O   GLY F 129 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR F 134 " --> pdb=" O   THR F 130 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 183 through 220
    Processing helix  chain 'G' and resid 21 through 43
      removed outlier: 3.736A  pdb=" N   GLU G  41 " --> pdb=" O   VAL G  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER G  42 " --> pdb=" O   VAL G  38 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 59 through 69
    Processing helix  chain 'G' and resid 72 through 107
      Proline residue:  G  87  - end of helix
    Processing helix  chain 'G' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP G 133 " --> pdb=" O   GLY G 129 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR G 134 " --> pdb=" O   THR G 130 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 183 through 220
    Processing helix  chain 'H' and resid 21 through 43
      removed outlier: 3.735A  pdb=" N   GLU H  41 " --> pdb=" O   VAL H  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER H  42 " --> pdb=" O   VAL H  38 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 59 through 69
    Processing helix  chain 'H' and resid 72 through 107
      Proline residue:  H  87  - end of helix
    Processing helix  chain 'H' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP H 133 " --> pdb=" O   GLY H 129 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR H 134 " --> pdb=" O   THR H 130 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 183 through 220
    Processing helix  chain 'I' and resid 21 through 43
      removed outlier: 3.736A  pdb=" N   GLU I  41 " --> pdb=" O   VAL I  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER I  42 " --> pdb=" O   VAL I  38 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 59 through 69
    Processing helix  chain 'I' and resid 72 through 107
      Proline residue:  I  87  - end of helix
    Processing helix  chain 'I' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP I 133 " --> pdb=" O   GLY I 129 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR I 134 " --> pdb=" O   THR I 130 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 183 through 220
    Processing helix  chain 'J' and resid 21 through 43
      removed outlier: 3.735A  pdb=" N   GLU J  41 " --> pdb=" O   VAL J  37 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER J  42 " --> pdb=" O   VAL J  38 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 59 through 69
    Processing helix  chain 'J' and resid 72 through 107
      Proline residue:  J  87  - end of helix
    Processing helix  chain 'J' and resid 123 through 157
      removed outlier: 3.598A  pdb=" N   TRP J 133 " --> pdb=" O   GLY J 129 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR J 134 " --> pdb=" O   THR J 130 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 183 through 220
    Processing helix  chain 'K' and resid 21 through 43
      removed outlier: 3.736A  pdb=" N   GLU K  41 " --> pdb=" O   VAL K  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER K  42 " --> pdb=" O   VAL K  38 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 59 through 69
    Processing helix  chain 'K' and resid 72 through 107
      Proline residue:  K  87  - end of helix
    Processing helix  chain 'K' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP K 133 " --> pdb=" O   GLY K 129 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR K 134 " --> pdb=" O   THR K 130 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 183 through 220
    Processing helix  chain 'L' and resid 21 through 43
      removed outlier: 3.736A  pdb=" N   GLU L  41 " --> pdb=" O   VAL L  37 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER L  42 " --> pdb=" O   VAL L  38 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 59 through 69
    Processing helix  chain 'L' and resid 72 through 107
      Proline residue:  L  87  - end of helix
    Processing helix  chain 'L' and resid 123 through 157
      removed outlier: 3.599A  pdb=" N   TRP L 133 " --> pdb=" O   GLY L 129 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR L 134 " --> pdb=" O   THR L 130 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 183 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE A  52 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE B  52 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE C  52 " --> pdb=" O   PHE C 180 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE D  52 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE E  52 " --> pdb=" O   PHE E 180 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE F  52 " --> pdb=" O   PHE F 180 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE G  52 " --> pdb=" O   PHE G 180 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE H  52 " --> pdb=" O   PHE H 180 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE I  52 " --> pdb=" O   PHE I 180 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE J  52 " --> pdb=" O   PHE J 180 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE K  52 " --> pdb=" O   PHE K 180 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53
      removed outlier: 3.841A  pdb=" N   ILE L  52 " --> pdb=" O   PHE L 180 " (cutoff:3.500A)

    1452 hydrogen bonds defined for protein.
