Starting phenix.real_space_refine
on Thu Sep 18 06:12:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5flu_3222/09_2025/5flu_3222.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5flu_3222/09_2025/5flu_3222.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5flu_3222/09_2025/5flu_3222.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5flu_3222/09_2025/5flu_3222.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5flu_3222/09_2025/5flu_3222.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5flu_3222/09_2025/5flu_3222.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.582 sd=   0.540
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      39      5.16       5
     C    9399      2.51       5
     N    2548      2.21       5
     O    3146      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15132
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1164
          Classifications: {'peptide': 163}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 157}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L, M
  Time building chain proxies: 1.69, per 1000 atoms: 0.11
  Number of scatterers: 15132
  At special positions: 0
  Unit cell: (95.7, 94.6, 145.2, 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      39     16.00
     O    3146      8.00
     N    2548      7.00
     C    9399      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  61 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  61 " distance=2.04

  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: 1.34
  Conformation dependent library (CDL) restraints added in 679.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3666

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 39 sheets defined
      11.8% alpha, 33.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 29
    Processing helix  chain 'A' and resid 40 through 45
    Processing helix  chain 'A' and resid 63 through 70
    Processing helix  chain 'B' and resid 25 through 30
    Processing helix  chain 'B' and resid 39 through 45
    Processing helix  chain 'B' and resid 63 through 70
    Processing helix  chain 'C' and resid 25 through 29
    Processing helix  chain 'C' and resid 40 through 45
    Processing helix  chain 'C' and resid 63 through 70
    Processing helix  chain 'D' and resid 25 through 29
    Processing helix  chain 'D' and resid 40 through 45
    Processing helix  chain 'D' and resid 63 through 70
    Processing helix  chain 'E' and resid 25 through 29
    Processing helix  chain 'E' and resid 40 through 45
    Processing helix  chain 'E' and resid 63 through 70
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 40 through 45
    Processing helix  chain 'F' and resid 63 through 70
    Processing helix  chain 'G' and resid 25 through 29
    Processing helix  chain 'G' and resid 40 through 45
    Processing helix  chain 'G' and resid 63 through 70
    Processing helix  chain 'H' and resid 25 through 29
    Processing helix  chain 'H' and resid 40 through 45
    Processing helix  chain 'H' and resid 63 through 70
    Processing helix  chain 'I' and resid 25 through 29
    Processing helix  chain 'I' and resid 40 through 45
    Processing helix  chain 'I' and resid 63 through 70
    Processing helix  chain 'J' and resid 25 through 29
    Processing helix  chain 'J' and resid 40 through 45
    Processing helix  chain 'J' and resid 63 through 70
    Processing helix  chain 'K' and resid 25 through 29
    Processing helix  chain 'K' and resid 40 through 45
    Processing helix  chain 'K' and resid 63 through 70
    Processing helix  chain 'L' and resid 25 through 29
    Processing helix  chain 'L' and resid 40 through 45
    Processing helix  chain 'L' and resid 63 through 70
    Processing helix  chain 'M' and resid 25 through 29
    Processing helix  chain 'M' and resid 40 through 45
    Processing helix  chain 'M' and resid 63 through 70
    Processing sheet with id=HA, first strand: chain 'H' and resid 30 through 39
      removed outlier: 5.810A  pdb=" N   THR A  16 " --> pdb=" O   PHE H  35 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLN H  37 " --> pdb=" O   THR A  16 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL A  18 " --> pdb=" O   GLN H  37 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   SER H  39 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
    Processing sheet with id=AA, first strand: chain 'A' and resid 23 through 24
    Processing sheet with id=AB, first strand: chain 'A' and resid 30 through 39
      removed outlier: 5.810A  pdb=" N   THR G  16 " --> pdb=" O   PHE A  35 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLN A  37 " --> pdb=" O   THR G  16 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL G  18 " --> pdb=" O   GLN A  37 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   SER A  39 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
    Processing sheet with id=AC, first strand: chain 'A' and resid 52 through 53
    Processing sheet with id=CA, first strand: chain 'C' and resid 30 through 39
      removed outlier: 5.811A  pdb=" N   THR B  16 " --> pdb=" O   PHE C  35 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLN C  37 " --> pdb=" O   THR B  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL B  18 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   SER C  39 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
    Processing sheet with id=BA, first strand: chain 'B' and resid 23 through 24
    Processing sheet with id=BB, first strand: chain 'B' and resid 52 through 53
    Processing sheet with id=BC, first strand: chain 'B' and resid 122 through 123
    Processing sheet with id=DA, first strand: chain 'D' and resid 30 through 39
      removed outlier: 5.809A  pdb=" N   THR C  16 " --> pdb=" O   PHE D  35 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLN D  37 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL C  18 " --> pdb=" O   GLN D  37 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   SER D  39 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing sheet with id=CB, first strand: chain 'C' and resid 23 through 24
    Processing sheet with id=CC, first strand: chain 'C' and resid 52 through 53
    Processing sheet with id=EA, first strand: chain 'E' and resid 30 through 39
      removed outlier: 5.810A  pdb=" N   THR D  16 " --> pdb=" O   PHE E  35 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLN E  37 " --> pdb=" O   THR D  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL D  18 " --> pdb=" O   GLN E  37 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   SER E  39 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
    Processing sheet with id=DB, first strand: chain 'D' and resid 23 through 24
    Processing sheet with id=DC, first strand: chain 'D' and resid 52 through 53
    Processing sheet with id=FA, first strand: chain 'F' and resid 30 through 39
      removed outlier: 5.810A  pdb=" N   THR E  16 " --> pdb=" O   PHE F  35 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLN F  37 " --> pdb=" O   THR E  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL E  18 " --> pdb=" O   GLN F  37 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   SER F  39 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
    Processing sheet with id=EB, first strand: chain 'E' and resid 23 through 24
    Processing sheet with id=EC, first strand: chain 'E' and resid 52 through 53
    Processing sheet with id=GA, first strand: chain 'G' and resid 30 through 39
      removed outlier: 5.810A  pdb=" N   THR F  16 " --> pdb=" O   PHE G  35 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLN G  37 " --> pdb=" O   THR F  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL F  18 " --> pdb=" O   GLN G  37 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   SER G  39 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
    Processing sheet with id=FB, first strand: chain 'F' and resid 23 through 24
    Processing sheet with id=FC, first strand: chain 'F' and resid 52 through 53
    Processing sheet with id=GB, first strand: chain 'G' and resid 23 through 24
    Processing sheet with id=GC, first strand: chain 'G' and resid 52 through 53
    Processing sheet with id=IA, first strand: chain 'I' and resid 30 through 39
      removed outlier: 5.809A  pdb=" N   THR H  16 " --> pdb=" O   PHE I  35 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLN I  37 " --> pdb=" O   THR H  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL H  18 " --> pdb=" O   GLN I  37 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   SER I  39 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
    Processing sheet with id=HB, first strand: chain 'H' and resid 23 through 24
    Processing sheet with id=HC, first strand: chain 'H' and resid 52 through 53
    Processing sheet with id=JA, first strand: chain 'J' and resid 30 through 39
      removed outlier: 5.810A  pdb=" N   THR I  16 " --> pdb=" O   PHE J  35 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLN J  37 " --> pdb=" O   THR I  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL I  18 " --> pdb=" O   GLN J  37 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   SER J  39 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
    Processing sheet with id=IB, first strand: chain 'I' and resid 23 through 24
    Processing sheet with id=IC, first strand: chain 'I' and resid 52 through 53
    Processing sheet with id=KA, first strand: chain 'K' and resid 30 through 39
      removed outlier: 5.809A  pdb=" N   THR J  16 " --> pdb=" O   PHE K  35 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLN K  37 " --> pdb=" O   THR J  16 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   VAL J  18 " --> pdb=" O   GLN K  37 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   SER K  39 " --> pdb=" O   VAL J  18 " (cutoff:3.500A)
    Processing sheet with id=JB, first strand: chain 'J' and resid 23 through 24
    Processing sheet with id=JC, first strand: chain 'J' and resid 52 through 53
    Processing sheet with id=LA, first strand: chain 'L' and resid 30 through 39
      removed outlier: 5.809A  pdb=" N   THR K  16 " --> pdb=" O   PHE L  35 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLN L  37 " --> pdb=" O   THR K  16 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL K  18 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   SER L  39 " --> pdb=" O   VAL K  18 " (cutoff:3.500A)
    Processing sheet with id=KB, first strand: chain 'K' and resid 23 through 24
    Processing sheet with id=KC, first strand: chain 'K' and resid 52 through 53
    Processing sheet with id=MA, first strand: chain 'M' and resid 30 through 39
      removed outlier: 5.810A  pdb=" N   THR L  16 " --> pdb=" O   PHE M  35 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLN M  37 " --> pdb=" O   THR L  16 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL L  18 " --> pdb=" O   GLN M  37 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   SER M  39 " --> pdb=" O   VAL L  18 " (cutoff:3.500A)
    Processing sheet with id=LB, first strand: chain 'L' and resid 23 through 24
    Processing sheet with id=LC, first strand: chain 'L' and resid 52 through 53
    Processing sheet with id=MB, first strand: chain 'M' and resid 23 through 24
    Processing sheet with id=MC, first strand: chain 'M' and resid 52 through 53

