Starting phenix.real_space_refine
on Sat May 10 02:00:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wyi_37929/05_2025/8wyi_37929.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wyi_37929/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wyi_37929/05_2025/8wyi_37929.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wyi_37929/05_2025/8wyi_37929.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wyi_37929/05_2025/8wyi_37929.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wyi_37929/05_2025/8wyi_37929.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.34, per 1000 atoms: 0.72
  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: 1.19
  Conformation dependent library (CDL) restraints added in 583.5 milliseconds
  

  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: 0.44
  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: 1.03

  Time building geometry restraints manager: 1.40 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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.080
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.590
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.037   0.003   TRP d  43 
 HIS   0.006   0.001   HIS d  89 
 PHE   0.018   0.002   PHE m 281 
 TYR   0.019   0.001   TYR g  34 
 ARG   0.006   0.001   ARG e 115 

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

*********************** 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  : 0.544 
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: 0.1636
  time to fit residues: 32.0761
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  : 0.542 
-------------------------------------------------------------------------------
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 46 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    0.4980
   chunk 43 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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  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 = 0.4087 r_free = 0.4087 target = 0.170183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.137460 restraints weight = 6398.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.141034 restraints weight = 4048.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.143529 restraints weight = 2998.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4754  Z= 0.160
  Angle     :  0.818   9.976   6444  Z= 0.400
  Chirality :  0.043   0.174    753
  Planarity :  0.005   0.054    791
  Dihedral  :  6.175  53.642    642
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  1.23 %
    Allowed  : 13.13 %
    Favored  : 85.64 %
  Rotamer:
    Outliers :  8.41 %
    Allowed  : 33.46 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.36), residues: 571
  helix:  3.44 (0.31), residues: 222
  sheet: -3.26 (0.58), residues: 64
  loop : -3.54 (0.28), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP d  43 
 HIS   0.003   0.001   HIS e  81 
 PHE   0.010   0.001   PHE g  56 
 TYR   0.019   0.001   TYR n 283 
 ARG   0.005   0.001   ARG e 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04470 (  222)
  hydrogen bonds       : angle       3.88649 (  639)
  SS BOND              : bond        0.00326 (    8)
  SS BOND              : angle       1.94452 (   16)
  covalent geometry    : bond        0.00366 ( 4746)
  covalent geometry    : angle       0.81314 ( 6428)

*********************** 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
  196 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 152
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
REVERT: d   91 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8693 (tmm160)
REVERT: g   55 TRP cc_start: 0.6164 (m100) cc_final: 0.5445 (m100)
  outliers start: 44
  outliers final: 27
  residues processed: 177
  average time/residue: 0.1458
  time to fit residues: 32.9810
Evaluate side-chains
  169 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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   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  114 LEU
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  136 VAL
Chi-restraints excluded: chain e residue  153 LYS
Chi-restraints excluded: chain f residue   47 LEU
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   35 ASP
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  268 VAL
Chi-restraints excluded: chain m residue  286 THR
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 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 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 = 0.4156 r_free = 0.4156 target = 0.176276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.145228 restraints weight = 6522.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.147906 restraints weight = 4161.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.148463 restraints weight = 3232.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2267

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= 0.152
  Angle     :  0.779   9.462   6444  Z= 0.384
  Chirality :  0.043   0.223    753
  Planarity :  0.004   0.045    791
  Dihedral  :  5.224  33.939    637
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 11.21 %
    Favored  : 87.74 %
  Rotamer:
    Outliers :  9.75 %
    Allowed  : 32.70 %
    Favored  : 57.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.35), residues: 571
  helix:  3.51 (0.31), residues: 222
  sheet: -3.14 (0.59), residues: 62
  loop : -3.47 (0.28), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP d  43 
 HIS   0.002   0.001   HIS e  81 
 PHE   0.007   0.001   PHE g  56 
 TYR   0.016   0.001   TYR b  33 
 ARG   0.003   0.000   ARG e 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04255 (  222)
  hydrogen bonds       : angle       3.69986 (  639)
  SS BOND              : bond        0.00372 (    8)
  SS BOND              : angle       1.78574 (   16)
  covalent geometry    : bond        0.00343 ( 4746)
  covalent geometry    : angle       0.77462 ( 6428)

*********************** 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
  203 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 152
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: e   36 TYR cc_start: 0.8661 (m-10) cc_final: 0.8332 (m-10)
REVERT: f   36 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.5457 (t80)
  outliers start: 51
  outliers final: 30
  residues processed: 183
  average time/residue: 0.1583
  time to fit residues: 36.6322
Evaluate side-chains
  176 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   32 CYS
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 d residue   31 ASP
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  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   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   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  290 TRP
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 36 optimal weight:    0.0670
   chunk 18 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0980
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0040
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.3530

-------------------------------------------------------------------------------
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 = 0.4185 r_free = 0.4185 target = 0.179148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.146675 restraints weight = 6554.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.150682 restraints weight = 4044.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.153374 restraints weight = 2941.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4754  Z= 0.135
  Angle     :  0.789  12.714   6444  Z= 0.377
  Chirality :  0.043   0.232    753
  Planarity :  0.004   0.040    791
  Dihedral  :  5.061  35.651    637
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.73 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  8.41 %
    Allowed  : 35.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.36), residues: 571
  helix:  3.49 (0.31), residues: 222
  sheet: -3.06 (0.53), residues: 82
  loop : -3.26 (0.29), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP d  43 
 HIS   0.002   0.001   HIS g  29 
 PHE   0.007   0.001   PHE g  56 
 TYR   0.016   0.001   TYR f  52 
 ARG   0.003   0.000   ARG d  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  222)
  hydrogen bonds       : angle       3.55870 (  639)
  SS BOND              : bond        0.00248 (    8)
  SS BOND              : angle       1.94498 (   16)
  covalent geometry    : bond        0.00293 ( 4746)
  covalent geometry    : angle       0.78412 ( 6428)