    4320 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 5544
        1.35 -     1.46: 4666
        1.46 -     1.58: 8474
        1.58 -     1.69: 0
        1.69 -     1.81: 240
  Bond restraints: 18924
  Sorted by residual:
  bond pdb=" CA  THR D  86 "
       pdb=" C   THR D  86 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.013 1.26e-02 6.30e+03 9.91e-01
  bond pdb=" CA  THR G  86 "
       pdb=" C   THR G  86 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.013 1.26e-02 6.30e+03 9.91e-01
  bond pdb=" CA  THR E  86 "
       pdb=" C   THR E  86 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.012 1.26e-02 6.30e+03 9.82e-01
  bond pdb=" CA  THR K  86 "
       pdb=" C   THR K  86 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.012 1.26e-02 6.30e+03 9.82e-01
  bond pdb=" CA  THR C  86 "
       pdb=" C   THR C  86 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.012 1.26e-02 6.30e+03 9.58e-01
  ... (remaining 18919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 25155
        1.15 -     2.30: 501
        2.30 -     3.46: 108
        3.46 -     4.61: 0
        4.61 -     5.76: 12
  Bond angle restraints: 25776
  Sorted by residual:
  angle pdb=" C   THR K  86 "
        pdb=" N   PRO K  87 "
        pdb=" CD  PRO K  87 "
      ideal   model   delta    sigma   weight residual
     125.00  130.76   -5.76 4.10e+00 5.95e-02 1.97e+00
  angle pdb=" C   THR I  86 "
        pdb=" N   PRO I  87 "
        pdb=" CD  PRO I  87 "
      ideal   model   delta    sigma   weight residual
     125.00  130.75   -5.75 4.10e+00 5.95e-02 1.96e+00
  angle pdb=" C   THR L  86 "
        pdb=" N   PRO L  87 "
        pdb=" CD  PRO L  87 "
      ideal   model   delta    sigma   weight residual
     125.00  130.75   -5.75 4.10e+00 5.95e-02 1.96e+00
  angle pdb=" C   THR H  86 "
        pdb=" N   PRO H  87 "
        pdb=" CD  PRO H  87 "
      ideal   model   delta    sigma   weight residual
     125.00  130.72   -5.72 4.10e+00 5.95e-02 1.95e+00
  angle pdb=" C   THR B  86 "
        pdb=" N   PRO B  87 "
        pdb=" CD  PRO B  87 "
      ideal   model   delta    sigma   weight residual
     125.00  130.71   -5.71 4.10e+00 5.95e-02 1.94e+00
  ... (remaining 25771 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.86: 9372
       12.86 -    25.72: 1032
       25.72 -    38.58: 420
       38.58 -    51.44: 240
       51.44 -    64.30: 36
  Dihedral angle restraints: 11100
    sinusoidal: 4320
      harmonic: 6780
  Sorted by residual:
  dihedral pdb=" CB  CYS J  64 "
           pdb=" SG  CYS J  64 "
           pdb=" SG  CYS J 168 "
           pdb=" CB  CYS J 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.20   31.20     1      1.00e+01 1.00e-02 1.39e+01
  dihedral pdb=" CB  CYS D  64 "
           pdb=" SG  CYS D  64 "
           pdb=" SG  CYS D 168 "
           pdb=" CB  CYS D 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.20   31.20     1      1.00e+01 1.00e-02 1.39e+01
  dihedral pdb=" CB  CYS E  64 "
           pdb=" SG  CYS E  64 "
           pdb=" SG  CYS E 168 "
           pdb=" CB  CYS E 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.19   31.19     1      1.00e+01 1.00e-02 1.39e+01
  ... (remaining 11097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 2182
       0.033 -    0.067: 590
       0.067 -    0.100: 228
       0.100 -    0.134: 12
       0.134 -    0.167: 36
  Chirality restraints: 3048
  Sorted by residual:
  chirality pdb=" CB  VAL C  95 "
            pdb=" CA  VAL C  95 "
            pdb=" CG1 VAL C  95 "
            pdb=" CG2 VAL C  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" CB  VAL F  95 "
            pdb=" CA  VAL F  95 "
            pdb=" CG1 VAL F  95 "
            pdb=" CG2 VAL F  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" CB  VAL L  95 "
            pdb=" CA  VAL L  95 "
            pdb=" CG1 VAL L  95 "
            pdb=" CG2 VAL L  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.99e-01
  ... (remaining 3045 not shown)

  Planarity restraints: 3084
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  29 "   -0.013 2.00e-02 2.50e+03   1.28e-02 2.88e+00
        pdb=" CG  PHE H  29 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  29 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  29 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  29 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  29 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE K  29 "   -0.013 2.00e-02 2.50e+03   1.28e-02 2.87e+00
        pdb=" CG  PHE K  29 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE K  29 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE K  29 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE K  29 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE K  29 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE K  29 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE J  29 "   -0.013 2.00e-02 2.50e+03   1.28e-02 2.86e+00
