Starting phenix.real_space_refine
on Fri Aug 22 15:04:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wyi_37929/08_2025/8wyi_37929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wyi_37929/08_2025/8wyi_37929.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wyi_37929/08_2025/8wyi_37929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wyi_37929/08_2025/8wyi_37929.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wyi_37929/08_2025/8wyi_37929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wyi_37929/08_2025/8wyi_37929.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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      37      5.16       5
     C    3018      2.51       5
     N     743      2.21       5
     O     861      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4659
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "a"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 245
          Classifications: {'peptide': 30}
          Link IDs: {'PTRANS': 1, 'TRANS': 28}
    Chain: "b"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 226
          Classifications: {'peptide': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 26}
    Chain: "d"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 821
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 3, 'TRANS': 102}
    Chain: "e"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 959
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
    Chain: "f"
      Number of atoms: 933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 933
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
          Chain breaks: 1
    Chain: "g"
      Number of atoms: 899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 899
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 2, 'TRANS': 111}
    Chain: "m"
      Number of atoms: 292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 292
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "n"
      Number of atoms: 284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 284
          Classifications: {'peptide': 35}
          Link IDs: {'TRANS': 34}
  Time building chain proxies: 1.45, per 1000 atoms: 0.31
  Number of scatterers: 4659
  At special positions: 0
  Unit cell: (70.0245, 89.4159, 107.73, 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      37     16.00
     O     861      8.00
     N     743      7.00
     C    3018      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS a  32 " - pdb=" SG  CYS b  32 " distance=2.03
    Simple disulfide: pdb=" SG  CYS d  37 " - pdb=" SG  CYS d  73 " distance=2.04
    Simple disulfide: pdb=" SG  CYS d  93 " - pdb=" SG  CYS d  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e  49 " - pdb=" SG  CYS e  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e 119 " - pdb=" SG  CYS e 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f  49 " - pdb=" SG  CYS f  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g  46 " - pdb=" SG  CYS g  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g 104 " - pdb=" SG  CYS g 107 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 182.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1094

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 7 sheets defined
      39.9% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'a' and resid 27 through 55
    Processing helix  chain 'b' and resid 28 through 54
      removed outlier: 3.691A  pdb=" N   CYS b  32 " --> pdb=" O   ASP b  28 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 100 through 127
    Processing helix  chain 'e' and resid 70 through 74
      removed outlier: 3.779A  pdb=" N   ASN e  74 " --> pdb=" O   ASP e  71 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 126 through 152
      removed outlier: 3.820A  pdb=" N   VAL e 130 " --> pdb=" O   ASP e 126 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 126 through 154
    Processing helix  chain 'g' and resid 113 through 137
    Processing helix  chain 'm' and resid 260 through 290
      removed outlier: 3.989A  pdb=" N   TRP m 290 " --> pdb=" O   THR m 286 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 272 through 305
    Processing sheet with id=AA1, first strand: chain 'd' and resid 45 through 46
      removed outlier: 3.573A  pdb=" N   GLU d  45 " --> pdb=" O   ILE d  70 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   THR d  85 " --> pdb=" O   TYR e 111 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   TYR e 113 " --> pdb=" O   THR d  85 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   GLN d  87 " --> pdb=" O   TYR e 113 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'd' and resid 96 through 97
    Processing sheet with id=AA3, first strand: chain 'e' and resid 37 through 41
      removed outlier: 3.667A  pdb=" N   LEU e  47 " --> pdb=" O   LEU e  82 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU e  82 " --> pdb=" O   LEU e  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 41
    Processing sheet with id=AA5, first strand: chain 'f' and resid 58 through 60
      removed outlier: 3.729A  pdb=" N   GLN f  60 " --> pdb=" O   VAL f  97 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL f  97 " --> pdb=" O   GLN f  60 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'f' and resid 114 through 116
      removed outlier: 7.024A  pdb=" N   ARG f 115 " --> pdb=" O   ARG g 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'g' and resid 32 through 34
      removed outlier: 4.548A  pdb=" N   LEU g  43 " --> pdb=" O   TYR g  34 " (cutoff:3.500A)

    222 hydrogen bonds defined for protein.