    561 hydrogen bonds defined for protein.
    1407 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: 3.03

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2962
        1.32 -     1.44: 3421
        1.44 -     1.57: 8905
        1.57 -     1.69: 0
        1.69 -     1.81: 52
  Bond restraints: 15340
  Sorted by residual:
  bond pdb=" CG  ASP D  19 "
       pdb=" OD2 ASP D  19 "
    ideal  model  delta    sigma   weight residual
    1.249  1.205  0.044 1.90e-02 2.77e+03 5.35e+00
  bond pdb=" CD  GLU A 118 "
       pdb=" OE1 GLU A 118 "
    ideal  model  delta    sigma   weight residual
    1.249  1.206  0.043 1.90e-02 2.77e+03 5.17e+00
  bond pdb=" CG  ASP M  19 "
       pdb=" OD2 ASP M  19 "
    ideal  model  delta    sigma   weight residual
    1.249  1.206  0.043 1.90e-02 2.77e+03 5.13e+00
  bond pdb=" CG  ASP E  19 "
       pdb=" OD2 ASP E  19 "
    ideal  model  delta    sigma   weight residual
    1.249  1.206  0.043 1.90e-02 2.77e+03 5.12e+00
  bond pdb=" CG  ASP B  19 "
       pdb=" OD2 ASP B  19 "
    ideal  model  delta    sigma   weight residual
    1.249  1.206  0.043 1.90e-02 2.77e+03 5.10e+00
  ... (remaining 15335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 17682
        1.27 -     2.53: 2619
        2.53 -     3.80: 382
        3.80 -     5.06: 78
        5.06 -     6.33: 26
  Bond angle restraints: 20787
  Sorted by residual:
  angle pdb=" C   ALA C 108 "
        pdb=" CA  ALA C 108 "
        pdb=" CB  ALA C 108 "
      ideal   model   delta    sigma   weight residual
     116.54  110.21    6.33 1.15e+00 7.56e-01 3.03e+01
  angle pdb=" C   ALA K 108 "
        pdb=" CA  ALA K 108 "
        pdb=" CB  ALA K 108 "
      ideal   model   delta    sigma   weight residual
     116.54  110.22    6.32 1.15e+00 7.56e-01 3.02e+01
  angle pdb=" C   ALA G 108 "
        pdb=" CA  ALA G 108 "
        pdb=" CB  ALA G 108 "
      ideal   model   delta    sigma   weight residual
     116.54  110.23    6.31 1.15e+00 7.56e-01 3.01e+01
  angle pdb=" C   ALA J 108 "
        pdb=" CA  ALA J 108 "
        pdb=" CB  ALA J 108 "
      ideal   model   delta    sigma   weight residual
     116.54  110.25    6.29 1.15e+00 7.56e-01 2.99e+01
  angle pdb=" C   ALA D 108 "
        pdb=" CA  ALA D 108 "
        pdb=" CB  ALA D 108 "
      ideal   model   delta    sigma   weight residual
     116.54  110.25    6.29 1.15e+00 7.56e-01 2.99e+01
  ... (remaining 20782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.78: 8639
       16.78 -    33.56: 279
       33.56 -    50.34: 26
       50.34 -    67.12: 52
       67.12 -    83.89: 65
  Dihedral angle restraints: 9061
    sinusoidal: 3263
      harmonic: 5798
  Sorted by residual:
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  61 "
           pdb=" CB  CYS E  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -54.93  -31.07     1      1.00e+01 1.00e-02 1.38e+01
  dihedral pdb=" CB  CYS J  22 "
           pdb=" SG  CYS J  22 "
           pdb=" SG  CYS J  61 "
           pdb=" CB  CYS J  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -54.94  -31.06     1      1.00e+01 1.00e-02 1.38e+01
  dihedral pdb=" CB  CYS M  22 "
           pdb=" SG  CYS M  22 "
           pdb=" SG  CYS M  61 "
           pdb=" CB  CYS M  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -54.96  -31.04     1      1.00e+01 1.00e-02 1.37e+01
  ... (remaining 9058 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1790
       0.025 -    0.049: 110
       0.049 -    0.074: 102
       0.074 -    0.099: 205
       0.099 -    0.123: 224
  Chirality restraints: 2431
  Sorted by residual:
  chirality pdb=" CA  VAL M 112 "
            pdb=" N   VAL M 112 "
            pdb=" C   VAL M 112 "
            pdb=" CB  VAL M 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  VAL G 112 "
            pdb=" N   VAL G 112 "
            pdb=" C   VAL G 112 "
            pdb=" CB  VAL G 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.47e-01
  chirality pdb=" CA  VAL B 112 "
            pdb=" N   VAL B 112 "
            pdb=" C   VAL B 112 "
            pdb=" CB  VAL B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.44e-01
  ... (remaining 2428 not shown)