        pdb=" CG  PHE J  29 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE J  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE J  29 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE J  29 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE J  29 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE J  29 "    0.000 2.00e-02 2.50e+03
  ... (remaining 3081 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 6007
        2.85 -     3.36: 18839
        3.36 -     3.87: 32223
        3.87 -     4.39: 32415
        4.39 -     4.90: 58673
  Nonbonded interactions: 148157
  Sorted by model distance:
  nonbonded pdb=" O   LEU D 131 "
            pdb=" OG1 THR D 134 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   LEU I 131 "
            pdb=" OG1 THR I 134 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   LEU L 131 "
            pdb=" OG1 THR L 134 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   LEU F 131 "
            pdb=" OG1 THR F 134 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   LEU C 131 "
            pdb=" OG1 THR C 134 "
     model   vdw
     2.332 3.040
  ... (remaining 148152 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

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:             3.420
  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:          0.270
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     12.760
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:5.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
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      :  0.002   0.020  18960  Z= 0.114
  Angle     :  0.423   5.761  25848  Z= 0.242
  Chirality :  0.039   0.167   3048
  Planarity :  0.003   0.017   3084
  Dihedral  : 14.726  64.301   6576
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 17.35 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.20 (0.17), residues: 2244
  helix:  4.00 (0.10), residues: 1632
  sheet: -0.27 (0.43), residues: 204
  loop : -1.17 (0.26), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  75 
 TYR   0.008   0.001   TYR G  65 
 PHE   0.030   0.002   PHE H  29 
 TRP   0.005   0.001   TRP E 132 
 HIS   0.003   0.001   HIS H  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 (18924)
  covalent geometry    : angle       0.42292 (25776)
  SS BOND              : bond        0.00063 (   36)
  SS BOND              : angle       0.58879 (   72)
  hydrogen bonds       : bond        0.08696 ( 1452)
  hydrogen bonds       : angle       3.55967 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 290
  time to evaluate  : 0.714 
Fit side-chains
  outliers start: 24
  outliers final: 16
  residues processed: 314
  average time/residue: 0.4116
  time to fit residues: 151.6618
Evaluate side-chains
  207 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 191
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain G residue   42 SER
Chi-restraints excluded: chain H residue   42 SER
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain I residue   42 SER
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain L residue   42 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 216 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 194 optimal weight:    0.9980
   chunk 227 optimal weight:    5.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 200 optimal weight:    4.9990
   overall best weight:    2.7184

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

Flipped N/Q/H residues before XYZ refinement:
A  73 HIS
B  73 HIS
D  73 HIS
E  73 HIS
F  73 HIS
G  73 HIS
H  73 HIS
J  73 HIS
K  73 HIS
L  73 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.132512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.081349 restraints weight = 25250.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 1.87
r_work: 0.2892 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  18960  Z= 0.170
  Angle     :  0.474   5.734  25848  Z= 0.257
  Chirality :  0.041   0.167   3048
  Planarity :  0.003   0.024   3084
  Dihedral  :  4.132  41.795   2504
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 16.52 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.30 (0.17), residues: 2244
  helix:  4.03 (0.10), residues: 1632
  sheet: -0.31 (0.42), residues: 204
  loop : -0.89 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  32 
 TYR   0.016   0.001   TYR A  65 
 PHE   0.013   0.002   PHE E 180 
 TRP   0.010   0.001   TRP J 133 
 HIS   0.006   0.001   HIS F  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (18924)
  covalent geometry    : angle       0.47048 (25776)
  SS BOND              : bond        0.00155 (   36)
  SS BOND              : angle       1.19540 (   72)
  hydrogen bonds       : bond        0.04574 ( 1452)
  hydrogen bonds       : angle       3.18044 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 205
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A  105 MET cc_start: 0.3239 (OUTLIER) cc_final: 0.2975 (tpp)
REVERT: B  105 MET cc_start: 0.3249 (OUTLIER) cc_final: 0.3001 (tpt)
REVERT: D  105 MET cc_start: 0.3237 (OUTLIER) cc_final: 0.2975 (tpp)
REVERT: E  105 MET cc_start: 0.3269 (OUTLIER) cc_final: 0.3029 (tpt)