    639 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: 0.53

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1447
        1.34 -     1.47: 1129
        1.47 -     1.59: 2119
        1.59 -     1.71: 0
        1.71 -     1.83: 51
  Bond restraints: 4746
  Sorted by residual:
  bond pdb=" CB  ARG m 288 "
       pdb=" CG  ARG m 288 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.99e+00
  bond pdb=" CB  GLU e  79 "
       pdb=" CG  GLU e  79 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.90e+00
  bond pdb=" C   ASP a  28 "
       pdb=" N   PRO a  29 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.017 1.30e-02 5.92e+03 1.72e+00
  bond pdb=" CB  LYS g  69 "
       pdb=" CG  LYS g  69 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.69e+00
  bond pdb=" N   ASP d  59 "
       pdb=" CA  ASP d  59 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.64e+00
  ... (remaining 4741 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 6050
        1.99 -     3.98: 302
        3.98 -     5.96: 45
        5.96 -     7.95: 22
        7.95 -     9.94: 9
  Bond angle restraints: 6428
  Sorted by residual:
  angle pdb=" N   GLN f  51 "
        pdb=" CA  GLN f  51 "
        pdb=" C   GLN f  51 "
      ideal   model   delta    sigma   weight residual
     114.75  108.19    6.56 1.26e+00 6.30e-01 2.71e+01
  angle pdb=" C   LEU d  58 "
        pdb=" N   ASP d  59 "
        pdb=" CA  ASP d  59 "
      ideal   model   delta    sigma   weight residual
     121.54  129.79   -8.25 1.91e+00 2.74e-01 1.87e+01
  angle pdb=" N   GLU e  70 "
        pdb=" CA  GLU e  70 "
        pdb=" C   GLU e  70 "
      ideal   model   delta    sigma   weight residual
     113.23  108.00    5.23 1.22e+00 6.72e-01 1.84e+01
  angle pdb=" CA  CYS d  96 "
        pdb=" CB  CYS d  96 "
        pdb=" SG  CYS d  96 "
      ideal   model   delta    sigma   weight residual
     114.40  123.30   -8.90 2.30e+00 1.89e-01 1.50e+01
  angle pdb=" CA  LYS g  69 "
        pdb=" CB  LYS g  69 "
        pdb=" CG  LYS g  69 "
      ideal   model   delta    sigma   weight residual
     114.10  121.75   -7.65 2.00e+00 2.50e-01 1.46e+01
  ... (remaining 6423 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 2353
       17.78 -    35.55: 372
       35.55 -    53.33: 97
       53.33 -    71.10: 11
       71.10 -    88.88: 8
  Dihedral angle restraints: 2841
    sinusoidal: 1132
      harmonic: 1709
  Sorted by residual:
  dihedral pdb=" CB  CYS g 104 "
           pdb=" SG  CYS g 104 "
           pdb=" SG  CYS g 107 "
           pdb=" CB  CYS g 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.98  -87.02     1      1.00e+01 1.00e-02 9.10e+01
  dihedral pdb=" CB  CYS e 119 "
           pdb=" SG  CYS e 119 "
           pdb=" SG  CYS e 122 "
           pdb=" CB  CYS e 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -151.04   65.04     1      1.00e+01 1.00e-02 5.55e+01
  dihedral pdb=" CB  CYS a  32 "
           pdb=" SG  CYS a  32 "
           pdb=" SG  CYS b  32 "
           pdb=" CB  CYS b  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.20  -49.20     1      1.00e+01 1.00e-02 3.33e+01
  ... (remaining 2838 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 550
       0.045 -    0.090: 160
       0.090 -    0.135: 37
       0.135 -    0.180: 4
       0.180 -    0.225: 2
  Chirality restraints: 753
  Sorted by residual:
  chirality pdb=" CA  ASP d  59 "
            pdb=" N   ASP d  59 "
            pdb=" C   ASP d  59 "
            pdb=" CB  ASP d  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  ILE n 299 "
            pdb=" CA  ILE n 299 "
            pdb=" CG1 ILE n 299 "
            pdb=" CG2 ILE n 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.98e-01
  chirality pdb=" CA  ASN d  36 "
            pdb=" N   ASN d  36 "
            pdb=" C   ASN d  36 "
            pdb=" CB  ASN d  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.43e-01
  ... (remaining 750 not shown)

  Planarity restraints: 791
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR e  52 "   -0.045 5.00e-02 4.00e+02   6.86e-02 7.54e+00
        pdb=" N   PRO e  53 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO e  53 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO e  53 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR f  99 "    0.041 5.00e-02 4.00e+02   6.25e-02 6.25e+00
        pdb=" N   PRO f 100 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO f 100 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO f 100 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP d  43 "    0.016 2.00e-02 2.50e+03   1.35e-02 4.56e+00
        pdb=" CG  TRP d  43 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP d  43 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP d  43 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP d  43 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP d  43 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP d  43 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP d  43 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP d  43 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP d  43 "    0.000 2.00e-02 2.50e+03
  ... (remaining 788 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 76
        2.63 -     3.20: 4388
        3.20 -     3.77: 7079
        3.77 -     4.33: 8814
        4.33 -     4.90: 14140
  Nonbonded interactions: 34497
  Sorted by model distance:
  nonbonded pdb=" O   LEU m 289 "
            pdb=" CE3 TRP m 290 "
     model   vdw
     2.068 3.340
  nonbonded pdb=" N   GLN f  33 "
            pdb=" NE2 GLN f  33 "
     model   vdw
     2.160 3.200
  nonbonded pdb=" OG  SER m 291 "
            pdb=" N   SER m 292 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" O   LEU m 289 "
            pdb=" CD2 TRP m 290 "
     model   vdw
     2.214 3.260
  nonbonded pdb=" ND2 ASN d  38 "
            pdb=" OG1 THR d  76 "
     model   vdw
     2.217 3.120
  ... (remaining 34492 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'a' and resid 27 through 54)
  selection = chain 'b'
}
ncs_group {
  reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153))
  selection = (chain 'f' and resid 33 through 153)
}

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:             0.680
  Set stop_for_unknowns flag:              0.010