  Planarity restraints: 2782
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA J   1 "   -0.063 5.00e-02 4.00e+02   9.56e-02 1.46e+01
        pdb=" N   PRO J   2 "    0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO J   2 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO J   2 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA I   1 "    0.062 5.00e-02 4.00e+02   9.55e-02 1.46e+01
        pdb=" N   PRO I   2 "   -0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO I   2 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO I   2 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A   1 "   -0.062 5.00e-02 4.00e+02   9.53e-02 1.45e+01
        pdb=" N   PRO A   2 "    0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO A   2 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A   2 "   -0.050 5.00e-02 4.00e+02
  ... (remaining 2779 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1545
        2.75 -     3.29: 16056
        3.29 -     3.83: 25346
        3.83 -     4.36: 31495
        4.36 -     4.90: 52126
  Nonbonded interactions: 126568
  Sorted by model distance:
  nonbonded pdb=" O   HIS M  89 "
            pdb=" OG  SER M  90 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   HIS K  89 "
            pdb=" OG  SER K  90 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   HIS F  89 "
            pdb=" OG  SER F  90 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   HIS C  89 "
            pdb=" OG  SER C  90 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   HIS D  89 "
            pdb=" OG  SER D  90 "
     model   vdw
     2.214 3.040
  ... (remaining 126563 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.940
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.044  15353  Z= 0.491
  Angle     :  0.953   6.325  20813  Z= 0.641
  Chirality :  0.045   0.123   2431
  Planarity :  0.007   0.096   2782
  Dihedral  : 12.312  83.894   5356
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  1.24 %
    Allowed  :  8.70 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.15), residues: 2093
  helix: -3.87 (0.19), residues: 260
  sheet:  0.11 (0.18), residues: 611
  loop : -2.01 (0.13), residues: 1222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR E 162 
 PHE   0.002   0.000   PHE B  66 
 HIS   0.001   0.000   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00871 (15340)
  covalent geometry    : angle       0.93455 (20787)
  SS BOND              : bond        0.00380 (   13)
  SS BOND              : angle       5.41484 (   26)
  hydrogen bonds       : bond        0.18688 (  561)
  hydrogen bonds       : angle       9.87816 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  595 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 595
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7822 (mm) cc_final: 0.7597 (mm)
REVERT: C   53 ASP cc_start: 0.7610 (m-30) cc_final: 0.7305 (m-30)
REVERT: C   91 ASP cc_start: 0.6961 (p0) cc_final: 0.6640 (p0)
REVERT: C  101 THR cc_start: 0.7957 (p) cc_final: 0.7095 (t)
REVERT: E   59 VAL cc_start: 0.7181 (m) cc_final: 0.6957 (p)
REVERT: F   53 ASP cc_start: 0.7699 (m-30) cc_final: 0.7455 (m-30)
REVERT: F  101 THR cc_start: 0.6753 (p) cc_final: 0.6329 (t)
REVERT: G   52 MET cc_start: 0.7140 (mmm) cc_final: 0.6757 (tpp)
REVERT: G   94 ASP cc_start: 0.7943 (t0) cc_final: 0.7741 (t70)
REVERT: H   59 VAL cc_start: 0.8635 (m) cc_final: 0.8354 (p)
REVERT: L   33 ILE cc_start: 0.7964 (mm) cc_final: 0.7614 (mm)
REVERT: L  101 THR cc_start: 0.7563 (p) cc_final: 0.7345 (t)
REVERT: L  126 ASP cc_start: 0.7016 (m-30) cc_final: 0.6755 (t70)
REVERT: M   94 ASP cc_start: 0.7469 (t0) cc_final: 0.7062 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 595
  average time/residue: 0.1270
  time to fit residues: 110.2385
Evaluate side-chains
  252 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 194 optimal weight:   10.0000
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:   40.0000
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    7.9990
   chunk 200 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:   30.0000
   overall best weight:    6.2788