REVERT: G  105 MET cc_start: 0.3228 (OUTLIER) cc_final: 0.2969 (tpp)
REVERT: H  105 MET cc_start: 0.3268 (OUTLIER) cc_final: 0.3028 (tpt)
REVERT: I  105 MET cc_start: 0.3171 (OUTLIER) cc_final: 0.2962 (tpp)
REVERT: J  105 MET cc_start: 0.3228 (OUTLIER) cc_final: 0.2970 (tpp)
REVERT: K  105 MET cc_start: 0.3257 (OUTLIER) cc_final: 0.3014 (tpt)
  outliers start: 76
  outliers final: 8
  residues processed: 255
  average time/residue: 0.4957
  time to fit residues: 144.4816
Evaluate side-chains
  193 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   97 HIS
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain G residue  105 MET
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue  105 MET
Chi-restraints excluded: chain I residue   97 HIS
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain J residue  105 MET
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain K residue  105 MET
Chi-restraints excluded: chain L residue   97 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 19 optimal weight:   20.0000
   chunk 64 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 116 optimal weight:    0.7980
   chunk 148 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3913 r_free = 0.3913 target = 0.135023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.084469 restraints weight = 25652.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 1.89
r_work: 0.2958 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8827
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  18960  Z= 0.097
  Angle     :  0.402   5.561  25848  Z= 0.211
  Chirality :  0.038   0.161   3048
  Planarity :  0.002   0.016   3084
  Dihedral  :  3.691  40.450   2492
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 17.15 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.60 (0.16), residues: 2244
  helix:  4.30 (0.10), residues: 1632
  sheet: -0.22 (0.43), residues: 204
  loop : -0.98 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  32 
 TYR   0.012   0.001   TYR K  65 
 PHE   0.007   0.001   PHE I 190 
 TRP   0.005   0.001   TRP D 133 
 HIS   0.003   0.000   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 (18924)
  covalent geometry    : angle       0.40043 (25776)
  SS BOND              : bond        0.00112 (   36)
  SS BOND              : angle       0.70470 (   72)
  hydrogen bonds       : bond        0.03664 ( 1452)
  hydrogen bonds       : angle       2.93978 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 173
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  105 MET cc_start: 0.3208 (OUTLIER) cc_final: 0.2930 (tpp)
REVERT: D  105 MET cc_start: 0.3205 (OUTLIER) cc_final: 0.2928 (tpp)
REVERT: G  105 MET cc_start: 0.3203 (OUTLIER) cc_final: 0.2925 (tpp)
REVERT: I  105 MET cc_start: 0.3080 (OUTLIER) cc_final: 0.2879 (tpp)
REVERT: J  105 MET cc_start: 0.3201 (OUTLIER) cc_final: 0.2922 (tpp)
  outliers start: 78
  outliers final: 28
  residues processed: 227
  average time/residue: 0.4160
  time to fit residues: 110.9583
Evaluate side-chains
  205 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   97 HIS
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   97 HIS
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain E residue   97 HIS
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   97 HIS
Chi-restraints excluded: chain G residue  105 MET
Chi-restraints excluded: chain H residue   18 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   97 HIS
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   97 HIS
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   97 HIS
Chi-restraints excluded: chain J residue  105 MET
Chi-restraints excluded: chain K residue   18 THR
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain K residue   97 HIS
Chi-restraints excluded: chain L residue   18 THR
Chi-restraints excluded: chain L residue   97 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 206 optimal weight:    0.9980
   chunk 182 optimal weight:    0.7980
   chunk 195 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 198 optimal weight:    7.9990
   chunk 215 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 171 optimal weight:   20.0000
   chunk 4 optimal weight:    0.8980
   chunk 144 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.135225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.084604 restraints weight = 25650.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.90
r_work: 0.2970 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  18960  Z= 0.091
  Angle     :  0.389   5.752  25848  Z= 0.204
  Chirality :  0.038   0.166   3048
  Planarity :  0.002   0.012   3084
  Dihedral  :  3.563  39.705   2492
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.13 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.73 (0.16), residues: 2244
  helix:  4.40 (0.10), residues: 1632
  sheet: -0.17 (0.43), residues: 204
  loop : -1.00 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J  32 
 TYR   0.010   0.001   TYR G  65 
 PHE   0.008   0.001   PHE D 180 
 TRP   0.004   0.001   TRP D 133 