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.400
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
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      :  0.004   0.042   4754  Z= 0.206
  Angle     :  1.066   9.939   6444  Z= 0.582
  Chirality :  0.044   0.225    753
  Planarity :  0.006   0.069    791
  Dihedral  : 18.199  88.877   1723
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  1.58 %
    Allowed  : 11.21 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 42.07 %
    Favored  : 56.02 %
  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: -1.04 (0.35), residues: 571
  helix:  3.06 (0.33), residues: 221
  sheet: -2.21 (0.73), residues: 52
  loop : -3.66 (0.27), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG e 115 
 TYR   0.019   0.001   TYR g  34 
 PHE   0.018   0.002   PHE m 281 
 TRP   0.037   0.003   TRP d  43 
 HIS   0.006   0.001   HIS d  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 4746)
  covalent geometry    : angle       1.06073 ( 6428)
  SS BOND              : bond        0.00439 (    8)
  SS BOND              : angle       2.37471 (   16)
  hydrogen bonds       : bond        0.14329 (  222)
  hydrogen bonds       : angle       4.93449 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 153
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: e   85 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8254 (pttm)
REVERT: e  117 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7318 (tpp80)
REVERT: f  126 ASP cc_start: 0.7698 (t70) cc_final: 0.7062 (p0)
REVERT: g   55 TRP cc_start: 0.5446 (m100) cc_final: 0.4702 (m100)
REVERT: g   72 TRP cc_start: 0.8170 (t-100) cc_final: 0.7878 (t-100)
REVERT: g   84 MET cc_start: 0.5874 (mmm) cc_final: 0.5316 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 156
  average time/residue: 0.0676
  time to fit residues: 13.4457
Evaluate side-chains
  152 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 147
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain d residue   31 ASP
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain m residue  258 THR
Chi-restraints excluded: chain m residue  290 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0170
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
e  62 ASN
f  33 GLN
** g  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
g  92 ASN
** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.172943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.140447 restraints weight = 6526.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.144106 restraints weight = 4086.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.146639 restraints weight = 3010.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.148222 restraints weight = 2428.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.149441 restraints weight = 2091.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4754  Z= 0.149
  Angle     :  0.810  10.384   6444  Z= 0.396
  Chirality :  0.043   0.174    753
  Planarity :  0.005   0.053    791
  Dihedral  :  6.151  55.209    642
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  1.23 %
    Allowed  : 12.61 %
    Favored  : 86.16 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 33.46 %
    Favored  : 58.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.36), residues: 571
  helix:  3.47 (0.31), residues: 222
  sheet: -3.22 (0.59), residues: 64
  loop : -3.50 (0.28), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG e 115 
 TYR   0.020   0.001   TYR n 283 
 PHE   0.009   0.001   PHE m 281 
 TRP   0.022   0.002   TRP d  43 
 HIS   0.002   0.001   HIS e  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4746)
  covalent geometry    : angle       0.80576 ( 6428)
  SS BOND              : bond        0.00320 (    8)
  SS BOND              : angle       1.90845 (   16)
  hydrogen bonds       : bond        0.04269 (  222)
  hydrogen bonds       : angle       3.86396 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: d   91 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8640 (tmm160)
REVERT: g   55 TRP cc_start: 0.6056 (m100) cc_final: 0.5391 (m100)
  outliers start: 41
  outliers final: 24
  residues processed: 174
  average time/residue: 0.0578
  time to fit residues: 12.9499
Evaluate side-chains
  168 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain d residue   58 LEU
Chi-restraints excluded: chain d residue   85 THR
Chi-restraints excluded: chain d residue   91 ARG
Chi-restraints excluded: chain d residue  115 THR
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   45 VAL
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  123 MET
Chi-restraints excluded: chain e residue  124 GLU
Chi-restraints excluded: chain e residue  153 LYS
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue   53 ILE
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  133 VAL
Chi-restraints excluded: chain m residue  286 THR
Chi-restraints excluded: chain m residue  290 TRP
Chi-restraints excluded: chain n residue  276 LEU
Chi-restraints excluded: chain n residue  293 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
f  33 GLN
f  92 GLN
n 275 GLN
** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.176866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.145625 restraints weight = 6516.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.148605 restraints weight = 4146.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.148974 restraints weight = 3195.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.149542 restraints weight = 2977.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.151970 restraints weight = 2734.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4754  Z= 0.151
  Angle     :  0.774   9.564   6444  Z= 0.382
  Chirality :  0.043   0.198    753
  Planarity :  0.004   0.044    791
  Dihedral  :  5.763  55.214    639
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 11.91 %
    Favored  : 87.04 %
  Rotamer:
    Outliers :  9.75 %
    Allowed  : 32.12 %
    Favored  : 58.13 %
  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: -0.69 (0.36), residues: 571
  helix:  3.55 (0.31), residues: 222
  sheet: -2.98 (0.54), residues: 80
  loop : -3.41 (0.29), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG e 115 