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
E  70 ASN
H  87 ASN
I  31 GLN
J  70 ASN
M  70 ASN
M  87 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.063958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.054044 restraints weight = 70037.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.055569 restraints weight = 41343.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.056458 restraints weight = 27902.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.057203 restraints weight = 21036.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.057626 restraints weight = 16936.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15353  Z= 0.160
  Angle     :  0.678  10.780  20813  Z= 0.351
  Chirality :  0.045   0.165   2431
  Planarity :  0.004   0.035   2782
  Dihedral  :  6.662  76.281   2145
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 13.77 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.29 (0.16), residues: 2093
  helix: -2.00 (0.26), residues: 260
  sheet:  0.14 (0.19), residues: 585
  loop : -1.10 (0.16), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR A 162 
 PHE   0.030   0.002   PHE H 158 
 HIS   0.003   0.001   HIS G 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (15340)
  covalent geometry    : angle       0.67732 (20787)
  SS BOND              : bond        0.01234 (   13)
  SS BOND              : angle       1.24970 (   26)
  hydrogen bonds       : bond        0.03475 (  561)
  hydrogen bonds       : angle       7.24788 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 286
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.8593 (mm) cc_final: 0.8114 (mm)
REVERT: A   52 MET cc_start: 0.7233 (mmm) cc_final: 0.6808 (mtp)
REVERT: B   85 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7731 (mt)
REVERT: B  114 PHE cc_start: 0.8147 (m-80) cc_final: 0.7881 (m-80)
REVERT: C   52 MET cc_start: 0.7219 (mmm) cc_final: 0.6685 (mtt)
REVERT: C  162 TYR cc_start: 0.6708 (m-80) cc_final: 0.6038 (m-10)
REVERT: E   52 MET cc_start: 0.7358 (mmm) cc_final: 0.7057 (mtp)
REVERT: E   57 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7610 (tm-30)
REVERT: E   85 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8571 (mt)
REVERT: E  106 GLN cc_start: 0.7092 (mm110) cc_final: 0.6874 (mm-40)
REVERT: F   34 ASP cc_start: 0.8188 (t0) cc_final: 0.7840 (t70)
REVERT: F   52 MET cc_start: 0.7621 (mmm) cc_final: 0.6843 (mtt)
REVERT: G   52 MET cc_start: 0.7437 (mmm) cc_final: 0.6921 (mpp)
REVERT: H   13 PHE cc_start: 0.8126 (m-80) cc_final: 0.7878 (m-80)
REVERT: J   52 MET cc_start: 0.6741 (mmm) cc_final: 0.6505 (mmm)
REVERT: L   33 ILE cc_start: 0.8624 (mm) cc_final: 0.8424 (mm)
REVERT: L   40 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8300 (tttp)
REVERT: M  126 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6477 (t70)
REVERT: M  148 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.7982 (p)
  outliers start: 72
  outliers final: 37
  residues processed: 331
  average time/residue: 0.1239
  time to fit residues: 60.7940
Evaluate side-chains
  263 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 221
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  110 LYS
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain D residue   50 LYS
Chi-restraints excluded: chain D residue   85 ILE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   16 THR
Chi-restraints excluded: chain E residue   85 ILE
Chi-restraints excluded: chain E residue  110 LYS
Chi-restraints excluded: chain F residue   30 ASP
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain G residue   85 ILE
Chi-restraints excluded: chain G residue   95 THR
Chi-restraints excluded: chain H residue   95 THR
Chi-restraints excluded: chain H residue  103 ILE
Chi-restraints excluded: chain H residue  152 PHE
Chi-restraints excluded: chain I residue   30 ASP
Chi-restraints excluded: chain I residue   31 GLN
Chi-restraints excluded: chain I residue   95 THR
Chi-restraints excluded: chain I residue  152 PHE
Chi-restraints excluded: chain J residue   85 ILE
Chi-restraints excluded: chain J residue  152 PHE
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue   56 ILE
Chi-restraints excluded: chain K residue  112 VAL
Chi-restraints excluded: chain L residue   30 ASP
Chi-restraints excluded: chain L residue   40 LYS
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain M residue   78 LYS
Chi-restraints excluded: chain M residue  126 ASP
Chi-restraints excluded: chain M residue  148 THR
Chi-restraints excluded: chain M residue  152 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 65 optimal weight:   20.0000
   chunk 202 optimal weight:   40.0000
   chunk 199 optimal weight:   30.0000
   chunk 200 optimal weight:    9.9990
   chunk 5 optimal weight:   20.0000
   chunk 57 optimal weight:   30.0000
   chunk 147 optimal weight:   40.0000
   chunk 105 optimal weight:   50.0000
   chunk 192 optimal weight:   50.0000
   chunk 85 optimal weight:   10.0000
   chunk 74 optimal weight:   50.0000
   overall best weight:   17.9998

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  70 ASN
** H  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 106 GLN
** K  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.059447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.049685 restraints weight = 72224.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.051081 restraints weight = 43184.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.051956 restraints weight = 29660.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.052665 restraints weight = 22622.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.053103 restraints weight = 18353.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.9986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  15353  Z= 0.290
  Angle     :  0.787   8.662  20813  Z= 0.414
  Chirality :  0.046   0.209   2431
  Planarity :  0.004   0.032   2782
  Dihedral  :  7.514  85.794   2145
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 14.76 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.17), residues: 2093
  helix: -1.46 (0.27), residues: 260
  sheet:  0.08 (0.21), residues: 585
  loop : -0.65 (0.16), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.021   0.003   TYR M 133 
 PHE   0.031   0.003   PHE E 158 
 HIS   0.005   0.002   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00647 (15340)
  covalent geometry    : angle       0.78516 (20787)
  SS BOND              : bond        0.00442 (   13)
  SS BOND              : angle       1.61824 (   26)
  hydrogen bonds       : bond        0.04277 (  561)
  hydrogen bonds       : angle       7.55322 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 229
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 MET cc_start: 0.7388 (mmm) cc_final: 0.7120 (mtp)
REVERT: B   57 GLU cc_start: 0.8619 (tt0) cc_final: 0.8320 (mp0)
REVERT: B   85 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8007 (mt)
REVERT: B  149 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6215 (mp0)
REVERT: C    8 GLN cc_start: 0.7827 (mt0) cc_final: 0.7442 (mt0)
REVERT: C   74 LYS cc_start: 0.8520 (tptt) cc_final: 0.8277 (mtmm)
REVERT: C  162 TYR cc_start: 0.8048 (m-80) cc_final: 0.6971 (m-10)
REVERT: D   27 LYS cc_start: 0.7267 (mmtp) cc_final: 0.7021 (mmmm)
REVERT: D   52 MET cc_start: 0.7761 (mmm) cc_final: 0.7373 (mtp)
REVERT: G   27 LYS cc_start: 0.7421 (mmmt) cc_final: 0.6840 (mmmm)
REVERT: G   52 MET cc_start: 0.8125 (mmm) cc_final: 0.7887 (mmt)
REVERT: G   54 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8488 (mm)
REVERT: G   56 ILE cc_start: 0.8972 (mt) cc_final: 0.8733 (pt)
REVERT: I   52 MET cc_start: 0.7577 (mpp) cc_final: 0.7082 (mmt)
REVERT: M   54 LEU cc_start: 0.8734 (mp) cc_final: 0.8480 (tt)
REVERT: M   67 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7679 (mtmm)
  outliers start: 85
  outliers final: 44
  residues processed: 294
  average time/residue: 0.1286
  time to fit residues: 56.3389
Evaluate side-chains
  196 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 150
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  128 GLU
Chi-restraints excluded: chain C residue  152 PHE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   16 THR
Chi-restraints excluded: chain E residue   50 LYS
Chi-restraints excluded: chain E residue  110 LYS
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain F residue   17 VAL
Chi-restraints excluded: chain F residue   30 ASP
Chi-restraints excluded: chain F residue  106 GLN
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue   54 LEU
Chi-restraints excluded: chain G residue   85 ILE
Chi-restraints excluded: chain G residue  152 PHE
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  105 VAL
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  152 PHE
Chi-restraints excluded: chain I residue   11 VAL
Chi-restraints excluded: chain I residue   33 ILE
Chi-restraints excluded: chain I residue   43 LEU
Chi-restraints excluded: chain I residue  112 VAL
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  152 PHE
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue  152 PHE
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue   17 VAL
Chi-restraints excluded: chain K residue   56 ILE
Chi-restraints excluded: chain K residue  112 VAL
Chi-restraints excluded: chain K residue  152 PHE
Chi-restraints excluded: chain L residue   30 ASP
Chi-restraints excluded: chain L residue   31 GLN
Chi-restraints excluded: chain L residue   43 LEU
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  134 THR
Chi-restraints excluded: chain M residue  152 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 146 optimal weight:   10.0000
   chunk 102 optimal weight:   20.0000
   chunk 99 optimal weight:   40.0000
   chunk 134 optimal weight:   30.0000
   chunk 154 optimal weight:    7.9990
   chunk 101 optimal weight:    3.9990
   chunk 25 optimal weight:   30.0000
   chunk 50 optimal weight:   20.0000
   chunk 71 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 64 optimal weight:   30.0000
   overall best weight:    7.5992