 HIS   0.003   0.000   HIS I  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 (18924)
  covalent geometry    : angle       0.38762 (25776)
  SS BOND              : bond        0.00154 (   36)
  SS BOND              : angle       0.67084 (   72)
  hydrogen bonds       : bond        0.03373 ( 1452)
  hydrogen bonds       : angle       2.78802 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 188
  time to evaluate  : 0.518 
Fit side-chains
REVERT: B  105 MET cc_start: 0.3253 (OUTLIER) cc_final: 0.3037 (tpp)
REVERT: C  105 MET cc_start: 0.3144 (OUTLIER) cc_final: 0.2822 (tpp)
REVERT: F  105 MET cc_start: 0.3126 (OUTLIER) cc_final: 0.2814 (tpp)
REVERT: L  105 MET cc_start: 0.3120 (OUTLIER) cc_final: 0.2809 (tpp)
  outliers start: 58
  outliers final: 28
  residues processed: 225
  average time/residue: 0.4321
  time to fit residues: 113.1879
Evaluate side-chains
  204 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 172
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   97 HIS
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   97 HIS
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain E residue   97 HIS
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   97 HIS
Chi-restraints excluded: chain H residue   18 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   97 HIS
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   97 HIS
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   97 HIS
Chi-restraints excluded: chain K residue   18 THR
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain K residue   97 HIS
Chi-restraints excluded: chain L residue   18 THR
Chi-restraints excluded: chain L residue   97 HIS
Chi-restraints excluded: chain L residue  105 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 203 optimal weight:    0.3980
   chunk 65 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 184 optimal weight:    0.6980
   chunk 160 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 186 optimal weight:    0.9980
   chunk 66 optimal weight:   30.0000
   chunk 195 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.134972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.084591 restraints weight = 25533.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.89
r_work: 0.2963 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8819
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  18960  Z= 0.091
  Angle     :  0.386   5.759  25848  Z= 0.203
  Chirality :  0.038   0.166   3048
  Planarity :  0.002   0.011   3084
  Dihedral  :  3.542  39.501   2492
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 18.52 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 (0.16), residues: 2244
  helix:  4.55 (0.09), residues: 1632
  sheet: -0.09 (0.44), residues: 204
  loop : -1.02 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  32 
 TYR   0.011   0.001   TYR J  65 
 PHE   0.007   0.001   PHE C 190 
 TRP   0.003   0.000   TRP J 133 
 HIS   0.003   0.000   HIS I  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 (18924)
  covalent geometry    : angle       0.38484 (25776)
  SS BOND              : bond        0.00117 (   36)
  SS BOND              : angle       0.67464 (   72)
  hydrogen bonds       : bond        0.03339 ( 1452)
  hydrogen bonds       : angle       2.72665 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 172
  time to evaluate  : 0.637 
Fit side-chains
REVERT: B  105 MET cc_start: 0.3328 (OUTLIER) cc_final: 0.3068 (tpp)
REVERT: C  105 MET cc_start: 0.3168 (OUTLIER) cc_final: 0.2792 (tpp)
REVERT: F  105 MET cc_start: 0.3174 (OUTLIER) cc_final: 0.2792 (tpp)
REVERT: I  105 MET cc_start: 0.3191 (OUTLIER) cc_final: 0.2829 (tpp)
REVERT: L  105 MET cc_start: 0.3172 (OUTLIER) cc_final: 0.2796 (tpp)
  outliers start: 66
  outliers final: 28
  residues processed: 218
  average time/residue: 0.4250
  time to fit residues: 108.2213
Evaluate side-chains
  205 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   97 HIS
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   97 HIS
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   97 HIS
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain E residue   97 HIS
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   97 HIS
Chi-restraints excluded: chain H residue   18 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   97 HIS
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   97 HIS
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   97 HIS
Chi-restraints excluded: chain K residue   18 THR
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain K residue   97 HIS
Chi-restraints excluded: chain L residue   18 THR
Chi-restraints excluded: chain L residue   97 HIS
Chi-restraints excluded: chain L residue  105 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 168 optimal weight:    6.9990
   chunk 169 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 204 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 212 optimal weight:    6.9990