 TYR   0.012   0.001   TYR f  96 
 PHE   0.008   0.001   PHE n 296 
 TRP   0.024   0.002   TRP d  43 
 HIS   0.002   0.001   HIS e  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4746)
  covalent geometry    : angle       0.76998 ( 6428)
  SS BOND              : bond        0.00391 (    8)
  SS BOND              : angle       1.76665 (   16)
  hydrogen bonds       : bond        0.04262 (  222)
  hydrogen bonds       : angle       3.68286 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 153
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: b   34 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7414 (tm)
REVERT: d   91 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8671 (tmm160)
REVERT: e   36 TYR cc_start: 0.8733 (m-10) cc_final: 0.8478 (m-10)
REVERT: e   61 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.5917 (p90)
REVERT: e  133 ILE cc_start: 0.8984 (tp) cc_final: 0.8775 (tp)
REVERT: f   36 TYR cc_start: 0.6007 (OUTLIER) cc_final: 0.5402 (t80)
REVERT: g   55 TRP cc_start: 0.5814 (m100) cc_final: 0.5578 (m100)
REVERT: m  285 MET cc_start: 0.8747 (tpp) cc_final: 0.8306 (tpp)
  outliers start: 51
  outliers final: 28
  residues processed: 182
  average time/residue: 0.0570
  time to fit residues: 13.6418
Evaluate side-chains
  175 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   34 LEU
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   45 ILE
Chi-restraints excluded: chain d residue   31 ASP
Chi-restraints excluded: chain d residue   64 ILE
Chi-restraints excluded: chain d residue   85 THR
Chi-restraints excluded: chain d residue   91 ARG
Chi-restraints excluded: chain d residue  113 ILE
Chi-restraints excluded: chain d residue  115 THR
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   45 VAL
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   57 ILE
Chi-restraints excluded: chain e residue   61 HIS
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  124 GLU
Chi-restraints excluded: chain e residue  153 LYS
Chi-restraints excluded: chain f residue   36 TYR
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue   44 LEU
Chi-restraints excluded: chain g residue   92 ASN
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  271 LEU
Chi-restraints excluded: chain m residue  291 SER
Chi-restraints excluded: chain n residue  276 LEU
Chi-restraints excluded: chain n residue  293 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
f  33 GLN
** n 278 ASN ** 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 = 0.4164 r_free = 0.4164 target = 0.177257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.146556 restraints weight = 6557.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.148360 restraints weight = 4227.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.150332 restraints weight = 3415.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.150613 restraints weight = 3103.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.151963 restraints weight = 2726.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4754  Z= 0.142
  Angle     :  0.797  12.319   6444  Z= 0.379
  Chirality :  0.043   0.232    753
  Planarity :  0.004   0.040    791
  Dihedral  :  5.099  35.009    637
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 11.73 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  9.56 %
    Allowed  : 34.61 %
    Favored  : 55.83 %
  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: -0.64 (0.36), residues: 571
  helix:  3.52 (0.31), residues: 222
  sheet: -3.06 (0.53), residues: 80
  loop : -3.26 (0.29), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG e 115 
 TYR   0.016   0.001   TYR f  52 
 PHE   0.007   0.001   PHE m 281 
 TRP   0.027   0.002   TRP d  43 
 HIS   0.002   0.001   HIS e  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4746)
  covalent geometry    : angle       0.79235 ( 6428)
  SS BOND              : bond        0.00413 (    8)
  SS BOND              : angle       1.93739 (   16)
  hydrogen bonds       : bond        0.04084 (  222)
  hydrogen bonds       : angle       3.58674 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 146
  time to evaluate  : 0.123 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7351 (tm)
REVERT: d   91 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8352 (tmm160)
REVERT: e   61 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6028 (p90)
REVERT: e   85 LYS cc_start: 0.8132 (pttp) cc_final: 0.7790 (mtpp)
REVERT: e  133 ILE cc_start: 0.8996 (tp) cc_final: 0.8778 (tp)
REVERT: f   92 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6444 (tp40)
REVERT: m  269 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9102 (tt)
REVERT: m  285 MET cc_start: 0.8739 (tpp) cc_final: 0.8375 (tpp)
REVERT: n  287 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8972 (tm)
  outliers start: 50
  outliers final: 30
  residues processed: 178
  average time/residue: 0.0561
  time to fit residues: 12.9261
Evaluate side-chains
  178 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 142
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain d residue   31 ASP
Chi-restraints excluded: chain d residue   53 SER
Chi-restraints excluded: chain d residue   58 LEU
Chi-restraints excluded: chain d residue   73 CYS
Chi-restraints excluded: chain d residue   85 THR
Chi-restraints excluded: chain d residue   91 ARG
Chi-restraints excluded: chain d residue  115 THR
Chi-restraints excluded: chain e residue   45 VAL
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   57 ILE
Chi-restraints excluded: chain e residue   61 HIS
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  124 GLU
Chi-restraints excluded: chain e residue  153 LYS
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   81 HIS
Chi-restraints excluded: chain f residue   92 GLN
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue   30 LEU
Chi-restraints excluded: chain g residue   44 LEU
Chi-restraints excluded: chain g residue   53 ILE
Chi-restraints excluded: chain g residue   92 ASN
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  133 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain m residue  290 TRP
Chi-restraints excluded: chain m residue  291 SER
Chi-restraints excluded: chain n residue  276 LEU
Chi-restraints excluded: chain n residue  287 LEU