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

Flipped N/Q/H residues before XYZ refinement:
F 163 GLN
G  70 ASN
H 122 ASN
K  70 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.060081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.050513 restraints weight = 71959.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.051954 restraints weight = 42599.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.052882 restraints weight = 28956.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.053485 restraints weight = 21739.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.053952 restraints weight = 17659.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          1.0208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15353  Z= 0.146
  Angle     :  0.616  12.064  20813  Z= 0.309
  Chirality :  0.044   0.154   2431
  Planarity :  0.003   0.022   2782
  Dihedral  :  6.552  80.249   2145
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 17.00 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.17), residues: 2093
  helix: -1.23 (0.26), residues: 273
  sheet:  0.33 (0.21), residues: 585
  loop : -0.60 (0.17), residues: 1235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR F 162 
 PHE   0.024   0.002   PHE E 158 
 HIS   0.002   0.001   HIS D  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (15340)
  covalent geometry    : angle       0.61569 (20787)
  SS BOND              : bond        0.00091 (   13)
  SS BOND              : angle       0.92028 (   26)
  hydrogen bonds       : bond        0.03076 (  561)
  hydrogen bonds       : angle       6.68973 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 173
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LEU cc_start: 0.8413 (tp) cc_final: 0.8149 (tt)
REVERT: B   54 LEU cc_start: 0.8856 (tp) cc_final: 0.8499 (tt)
REVERT: B   85 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7882 (mt)
REVERT: B  149 GLU cc_start: 0.6060 (mt-10) cc_final: 0.5857 (mp0)
REVERT: C    8 GLN cc_start: 0.7842 (mt0) cc_final: 0.7325 (mt0)
REVERT: C  110 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7504 (tttt)
REVERT: H   67 LYS cc_start: 0.6938 (pttp) cc_final: 0.6505 (mtmm)
REVERT: I   52 MET cc_start: 0.7706 (mpp) cc_final: 0.6799 (mpp)
REVERT: I   54 LEU cc_start: 0.8837 (mm) cc_final: 0.8530 (mm)
REVERT: M  149 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6766 (tm-30)
  outliers start: 60
  outliers final: 35
  residues processed: 211
  average time/residue: 0.1140
  time to fit residues: 37.4733
Evaluate side-chains
  180 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 143
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain C residue  110 LYS
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue  110 LYS
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain F residue  152 PHE
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   54 LEU
Chi-restraints excluded: chain G residue  152 PHE
Chi-restraints excluded: chain G residue  160 LEU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  152 PHE
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain I residue   33 ILE
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  152 PHE
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   85 ILE
Chi-restraints excluded: chain J residue  152 PHE
Chi-restraints excluded: chain K residue   56 ILE
Chi-restraints excluded: chain K residue  112 VAL
Chi-restraints excluded: chain K residue  152 PHE
Chi-restraints excluded: chain L residue   30 ASP
Chi-restraints excluded: chain M residue  103 ILE
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  134 THR
Chi-restraints excluded: chain M residue  152 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 54 optimal weight:    0.0770
   chunk 205 optimal weight:    8.9990
   chunk 50 optimal weight:   30.0000
   chunk 155 optimal weight:   20.0000
   chunk 164 optimal weight:   20.0000
   chunk 188 optimal weight:    7.9990
   chunk 127 optimal weight:   20.0000
   chunk 193 optimal weight:    4.9990
   chunk 24 optimal weight:   40.0000
   chunk 130 optimal weight:   30.0000
   chunk 126 optimal weight:   50.0000
   overall best weight:    8.4148