   chunk 165 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   chunk 144 optimal weight:    4.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.132210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.081161 restraints weight = 25178.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.85
r_work: 0.2892 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  18960  Z= 0.138
  Angle     :  0.430   5.788  25848  Z= 0.230
  Chirality :  0.040   0.170   3048
  Planarity :  0.002   0.015   3084
  Dihedral  :  3.790  41.473   2492
  Min Nonbonded Distance : 2.662

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 18.37 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.78 (0.16), residues: 2244
  helix:  4.44 (0.09), residues: 1632
  sheet: -0.17 (0.43), residues: 204
  loop : -0.96 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J  32 
 TYR   0.011   0.001   TYR K  65 
 PHE   0.012   0.002   PHE J  68 
 TRP   0.003   0.001   TRP F 133 
 HIS   0.004   0.001   HIS I  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (18924)
  covalent geometry    : angle       0.42791 (25776)
  SS BOND              : bond        0.00136 (   36)
  SS BOND              : angle       0.97601 (   72)
  hydrogen bonds       : bond        0.03991 ( 1452)
  hydrogen bonds       : angle       2.88818 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 184
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7424 (tp)
REVERT: B  105 MET cc_start: 0.3221 (OUTLIER) cc_final: 0.2945 (tpp)
REVERT: C  105 MET cc_start: 0.3306 (OUTLIER) cc_final: 0.2906 (tpp)
REVERT: F  105 MET cc_start: 0.3308 (OUTLIER) cc_final: 0.2911 (tpp)
REVERT: I  105 MET cc_start: 0.3323 (OUTLIER) cc_final: 0.2929 (tpp)
REVERT: L  105 MET cc_start: 0.3300 (OUTLIER) cc_final: 0.2903 (tpp)
  outliers start: 71
  outliers final: 28
  residues processed: 219
  average time/residue: 0.4194
  time to fit residues: 107.3523
Evaluate side-chains
  214 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 180
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   97 HIS
Chi-restraints excluded: chain C residue  105 MET
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   95 VAL
Chi-restraints excluded: chain H residue   18 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   95 VAL
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   97 HIS
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   95 VAL
Chi-restraints excluded: chain K residue   18 THR
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain K residue   95 VAL
Chi-restraints excluded: chain L residue   18 THR
Chi-restraints excluded: chain L residue   97 HIS
Chi-restraints excluded: chain L residue  105 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 194 optimal weight:    0.5980
   chunk 124 optimal weight:    9.9990
   chunk 94 optimal weight:    1.9990
   chunk 220 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 9 optimal weight:   40.0000
   chunk 213 optimal weight:    0.9990
   chunk 123 optimal weight:   30.0000
   chunk 77 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 208 optimal weight:    0.9980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.133061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.082640 restraints weight = 25536.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.87
r_work: 0.2916 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017  18960  Z= 0.111
  Angle     :  0.401   5.758  25848  Z= 0.214
  Chirality :  0.039   0.166   3048
  Planarity :  0.002   0.014   3084
  Dihedral  :  3.680  41.052   2492
  Min Nonbonded Distance : 2.659

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.37 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.84 (0.16), residues: 2244
  helix:  4.51 (0.09), residues: 1632
  sheet: -0.16 (0.43), residues: 204
  loop : -1.06 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J  32 
 TYR   0.012   0.001   TYR J  65 
 PHE   0.009   0.002   PHE J  68 
 TRP   0.003   0.001   TRP K  24 
 HIS   0.003   0.000   HIS I  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (18924)
  covalent geometry    : angle       0.39899 (25776)
  SS BOND              : bond        0.00105 (   36)
  SS BOND              : angle       0.81364 (   72)
  hydrogen bonds       : bond        0.03620 ( 1452)
  hydrogen bonds       : angle       2.80259 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 186
  time to evaluate  : 0.727 
Fit side-chains
REVERT: B  131 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7340 (tp)
REVERT: E  131 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7327 (tp)
REVERT: K  131 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7326 (tp)
  outliers start: 70
  outliers final: 36
  residues processed: 213
  average time/residue: 0.4346
  time to fit residues: 107.8996
Evaluate side-chains
  220 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 181
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue   97 HIS
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue   97 HIS
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   95 VAL
Chi-restraints excluded: chain G residue   97 HIS