Chi-restraints excluded: chain n residue  293 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
f  33 GLN
g  98 GLN
** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.174170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.143637 restraints weight = 6603.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.145657 restraints weight = 4326.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.147095 restraints weight = 3414.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.147547 restraints weight = 2997.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.147972 restraints weight = 2786.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4754  Z= 0.154
  Angle     :  0.788  10.792   6444  Z= 0.381
  Chirality :  0.043   0.230    753
  Planarity :  0.004   0.037    791
  Dihedral  :  5.173  34.481    637
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.73 %
    Favored  : 87.39 %
  Rotamer:
    Outliers : 10.90 %
    Allowed  : 33.27 %
    Favored  : 55.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 (0.36), residues: 571
  helix:  3.56 (0.31), residues: 222
  sheet: -3.02 (0.52), residues: 80
  loop : -3.18 (0.30), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG d  57 
 TYR   0.019   0.001   TYR f  52 
 PHE   0.010   0.001   PHE f 110 
 TRP   0.031   0.002   TRP d  43 
 HIS   0.002   0.001   HIS g  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4746)
  covalent geometry    : angle       0.78290 ( 6428)
  SS BOND              : bond        0.00318 (    8)
  SS BOND              : angle       1.94651 (   16)
  hydrogen bonds       : bond        0.04249 (  222)
  hydrogen bonds       : angle       3.55617 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 149
  time to evaluate  : 0.175 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7429 (tm)
REVERT: e   61 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.6193 (p90)
REVERT: e   64 LYS cc_start: 0.7785 (pptt) cc_final: 0.7470 (pptt)
REVERT: e  128 MET cc_start: 0.6501 (tmm) cc_final: 0.6212 (tmm)
REVERT: e  133 ILE cc_start: 0.9106 (tp) cc_final: 0.8871 (tp)
REVERT: f   36 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.5292 (t80)
REVERT: m  260 LYS cc_start: 0.9015 (mppt) cc_final: 0.8789 (mppt)
REVERT: m  285 MET cc_start: 0.8746 (tpp) cc_final: 0.8490 (tpp)
  outliers start: 57
  outliers final: 40
  residues processed: 183
  average time/residue: 0.0624
  time to fit residues: 14.7620
Evaluate side-chains
  189 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 146
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   34 LEU
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   31 ASP
Chi-restraints excluded: chain d residue   53 SER
Chi-restraints excluded: chain d residue   58 LEU
Chi-restraints excluded: chain d residue   64 ILE
Chi-restraints excluded: chain d residue   73 CYS
Chi-restraints excluded: chain d residue   85 THR
Chi-restraints excluded: chain d residue  113 ILE
Chi-restraints excluded: chain d residue  115 THR
Chi-restraints excluded: chain e residue   45 VAL
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   57 ILE
Chi-restraints excluded: chain e residue   61 HIS
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  124 GLU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain e residue  153 LYS
Chi-restraints excluded: chain f residue   36 TYR
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   81 HIS
Chi-restraints excluded: chain f residue   92 GLN
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue   30 LEU
Chi-restraints excluded: chain g residue   44 LEU
Chi-restraints excluded: chain g residue   53 ILE
Chi-restraints excluded: chain g residue   92 ASN
Chi-restraints excluded: chain g residue   95 LYS
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain g residue  133 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  271 LEU
Chi-restraints excluded: chain m residue  291 SER
Chi-restraints excluded: chain n residue  276 LEU
Chi-restraints excluded: chain n residue  293 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 8 optimal weight:    0.3980
   chunk 54 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
f  33 GLN
** g  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.176000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.144984 restraints weight = 6732.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.148266 restraints weight = 4338.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.149287 restraints weight = 3277.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.149681 restraints weight = 2950.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.150822 restraints weight = 2693.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4754  Z= 0.148
  Angle     :  0.810   9.875   6444  Z= 0.390
  Chirality :  0.043   0.232    753
  Planarity :  0.004   0.036    791
  Dihedral  :  5.154  35.841    637
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.21 %
    Favored  : 87.92 %
  Rotamer:
    Outliers :  9.56 %
    Allowed  : 33.84 %
    Favored  : 56.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.50 (0.36), residues: 571
  helix:  3.64 (0.31), residues: 221
  sheet: -2.88 (0.53), residues: 80
  loop : -3.19 (0.29), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG d  91 
 TYR   0.038   0.001   TYR f  99 
 PHE   0.010   0.001   PHE g  56 
 TRP   0.032   0.002   TRP d  43 
 HIS   0.003   0.001   HIS g  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4746)
  covalent geometry    : angle       0.80584 ( 6428)
  SS BOND              : bond        0.00384 (    8)
  SS BOND              : angle       1.76283 (   16)
  hydrogen bonds       : bond        0.04098 (  222)
  hydrogen bonds       : angle       3.54445 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 145
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: b   34 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7401 (tm)
REVERT: e   61 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.6450 (p90)
REVERT: e   85 LYS cc_start: 0.8076 (pttp) cc_final: 0.7860 (mtpp)
REVERT: e  128 MET cc_start: 0.6480 (tmm) cc_final: 0.6135 (tmm)
REVERT: f   36 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5228 (t80)
REVERT: g   55 TRP cc_start: 0.4979 (m100) cc_final: 0.4727 (m100)