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  70 ASN
** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.059553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.050182 restraints weight = 71049.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.051613 restraints weight = 41502.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.052533 restraints weight = 27947.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.053126 restraints weight = 20763.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.053564 restraints weight = 16845.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          1.0481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15353  Z= 0.151
  Angle     :  0.585  10.107  20813  Z= 0.297
  Chirality :  0.043   0.130   2431
  Planarity :  0.003   0.021   2782
  Dihedral  :  6.256  72.683   2145
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.68 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.17), residues: 2093
  helix: -1.47 (0.26), residues: 260
  sheet:  0.43 (0.21), residues: 585
  loop : -0.46 (0.17), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.001   TYR K 162 
 PHE   0.022   0.002   PHE E 158 
 HIS   0.002   0.001   HIS D  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (15340)
  covalent geometry    : angle       0.58442 (20787)
  SS BOND              : bond        0.00072 (   13)
  SS BOND              : angle       0.81567 (   26)
  hydrogen bonds       : bond        0.02906 (  561)
  hydrogen bonds       : angle       6.47856 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 159
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 LYS cc_start: 0.4542 (mptt) cc_final: 0.2076 (mmtt)
REVERT: B   85 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7757 (mt)
REVERT: C    8 GLN cc_start: 0.7928 (mt0) cc_final: 0.7451 (mt0)
REVERT: C  110 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7491 (tttt)
REVERT: D  152 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5010 (m-80)
REVERT: H   67 LYS cc_start: 0.6989 (pttp) cc_final: 0.6442 (ttpt)
REVERT: I   52 MET cc_start: 0.7496 (mpp) cc_final: 0.7166 (mpp)
REVERT: I   54 LEU cc_start: 0.8824 (mm) cc_final: 0.8520 (mm)
REVERT: J  149 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6471 (tm-30)
REVERT: M   52 MET cc_start: 0.7841 (mmm) cc_final: 0.7001 (mtt)
  outliers start: 57
  outliers final: 44
  residues processed: 199
  average time/residue: 0.1073
  time to fit residues: 34.0621
Evaluate side-chains
  186 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 139
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue  110 LYS
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  152 PHE
Chi-restraints excluded: chain D residue  152 PHE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   16 THR
Chi-restraints excluded: chain E residue  110 LYS
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain F residue  152 PHE
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue   54 LEU
Chi-restraints excluded: chain G residue  152 PHE
Chi-restraints excluded: chain G residue  160 LEU
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  152 PHE
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain I residue   33 ILE
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  152 PHE
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   85 ILE
Chi-restraints excluded: chain J residue  152 PHE
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue   56 ILE
Chi-restraints excluded: chain K residue  112 VAL
Chi-restraints excluded: chain K residue  152 PHE
Chi-restraints excluded: chain M residue   82 THR
Chi-restraints excluded: chain M residue  103 ILE
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  134 THR
Chi-restraints excluded: chain M residue  152 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 144 optimal weight:   40.0000
   chunk 139 optimal weight:    0.9980
   chunk 138 optimal weight:    6.9990
   chunk 160 optimal weight:   50.0000
   chunk 106 optimal weight:   50.0000
   chunk 161 optimal weight:   40.0000
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:   50.0000
   chunk 136 optimal weight:    0.9990
   chunk 149 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.060414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.050995 restraints weight = 70954.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.052387 restraints weight = 41531.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.053296 restraints weight = 28250.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.053944 restraints weight = 21088.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.054383 restraints weight = 16920.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          1.0575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  15353  Z= 0.107
  Angle     :  0.561  12.568  20813  Z= 0.278
  Chirality :  0.043   0.133   2431
  Planarity :  0.003   0.023   2782
  Dihedral  :  5.854  69.111   2145
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.67 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.17), residues: 2093
  helix: -1.29 (0.28), residues: 273
  sheet:  0.76 (0.21), residues: 572
  loop : -0.31 (0.17), residues: 1248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.001   TYR K 162 
 PHE   0.019   0.001   PHE E 158 
 HIS   0.002   0.001   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (15340)
  covalent geometry    : angle       0.56076 (20787)
  SS BOND              : bond        0.00058 (   13)
  SS BOND              : angle       0.68301 (   26)
  hydrogen bonds       : bond        0.02533 (  561)
  hydrogen bonds       : angle       6.13958 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 165
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 LYS cc_start: 0.4357 (mptt) cc_final: 0.1962 (mmtt)
REVERT: B   57 GLU cc_start: 0.8645 (tt0) cc_final: 0.7841 (tm-30)
REVERT: C    8 GLN cc_start: 0.7917 (mt0) cc_final: 0.7470 (mt0)
REVERT: C  110 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7675 (tttt)
REVERT: D  152 PHE cc_start: 0.5836 (OUTLIER) cc_final: 0.4850 (m-80)
REVERT: H   67 LYS cc_start: 0.7091 (pttp) cc_final: 0.6690 (ttpp)
REVERT: I   52 MET cc_start: 0.7377 (mpp) cc_final: 0.7129 (mpp)
REVERT: J   74 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7380 (mptt)
REVERT: J  149 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6489 (tm-30)
REVERT: M   52 MET cc_start: 0.7772 (mmm) cc_final: 0.7295 (mtt)
  outliers start: 47
  outliers final: 38
  residues processed: 192
  average time/residue: 0.1065
  time to fit residues: 32.6430
Evaluate side-chains
  182 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 141
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue  110 LYS
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  152 PHE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain D residue  152 PHE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain F residue  152 PHE
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  152 PHE
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  152 PHE
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain I residue   33 ILE
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  152 PHE
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   24 ILE
Chi-restraints excluded: chain J residue   74 LYS
Chi-restraints excluded: chain J residue  152 PHE
Chi-restraints excluded: chain K residue   56 ILE
Chi-restraints excluded: chain K residue  112 VAL
Chi-restraints excluded: chain K residue  152 PHE
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain L residue  152 PHE
Chi-restraints excluded: chain M residue  103 ILE
Chi-restraints excluded: chain M residue  152 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 115 optimal weight:   50.0000
   chunk 186 optimal weight:   50.0000
   chunk 23 optimal weight:    4.9990
   chunk 66 optimal weight:    8.9990
   chunk 181 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 203 optimal weight:   50.0000
   chunk 98 optimal weight:   30.0000
   chunk 131 optimal weight:    8.9990
   chunk 144 optimal weight:   40.0000
   overall best weight:   10.5994

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  96 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.059459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.049965 restraints weight = 71138.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.051348 restraints weight = 42824.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.052219 restraints weight = 29322.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.052812 restraints weight = 22243.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.053314 restraints weight = 18143.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          1.0860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  15353  Z= 0.176
  Angle     :  0.601  10.780  20813  Z= 0.304
  Chirality :  0.043   0.168   2431
  Planarity :  0.003   0.022   2782
  Dihedral  :  6.074  67.817   2145
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.61 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.17), residues: 2093
  helix: -1.06 (0.29), residues: 260
  sheet:  0.78 (0.21), residues: 572
  loop : -0.41 (0.17), residues: 1261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.001   TYR K 162 
 PHE   0.023   0.002   PHE M 158 
 HIS   0.002   0.001   HIS K 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (15340)
  covalent geometry    : angle       0.60026 (20787)
  SS BOND              : bond        0.00110 (   13)
  SS BOND              : angle       0.88038 (   26)
  hydrogen bonds       : bond        0.02928 (  561)
  hydrogen bonds       : angle       6.41598 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 131
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 LYS cc_start: 0.4448 (mptt) cc_final: 0.1998 (mmtt)
REVERT: B   54 LEU cc_start: 0.8835 (tp) cc_final: 0.8460 (tt)
REVERT: B   85 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7858 (mt)
REVERT: D  152 PHE cc_start: 0.5837 (OUTLIER) cc_final: 0.4611 (m-80)
REVERT: H   67 LYS cc_start: 0.7119 (pttp) cc_final: 0.6633 (tmmt)
REVERT: I   52 MET cc_start: 0.7339 (mpp) cc_final: 0.7080 (mpp)
REVERT: J   73 LYS cc_start: 0.6655 (mtpt) cc_final: 0.6414 (mtmm)
REVERT: J   74 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7306 (mptt)
REVERT: J  149 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6545 (tm-30)
REVERT: M   52 MET cc_start: 0.7942 (mmm) cc_final: 0.7417 (mtt)
  outliers start: 57
  outliers final: 44
  residues processed: 170
  average time/residue: 0.1062
  time to fit residues: 29.1733
Evaluate side-chains
  170 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 123
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  152 PHE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain D residue  152 PHE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   16 THR
Chi-restraints excluded: chain E residue  110 LYS
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain F residue  152 PHE
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  152 PHE
Chi-restraints excluded: chain G residue  160 LEU
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   24 ILE
Chi-restraints excluded: chain H residue  152 PHE
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain I residue   11 VAL
Chi-restraints excluded: chain I residue   33 ILE
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  152 PHE
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   74 LYS
Chi-restraints excluded: chain J residue  152 PHE
Chi-restraints excluded: chain K residue   56 ILE
Chi-restraints excluded: chain K residue  112 VAL
Chi-restraints excluded: chain K residue  152 PHE
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain L residue  152 PHE
Chi-restraints excluded: chain M residue  103 ILE
Chi-restraints excluded: chain M residue  134 THR
Chi-restraints excluded: chain M residue  152 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 177 optimal weight:    8.9990
   chunk 111 optimal weight:   20.0000
   chunk 154 optimal weight:   50.0000
   chunk 114 optimal weight:    5.9990
   chunk 176 optimal weight:   50.0000
   chunk 127 optimal weight:   50.0000
   chunk 72 optimal weight:    0.6980
   chunk 164 optimal weight:   20.0000
   chunk 87 optimal weight:   50.0000
   chunk 24 optimal weight:   30.0000
   chunk 97 optimal weight:   20.0000
   overall best weight:   11.1392