Chi-restraints excluded: chain H residue   18 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   95 VAL
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   95 VAL
Chi-restraints excluded: chain I residue   97 HIS
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   95 VAL
Chi-restraints excluded: chain J residue   97 HIS
Chi-restraints excluded: chain K residue   18 THR
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain K residue   95 VAL
Chi-restraints excluded: chain K residue  131 LEU
Chi-restraints excluded: chain L residue   18 THR
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   97 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 182 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 156 optimal weight:    0.6980
   chunk 183 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 195 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 202 optimal weight:    3.9990
   chunk 154 optimal weight:    7.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B  97 HIS
C  97 HIS
D  97 HIS
G  97 HIS
H  97 HIS
I  97 HIS
J  97 HIS
L  97 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.131429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.080999 restraints weight = 25552.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.84
r_work: 0.2871 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  18960  Z= 0.141
  Angle     :  0.429   5.825  25848  Z= 0.231
  Chirality :  0.040   0.172   3048
  Planarity :  0.002   0.015   3084
  Dihedral  :  3.810  41.606   2492
  Min Nonbonded Distance : 2.665

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.64 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.72 (0.16), residues: 2244
  helix:  4.40 (0.09), residues: 1632
  sheet: -0.14 (0.43), residues: 204
  loop : -1.02 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J  32 
 TYR   0.012   0.001   TYR J  65 
 PHE   0.012   0.002   PHE J 180 
 TRP   0.003   0.001   TRP E  44 
 HIS   0.004   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (18924)
  covalent geometry    : angle       0.42636 (25776)
  SS BOND              : bond        0.00125 (   36)
  SS BOND              : angle       0.95516 (   72)
  hydrogen bonds       : bond        0.03971 ( 1452)
  hydrogen bonds       : angle       2.87816 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 182
  time to evaluate  : 0.627 
Fit side-chains
  outliers start: 51
  outliers final: 29
  residues processed: 201
  average time/residue: 0.4615
  time to fit residues: 107.6238
Evaluate side-chains
  211 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue   97 HIS
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   95 VAL
Chi-restraints excluded: chain H residue   18 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   95 VAL
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   95 VAL
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   95 VAL
Chi-restraints excluded: chain K residue   18 THR
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain K residue   95 VAL
Chi-restraints excluded: chain L residue   18 THR
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 138 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 141 optimal weight:    7.9990
   chunk 125 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 107 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 172 optimal weight:    0.5980
   chunk 175 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B  97 HIS
C  97 HIS
E  97 HIS
F  97 HIS
H  97 HIS
I  97 HIS
K  97 HIS
L  97 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.129590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.077569 restraints weight = 25401.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 1.89
r_work: 0.2807 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  18960  Z= 0.135
  Angle     :  0.418   5.825  25848  Z= 0.226
  Chirality :  0.040   0.169   3048
  Planarity :  0.002   0.015   3084
  Dihedral  :  3.787  41.409   2492
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.35 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.65 (0.16), residues: 2244
  helix:  4.35 (0.09), residues: 1632
  sheet: -0.14 (0.43), residues: 204
  loop : -1.06 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  32 
 TYR   0.012   0.001   TYR G  65 
 PHE   0.011   0.002   PHE A  68 
 TRP   0.004   0.001   TRP F  44 
 HIS   0.004   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (18924)
  covalent geometry    : angle       0.41517 (25776)
  SS BOND              : bond        0.00161 (   36)
  SS BOND              : angle       0.96220 (   72)
  hydrogen bonds       : bond        0.03795 ( 1452)
  hydrogen bonds       : angle       2.87182 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 196
  time to evaluate  : 0.727 
Fit side-chains
  outliers start: 50
  outliers final: 28
  residues processed: 226
  average time/residue: 0.4428
  time to fit residues: 116.7684
Evaluate side-chains
  220 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 192
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   95 VAL