REVERT: m  285 MET cc_start: 0.8686 (tpp) cc_final: 0.8464 (tpp)
  outliers start: 50
  outliers final: 38
  residues processed: 175
  average time/residue: 0.0611
  time to fit residues: 13.9943
Evaluate side-chains
  182 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 141
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   28 ASP
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   31 ASP
Chi-restraints excluded: chain d residue   53 SER
Chi-restraints excluded: chain d residue   64 ILE
Chi-restraints excluded: chain d residue   73 CYS
Chi-restraints excluded: chain d residue   85 THR
Chi-restraints excluded: chain d residue  107 ILE
Chi-restraints excluded: chain d residue  115 THR
Chi-restraints excluded: chain e residue   45 VAL
Chi-restraints excluded: chain e residue   57 ILE
Chi-restraints excluded: chain e residue   61 HIS
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  124 GLU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain e residue  153 LYS
Chi-restraints excluded: chain f residue   36 TYR
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   81 HIS
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue   29 HIS
Chi-restraints excluded: chain g residue   30 LEU
Chi-restraints excluded: chain g residue   35 ASP
Chi-restraints excluded: chain g residue   54 THR
Chi-restraints excluded: chain g residue   92 ASN
Chi-restraints excluded: chain g residue   95 LYS
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain g residue  135 PHE
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  291 SER
Chi-restraints excluded: chain n residue  276 LEU
Chi-restraints excluded: chain n residue  293 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 22 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
f  33 GLN
f  92 GLN
g  29 HIS
** g  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.176371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.146175 restraints weight = 6573.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.149121 restraints weight = 4211.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.149733 restraints weight = 3248.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.150236 restraints weight = 2998.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.152334 restraints weight = 2730.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4754  Z= 0.142
  Angle     :  0.795   9.430   6444  Z= 0.384
  Chirality :  0.042   0.222    753
  Planarity :  0.004   0.036    791
  Dihedral  :  5.109  36.817    637
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.56 %
    Favored  : 87.57 %
  Rotamer:
    Outliers :  9.37 %
    Allowed  : 34.42 %
    Favored  : 56.21 %
  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: -0.36 (0.36), residues: 571
  helix:  3.72 (0.31), residues: 222
  sheet: -2.73 (0.55), residues: 82
  loop : -3.12 (0.30), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG d  91 
 TYR   0.031   0.001   TYR f  99 
 PHE   0.007   0.001   PHE g  56 
 TRP   0.035   0.002   TRP d  43 
 HIS   0.003   0.001   HIS g  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4746)
  covalent geometry    : angle       0.79160 ( 6428)
  SS BOND              : bond        0.00363 (    8)
  SS BOND              : angle       1.61201 (   16)
  hydrogen bonds       : bond        0.04029 (  222)
  hydrogen bonds       : angle       3.47882 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 149
  time to evaluate  : 0.146 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7396 (tm)
REVERT: b   54 LYS cc_start: 0.7875 (tptp) cc_final: 0.7413 (tptp)
REVERT: e   61 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.6307 (p90)
REVERT: e   85 LYS cc_start: 0.8098 (pttp) cc_final: 0.7880 (mtpp)
REVERT: e  128 MET cc_start: 0.6401 (tmm) cc_final: 0.6040 (tmm)
REVERT: f   36 TYR cc_start: 0.6351 (OUTLIER) cc_final: 0.4936 (t80)
REVERT: f  137 ASP cc_start: 0.8728 (t70) cc_final: 0.8236 (t0)
REVERT: g   55 TRP cc_start: 0.5008 (m100) cc_final: 0.4742 (m100)
REVERT: g  110 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8148 (mt)
  outliers start: 49
  outliers final: 34
  residues processed: 178
  average time/residue: 0.0566
  time to fit residues: 13.0818
Evaluate side-chains
  182 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 144
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain d residue   53 SER
Chi-restraints excluded: chain d residue   58 LEU
Chi-restraints excluded: chain d residue   64 ILE
Chi-restraints excluded: chain d residue   73 CYS
Chi-restraints excluded: chain d residue   78 ILE
Chi-restraints excluded: chain d residue   85 THR
Chi-restraints excluded: chain d residue  107 ILE
Chi-restraints excluded: chain d residue  115 THR
Chi-restraints excluded: chain e residue   45 VAL
Chi-restraints excluded: chain e residue   57 ILE
Chi-restraints excluded: chain e residue   61 HIS
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  124 GLU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   36 TYR
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  145 LEU
Chi-restraints excluded: chain g residue   30 LEU
Chi-restraints excluded: chain g residue   35 ASP
Chi-restraints excluded: chain g residue   44 LEU
Chi-restraints excluded: chain g residue   54 THR
Chi-restraints excluded: chain g residue   92 ASN
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain g residue  133 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  291 SER
Chi-restraints excluded: chain n residue  276 LEU
Chi-restraints excluded: chain n residue  293 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0270
   chunk 41 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
f  33 GLN
** g  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n 278 ASN ** 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 = 0.4150 r_free = 0.4150 target = 0.176180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.142918 restraints weight = 6698.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.147090 restraints weight = 4102.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.149888 restraints weight = 2964.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.151817 restraints weight = 2368.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.152988 restraints weight = 2021.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4754  Z= 0.145
  Angle     :  0.795   9.514   6444  Z= 0.384