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  96 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.058625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.049423 restraints weight = 71973.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.050809 restraints weight = 41709.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.051707 restraints weight = 27992.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.052314 restraints weight = 20876.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.052793 restraints weight = 16894.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          1.1116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  15353  Z= 0.180
  Angle     :  0.617  12.411  20813  Z= 0.309
  Chirality :  0.043   0.138   2431
  Planarity :  0.003   0.027   2782
  Dihedral  :  6.108  65.340   2145
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 19.23 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.17), residues: 2093
  helix: -1.39 (0.32), residues: 182
  sheet:  0.68 (0.20), residues: 637
  loop : -0.55 (0.17), residues: 1274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.001   TYR K 162 
 PHE   0.021   0.002   PHE M 158 
 HIS   0.003   0.001   HIS J 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (15340)
  covalent geometry    : angle       0.61613 (20787)
  SS BOND              : bond        0.00125 (   13)
  SS BOND              : angle       0.90594 (   26)
  hydrogen bonds       : bond        0.02941 (  561)
  hydrogen bonds       : angle       6.41332 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 118
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 LYS cc_start: 0.4659 (mptt) cc_final: 0.2009 (mmtt)
REVERT: B   85 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7844 (mt)
REVERT: D  152 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.4615 (m-80)
REVERT: I   52 MET cc_start: 0.7221 (mpp) cc_final: 0.6890 (mpp)
REVERT: J   73 LYS cc_start: 0.6754 (mtpt) cc_final: 0.6530 (mtmm)
REVERT: J   74 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7229 (mptt)
REVERT: J  149 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6634 (tm-30)
REVERT: M   52 MET cc_start: 0.7851 (mmm) cc_final: 0.7039 (mtt)
  outliers start: 53
  outliers final: 46
  residues processed: 157
  average time/residue: 0.1049
  time to fit residues: 26.5935
Evaluate side-chains
  162 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 113
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  152 PHE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain D residue  152 PHE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue  110 LYS
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain F residue   11 VAL
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain F residue  152 PHE
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  152 PHE
Chi-restraints excluded: chain G residue  160 LEU
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  152 PHE
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain I residue   11 VAL
Chi-restraints excluded: chain I residue   33 ILE
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  152 PHE
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   74 LYS
Chi-restraints excluded: chain J residue  152 PHE
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue   56 ILE
Chi-restraints excluded: chain K residue  112 VAL
Chi-restraints excluded: chain K residue  152 PHE
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain L residue  152 PHE
Chi-restraints excluded: chain M residue   56 ILE
Chi-restraints excluded: chain M residue  103 ILE
Chi-restraints excluded: chain M residue  134 THR
Chi-restraints excluded: chain M residue  152 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 42 optimal weight:   40.0000
   chunk 81 optimal weight:   20.0000
   chunk 1 optimal weight:   30.0000
   chunk 5 optimal weight:   10.0000
   chunk 201 optimal weight:    5.9990
   chunk 120 optimal weight:    0.9990
   chunk 9 optimal weight:   50.0000
   chunk 177 optimal weight:    8.9990
   chunk 153 optimal weight:   30.0000
   chunk 62 optimal weight:   50.0000
   chunk 79 optimal weight:   20.0000
   overall best weight:    9.1994

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   8 GLN
G  70 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.058924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.049808 restraints weight = 71766.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.051222 restraints weight = 41400.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.052126 restraints weight = 27647.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.052719 restraints weight = 20552.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.053191 restraints weight = 16622.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          1.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  15353  Z= 0.157
  Angle     :  0.597  11.805  20813  Z= 0.297
  Chirality :  0.043   0.143   2431
  Planarity :  0.003   0.025   2782
  Dihedral  :  5.927  64.065   2145
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.67 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.18), residues: 2093
  helix: -1.38 (0.32), residues: 182
  sheet:  0.72 (0.20), residues: 637
  loop : -0.53 (0.17), residues: 1274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.001   TYR K 162 
 PHE   0.022   0.002   PHE M 158 
 HIS   0.002   0.001   HIS K 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (15340)
  covalent geometry    : angle       0.59692 (20787)
  SS BOND              : bond        0.00105 (   13)
  SS BOND              : angle       0.82679 (   26)
  hydrogen bonds       : bond        0.02800 (  561)
  hydrogen bonds       : angle       6.32222 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 121
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 LYS cc_start: 0.4638 (mptt) cc_final: 0.1992 (mmtt)
REVERT: B   85 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7841 (mt)
REVERT: D  152 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.4617 (m-80)
REVERT: I   52 MET cc_start: 0.7174 (mpp) cc_final: 0.6862 (mpp)
REVERT: J   74 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.7075 (mptt)
REVERT: J  149 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6772 (tm-30)
REVERT: M   52 MET cc_start: 0.7836 (mmm) cc_final: 0.7031 (mtt)
  outliers start: 54
  outliers final: 46
  residues processed: 160
  average time/residue: 0.0960
  time to fit residues: 25.2168
Evaluate side-chains
  162 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 113
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  152 PHE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain D residue  152 PHE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue  110 LYS
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain F residue  152 PHE
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  152 PHE
Chi-restraints excluded: chain G residue  160 LEU
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  152 PHE
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain I residue   11 VAL
Chi-restraints excluded: chain I residue   17 VAL
Chi-restraints excluded: chain I residue   33 ILE
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  152 PHE
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   74 LYS
Chi-restraints excluded: chain J residue   85 ILE
Chi-restraints excluded: chain J residue  152 PHE
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue   56 ILE
Chi-restraints excluded: chain K residue  112 VAL
Chi-restraints excluded: chain K residue  152 PHE
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain L residue  152 PHE
Chi-restraints excluded: chain M residue   56 ILE
Chi-restraints excluded: chain M residue  103 ILE
Chi-restraints excluded: chain M residue  134 THR
Chi-restraints excluded: chain M residue  152 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 49 optimal weight:   30.0000
   chunk 104 optimal weight:    0.0570
   chunk 127 optimal weight:   40.0000
   chunk 99 optimal weight:   30.0000
   chunk 64 optimal weight:   40.0000
   chunk 200 optimal weight:    2.9990
   chunk 78 optimal weight:    9.9990
   chunk 68 optimal weight:   20.0000
   chunk 26 optimal weight:   20.0000
   chunk 115 optimal weight:   50.0000
   chunk 29 optimal weight:    7.9990
   overall best weight:    8.2108