Chi-restraints excluded: chain H residue   18 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   95 VAL
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain I residue   95 VAL
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   95 VAL
Chi-restraints excluded: chain K residue   18 THR
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain K residue   95 VAL
Chi-restraints excluded: chain L residue   18 THR
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 168 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9990
   chunk 213 optimal weight:    0.8980
   chunk 181 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 161 optimal weight:    0.9990
   chunk 188 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 124 optimal weight:    7.9990
   chunk 144 optimal weight:    5.9990
   chunk 140 optimal weight:    1.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B  97 HIS
C  97 HIS
D  97 HIS
E  97 HIS
F  97 HIS
G  97 HIS
H  97 HIS
I  97 HIS
J  97 HIS
K  97 HIS
L  97 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.130593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.079141 restraints weight = 25575.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 1.89
r_work: 0.2840 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  18960  Z= 0.104
  Angle     :  0.399   5.800  25848  Z= 0.216
  Chirality :  0.038   0.167   3048
  Planarity :  0.002   0.013   3084
  Dihedral  :  3.657  40.775   2492
  Min Nonbonded Distance : 2.659

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 20.37 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.84 (0.16), residues: 2244
  helix:  4.50 (0.09), residues: 1632
  sheet: -0.07 (0.44), residues: 204
  loop : -1.08 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  32 
 TYR   0.014   0.001   TYR B 211 
 PHE   0.008   0.001   PHE C  68 
 TRP   0.004   0.001   TRP G  44 
 HIS   0.003   0.000   HIS I  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (18924)
  covalent geometry    : angle       0.39725 (25776)
  SS BOND              : bond        0.00112 (   36)
  SS BOND              : angle       0.77259 (   72)
  hydrogen bonds       : bond        0.03461 ( 1452)
  hydrogen bonds       : angle       2.75709 ( 4320)

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

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

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4488 Ramachandran restraints generated.
    2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 212
  time to evaluate  : 0.783 
Fit side-chains
  outliers start: 30
  outliers final: 16
  residues processed: 238
  average time/residue: 0.4469
  time to fit residues: 123.4499
Evaluate side-chains
  217 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 201
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   52 ILE
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain H residue   18 THR
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain I residue   18 THR
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain K residue   18 THR
Chi-restraints excluded: chain K residue   52 ILE
Chi-restraints excluded: chain L residue   18 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 221 optimal weight:    3.9990
   chunk 101 optimal weight:    7.9990
   chunk 187 optimal weight:    4.9990
   chunk 179 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 222 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 119 optimal weight:    0.3980
   chunk 76 optimal weight:   20.0000
   chunk 55 optimal weight:    0.0570
   overall best weight:    2.8904

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B  97 HIS
C  97 HIS
D  97 HIS
E  97 HIS
F  97 HIS
G  97 HIS
H  97 HIS
I  97 HIS
J  97 HIS
K  97 HIS
L  97 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.128298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.076432 restraints weight = 25678.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 1.87
r_work: 0.2779 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023  18960  Z= 0.171
  Angle     :  0.453   5.845  25848  Z= 0.247
  Chirality :  0.041   0.175   3048
  Planarity :  0.003   0.017   3084
  Dihedral  :  3.907  42.272   2492
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 21.30 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  4.60 (0.16), residues: 2244
  helix:  4.31 (0.09), residues: 1632
  sheet: -0.21 (0.43), residues: 204
  loop : -1.05 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  32 
 TYR   0.019   0.002   TYR C 211 
 PHE   0.013   0.002   PHE E 180 
 TRP   0.004   0.001   TRP L  44 
 HIS   0.004   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (18924)
  covalent geometry    : angle       0.44996 (25776)
  SS BOND              : bond        0.00154 (   36)
  SS BOND              : angle       1.09279 (   72)
  hydrogen bonds       : bond        0.04108 ( 1452)
  hydrogen bonds       : angle       2.89275 ( 4320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7604.65 seconds
wall clock time: 129 minutes 57.17 seconds (7797.17 seconds total)