  Chirality :  0.043   0.221    753
  Planarity :  0.004   0.037    791
  Dihedral  :  5.107  39.017    637
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.56 %
    Favored  : 87.57 %
  Rotamer:
    Outliers :  8.99 %
    Allowed  : 35.18 %
    Favored  : 55.83 %
  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 (0.36), residues: 571
  helix:  3.69 (0.31), residues: 222
  sheet: -2.61 (0.56), residues: 82
  loop : -3.14 (0.29), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG d  57 
 TYR   0.034   0.002   TYR f  99 
 PHE   0.010   0.001   PHE g  56 
 TRP   0.037   0.002   TRP d  43 
 HIS   0.001   0.000   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4746)
  covalent geometry    : angle       0.79214 ( 6428)
  SS BOND              : bond        0.00320 (    8)
  SS BOND              : angle       1.52059 (   16)
  hydrogen bonds       : bond        0.04034 (  222)
  hydrogen bonds       : angle       3.51316 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 148
  time to evaluate  : 0.186 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7407 (tm)
REVERT: b   54 LYS cc_start: 0.7967 (tptp) cc_final: 0.7538 (tptp)
REVERT: e   61 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6551 (p90)
REVERT: e  128 MET cc_start: 0.6374 (tmm) cc_final: 0.6025 (tmm)
REVERT: f   37 LYS cc_start: 0.6884 (tppt) cc_final: 0.6018 (ttmm)
REVERT: f  137 ASP cc_start: 0.8691 (t70) cc_final: 0.8213 (t0)
REVERT: g   55 TRP cc_start: 0.5126 (m100) cc_final: 0.4877 (m100)
REVERT: g  110 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8252 (mt)
REVERT: m  260 LYS cc_start: 0.9029 (mppt) cc_final: 0.8796 (mppt)
REVERT: m  289 LEU cc_start: 0.8574 (mt) cc_final: 0.8307 (mt)
  outliers start: 47
  outliers final: 37
  residues processed: 177
  average time/residue: 0.0637
  time to fit residues: 14.5593
Evaluate side-chains
  182 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 142
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   28 ASP
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   31 ASP
Chi-restraints excluded: chain d residue   58 LEU
Chi-restraints excluded: chain d residue   64 ILE
Chi-restraints excluded: chain d residue   73 CYS
Chi-restraints excluded: chain d residue   85 THR
Chi-restraints excluded: chain d residue  107 ILE
Chi-restraints excluded: chain d residue  115 THR
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   45 VAL
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   57 ILE
Chi-restraints excluded: chain e residue   61 HIS
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  124 GLU
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   36 TYR
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  145 LEU
Chi-restraints excluded: chain g residue   30 LEU
Chi-restraints excluded: chain g residue   35 ASP
Chi-restraints excluded: chain g residue   44 LEU
Chi-restraints excluded: chain g residue   54 THR
Chi-restraints excluded: chain g residue   92 ASN
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  291 SER
Chi-restraints excluded: chain n residue  276 LEU
Chi-restraints excluded: chain n residue  293 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0570
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0570
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4816

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS
f  33 GLN
** g  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.178323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.146226 restraints weight = 6698.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.150020 restraints weight = 4223.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.152762 restraints weight = 3123.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.154518 restraints weight = 2513.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.155784 restraints weight = 2159.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4754  Z= 0.142
  Angle     :  0.808  10.021   6444  Z= 0.390
  Chirality :  0.043   0.216    753
  Planarity :  0.004   0.039    791
  Dihedral  :  5.083  37.539    637
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.21 %
    Favored  : 87.92 %
  Rotamer:
    Outliers :  7.46 %
    Allowed  : 37.28 %
    Favored  : 55.26 %
  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 (0.36), residues: 571
  helix:  3.74 (0.31), residues: 222
  sheet: -2.50 (0.56), residues: 82
  loop : -3.09 (0.30), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG d  57 
 TYR   0.033   0.001   TYR f  99 
 PHE   0.006   0.001   PHE m 281 
 TRP   0.039   0.002   TRP d  43 
 HIS   0.002   0.001   HIS g  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4746)
  covalent geometry    : angle       0.80513 ( 6428)
  SS BOND              : bond        0.00295 (    8)
  SS BOND              : angle       1.49323 (   16)
  hydrogen bonds       : bond        0.03864 (  222)
  hydrogen bonds       : angle       3.46457 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 141
  time to evaluate  : 0.201 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7387 (tm)
REVERT: b   54 LYS cc_start: 0.7954 (tptp) cc_final: 0.7523 (tptp)
REVERT: d   91 ARG cc_start: 0.8892 (tmt170) cc_final: 0.8692 (ttt-90)
REVERT: e   34 THR cc_start: 0.8953 (p) cc_final: 0.8737 (p)
REVERT: e   61 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.6586 (p90)
REVERT: e  128 MET cc_start: 0.6332 (tmm) cc_final: 0.5994 (tmm)
REVERT: f   37 LYS cc_start: 0.6889 (tppt) cc_final: 0.6063 (ttmm)
REVERT: f  128 MET cc_start: 0.7174 (tmm) cc_final: 0.5936 (tpt)
REVERT: f  137 ASP cc_start: 0.8704 (t70) cc_final: 0.8213 (t0)
REVERT: g   55 TRP cc_start: 0.5279 (m100) cc_final: 0.5062 (m100)
REVERT: g  110 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8165 (mt)
  outliers start: 39
  outliers final: 30
  residues processed: 167
  average time/residue: 0.0707
  time to fit residues: 15.1849
Evaluate side-chains
  170 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   28 ASP
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   64 ILE
Chi-restraints excluded: chain d residue   73 CYS
Chi-restraints excluded: chain d residue   85 THR
Chi-restraints excluded: chain d residue  107 ILE