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

Flipped N/Q/H residues before XYZ refinement:
B  70 ASN
** C  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.059251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.049994 restraints weight = 72828.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.051379 restraints weight = 43000.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.052225 restraints weight = 29167.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.052911 restraints weight = 22012.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.053324 restraints weight = 17660.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          1.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092  15353  Z= 0.149
  Angle     :  0.617  13.376  20813  Z= 0.303
  Chirality :  0.044   0.213   2431
  Planarity :  0.003   0.025   2782
  Dihedral  :  5.900  70.819   2145
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.79 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.18), residues: 2093
  helix: -1.34 (0.33), residues: 182
  sheet:  0.77 (0.21), residues: 637
  loop : -0.53 (0.17), residues: 1274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.001   TYR K 162 
 PHE   0.021   0.002   PHE M 158 
 HIS   0.002   0.001   HIS D  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (15340)
  covalent geometry    : angle       0.61348 (20787)
  SS BOND              : bond        0.00795 (   13)
  SS BOND              : angle       1.99535 (   26)
  hydrogen bonds       : bond        0.02775 (  561)
  hydrogen bonds       : angle       6.24552 ( 1407)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 121
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 LYS cc_start: 0.4586 (mptt) cc_final: 0.1961 (mmtt)
REVERT: B   85 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7843 (mt)
REVERT: D  152 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.4500 (m-80)
REVERT: I   52 MET cc_start: 0.7126 (mpp) cc_final: 0.6812 (mpp)
REVERT: J   74 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7140 (mptt)
REVERT: J  149 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6810 (tm-30)
REVERT: M   52 MET cc_start: 0.7825 (mmm) cc_final: 0.7047 (mtt)
  outliers start: 52
  outliers final: 47
  residues processed: 159
  average time/residue: 0.0987
  time to fit residues: 25.7896
Evaluate side-chains
  165 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 115
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue  152 PHE
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain C residue   11 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  152 PHE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain D residue  152 PHE
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   17 VAL
Chi-restraints excluded: chain E residue  110 LYS
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain F residue  112 VAL
Chi-restraints excluded: chain F residue  152 PHE
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  152 PHE
Chi-restraints excluded: chain G residue  160 LEU
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  152 PHE
Chi-restraints excluded: chain H residue  160 LEU
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain I residue   11 VAL
Chi-restraints excluded: chain I residue   17 VAL
Chi-restraints excluded: chain I residue   33 ILE
Chi-restraints excluded: chain I residue  118 GLU
Chi-restraints excluded: chain I residue  152 PHE
Chi-restraints excluded: chain J residue   16 THR
Chi-restraints excluded: chain J residue   74 LYS
Chi-restraints excluded: chain J residue   85 ILE
Chi-restraints excluded: chain J residue  152 PHE
Chi-restraints excluded: chain K residue   11 VAL
Chi-restraints excluded: chain K residue   56 ILE
Chi-restraints excluded: chain K residue  112 VAL
Chi-restraints excluded: chain K residue  152 PHE
Chi-restraints excluded: chain K residue  155 VAL
Chi-restraints excluded: chain L residue  152 PHE
Chi-restraints excluded: chain M residue   56 ILE
Chi-restraints excluded: chain M residue  103 ILE
Chi-restraints excluded: chain M residue  134 THR
Chi-restraints excluded: chain M residue  152 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 167 optimal weight:   10.0000
   chunk 190 optimal weight:    0.7980
   chunk 29 optimal weight:   30.0000
   chunk 50 optimal weight:   40.0000
   chunk 86 optimal weight:   10.0000
   chunk 82 optimal weight:   20.0000
   chunk 106 optimal weight:   40.0000
   chunk 72 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 201 optimal weight:   30.0000
   chunk 199 optimal weight:   50.0000
   overall best weight:    7.7592

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

Flipped N/Q/H residues before XYZ refinement:
** C  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.059305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.050194 restraints weight = 71688.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.051595 restraints weight = 41776.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.052474 restraints weight = 28051.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.053149 restraints weight = 21006.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.053571 restraints weight = 16803.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          1.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  15353  Z= 0.145
  Angle     :  0.625  17.708  20813  Z= 0.305
  Chirality :  0.044   0.176   2431
  Planarity :  0.003   0.028   2782
  Dihedral  :  5.878  68.165   2145
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.29 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.18), residues: 2093
  helix: -1.11 (0.29), residues: 260
  sheet:  0.77 (0.21), residues: 637
  loop : -0.35 (0.17), residues: 1196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.001   TYR K 162 
 PHE   0.018   0.002   PHE D 152 
 HIS   0.002   0.001   HIS K  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (15340)
  covalent geometry    : angle       0.62166 (20787)
  SS BOND              : bond        0.00738 (   13)
  SS BOND              : angle       2.02065 (   26)
  hydrogen bonds       : bond        0.02721 (  561)
  hydrogen bonds       : angle       6.22920 ( 1407)

===============================================================================
Job complete
usr+sys time: 2045.69 seconds
wall clock time: 36 minutes 47.71 seconds (2207.71 seconds total)