Chi-restraints excluded: chain d residue  115 THR
Chi-restraints excluded: chain e residue   45 VAL
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   57 ILE
Chi-restraints excluded: chain e residue   61 HIS
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  145 LEU
Chi-restraints excluded: chain g residue   30 LEU
Chi-restraints excluded: chain g residue   44 LEU
Chi-restraints excluded: chain g residue   54 THR
Chi-restraints excluded: chain g residue   92 ASN
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  290 TRP
Chi-restraints excluded: chain n residue  276 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0060
   chunk 36 optimal weight:    0.0970
   chunk 43 optimal weight:    0.0070
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.2612

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

Flipped N/Q/H residues before XYZ refinement:
f  33 GLN
** g  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n 278 ASN ** 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 = 0.4205 r_free = 0.4205 target = 0.180973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.149084 restraints weight = 6642.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.152847 restraints weight = 4167.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.155553 restraints weight = 3072.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.157125 restraints weight = 2468.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.158492 restraints weight = 2132.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.4529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4754  Z= 0.139
  Angle     :  0.809   9.990   6444  Z= 0.386
  Chirality :  0.043   0.208    753
  Planarity :  0.004   0.041    791
  Dihedral  :  4.993  37.707    637
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.21 %
    Favored  : 87.92 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 39.20 %
    Favored  : 54.49 %
  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 (0.36), residues: 571
  helix:  3.72 (0.31), residues: 222
  sheet: -2.44 (0.56), residues: 82
  loop : -3.08 (0.30), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG f 101 
 TYR   0.032   0.001   TYR f  99 
 PHE   0.008   0.001   PHE g  56 
 TRP   0.040   0.002   TRP d  43 
 HIS   0.005   0.001   HIS g  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4746)
  covalent geometry    : angle       0.80654 ( 6428)
  SS BOND              : bond        0.00286 (    8)
  SS BOND              : angle       1.43928 (   16)
  hydrogen bonds       : bond        0.03584 (  222)
  hydrogen bonds       : angle       3.43730 (  639)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 0.250 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7301 (tm)
REVERT: b   54 LYS cc_start: 0.7817 (tptp) cc_final: 0.7395 (tptp)
REVERT: e   34 THR cc_start: 0.8937 (p) cc_final: 0.8718 (p)
REVERT: e   59 TRP cc_start: 0.6922 (m-10) cc_final: 0.6702 (m100)
REVERT: e  128 MET cc_start: 0.6254 (tmm) cc_final: 0.5922 (tmm)
REVERT: f   37 LYS cc_start: 0.6827 (tppt) cc_final: 0.6007 (ttmm)
REVERT: f  128 MET cc_start: 0.7034 (tmm) cc_final: 0.5725 (tpt)
REVERT: f  137 ASP cc_start: 0.8692 (t70) cc_final: 0.8215 (t0)
REVERT: g   55 TRP cc_start: 0.5248 (m100) cc_final: 0.4984 (m100)
REVERT: g  110 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7899 (mt)
REVERT: m  290 TRP cc_start: 0.5616 (OUTLIER) cc_final: 0.5196 (m100)
  outliers start: 33
  outliers final: 25
  residues processed: 164
  average time/residue: 0.0770
  time to fit residues: 16.1227
Evaluate side-chains
  166 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   28 ASP
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain d residue   73 CYS
Chi-restraints excluded: chain d residue  107 ILE
Chi-restraints excluded: chain d residue  115 THR
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   45 VAL
Chi-restraints excluded: chain e residue   57 ILE
Chi-restraints excluded: chain e residue  119 CYS
Chi-restraints excluded: chain e residue  152 SER
Chi-restraints excluded: chain f residue   33 GLN
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  145 LEU
Chi-restraints excluded: chain g residue   30 LEU
Chi-restraints excluded: chain g residue   44 LEU
Chi-restraints excluded: chain g residue   54 THR
Chi-restraints excluded: chain g residue   92 ASN
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  290 TRP
Chi-restraints excluded: chain n residue  276 LEU
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
f  33 GLN
** n 278 ASN ** 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 = 0.4142 r_free = 0.4142 target = 0.174872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.142172 restraints weight = 6607.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.145762 restraints weight = 4269.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.148228 restraints weight = 3196.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.149955 restraints weight = 2621.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.150780 restraints weight = 2274.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4754  Z= 0.164
  Angle     :  0.850  11.430   6444  Z= 0.408
  Chirality :  0.044   0.208    753
  Planarity :  0.005   0.039    791
  Dihedral  :  5.033  37.258    637
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 12.43 %
    Favored  : 86.69 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 40.54 %
    Favored  : 52.96 %
  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: -0.30 (0.36), residues: 571
  helix:  3.70 (0.31), residues: 222
  sheet: -2.45 (0.56), residues: 82
  loop : -3.12 (0.30), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG d  91 
 TYR   0.032   0.002   TYR f  99 
 PHE   0.007   0.001   PHE n 296 
 TRP   0.043   0.002   TRP d  43 
 HIS   0.006   0.001   HIS g  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4746)
  covalent geometry    : angle       0.84755 ( 6428)
  SS BOND              : bond        0.00287 (    8)
  SS BOND              : angle       1.48710 (   16)
  hydrogen bonds       : bond        0.04113 (  222)
  hydrogen bonds       : angle       3.51086 (  639)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 934.79 seconds
wall clock time: 16 minutes 51.64 seconds (1011.64 seconds total)