*********************** 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
  193 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 149
  time to evaluate  : 0.497 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7289 (tm)
REVERT: e   85 LYS cc_start: 0.8115 (pttp) cc_final: 0.7787 (mtpp)
REVERT: f   92 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6412 (tp40)
REVERT: n  287 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8959 (tm)
  outliers start: 44
  outliers final: 28
  residues processed: 175
  average time/residue: 0.1446
  time to fit residues: 32.3990
Evaluate side-chains
  172 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   35 LEU
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   58 LEU
Chi-restraints excluded: chain d residue   85 THR
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  125 MET
Chi-restraints excluded: chain f residue  138 ILE
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   53 ILE
Chi-restraints excluded: chain g residue   92 ASN
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain m residue  271 LEU
Chi-restraints excluded: chain n residue  276 LEU
Chi-restraints excluded: chain n residue  287 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 45 optimal weight:    0.5980
   chunk 16 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4146 r_free = 0.4146 target = 0.175485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.142490 restraints weight = 6682.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.146471 restraints weight = 4132.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.149178 restraints weight = 3015.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4754  Z= 0.151
  Angle     :  0.787  10.944   6444  Z= 0.381
  Chirality :  0.043   0.230    753
  Planarity :  0.004   0.035    791
  Dihedral  :  5.140  34.361    637
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.56 %
    Favored  : 87.57 %
  Rotamer:
    Outliers : 10.52 %
    Allowed  : 33.84 %
    Favored  : 55.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.36), residues: 571
  helix:  3.51 (0.31), residues: 222
  sheet: -2.96 (0.54), residues: 80
  loop : -3.22 (0.29), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP d  43 
 HIS   0.003   0.001   HIS g  29 
 PHE   0.010   0.001   PHE f 110 
 TYR   0.019   0.001   TYR f  52 
 ARG   0.004   0.000   ARG d  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  222)
  hydrogen bonds       : angle       3.55692 (  639)
  SS BOND              : bond        0.00372 (    8)
  SS BOND              : angle       1.95740 (   16)
  covalent geometry    : bond        0.00334 ( 4746)
  covalent geometry    : angle       0.78186 ( 6428)

*********************** 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
  199 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 144
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: b   34 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7437 (tm)
REVERT: b   54 LYS cc_start: 0.7898 (tptp) cc_final: 0.7412 (tptp)
REVERT: e   61 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6333 (p90)
REVERT: e   85 LYS cc_start: 0.8072 (pttp) cc_final: 0.7793 (mtpp)
REVERT: e  128 MET cc_start: 0.6507 (tmm) cc_final: 0.6183 (tmm)
REVERT: f   36 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5335 (t80)
REVERT: f   90 LEU cc_start: 0.7899 (mt) cc_final: 0.7682 (mt)
  outliers start: 55
  outliers final: 40
  residues processed: 179
  average time/residue: 0.1463
  time to fit residues: 33.3987
Evaluate side-chains
  186 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 143
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   32 CYS
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   45 ILE
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  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   84 LEU
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  125 MET
Chi-restraints excluded: chain f residue  138 ILE
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0060
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.8800

-------------------------------------------------------------------------------
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
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.174516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.141654 restraints weight = 6597.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.145645 restraints weight = 4083.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.148381 restraints weight = 2968.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4754  Z= 0.153
  Angle     :  0.806  10.533   6444  Z= 0.389
  Chirality :  0.043   0.227    753
  Planarity :  0.004   0.036    791
  Dihedral  :  5.095  35.816    637
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.21 %
    Favored  : 87.92 %
  Rotamer:
    Outliers : 11.09 %
    Allowed  : 34.80 %
    Favored  : 54.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.36), residues: 571
  helix:  3.54 (0.31), residues: 222
  sheet: -2.73 (0.55), residues: 80
  loop : -3.19 (0.29), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP d  43 
 HIS   0.006   0.001   HIS g  29 
 PHE   0.011   0.001   PHE g  56 
 TYR   0.037   0.002   TYR f  99 
 ARG   0.003   0.001   ARG d  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04254 (  222)
  hydrogen bonds       : angle       3.55022 (  639)
  SS BOND              : bond        0.00384 (    8)
  SS BOND              : angle       1.73610 (   16)
  covalent geometry    : bond        0.00351 ( 4746)
  covalent geometry    : angle       0.80265 ( 6428)

*********************** 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
  205 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 147
  time to evaluate  : 0.540 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7459 (tm)
REVERT: e   61 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6256 (p90)
REVERT: e  128 MET cc_start: 0.6509 (tmm) cc_final: 0.6170 (tmm)
REVERT: f   36 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.5271 (t80)
REVERT: m  260 LYS cc_start: 0.9028 (mppt) cc_final: 0.8777 (mppt)
  outliers start: 58
  outliers final: 43
  residues processed: 184
  average time/residue: 0.1333
  time to fit residues: 31.6943
Evaluate side-chains
  187 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 141
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
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   28 ASP
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   45 ILE
Chi-restraints excluded: chain b residue   46 LEU
Chi-restraints excluded: chain d residue   31 ASP
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  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   84 LEU
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  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
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    0.0970
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0870
   chunk 51 optimal weight:    0.1980
   overall best weight:    0.2956

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.179630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.148070 restraints weight = 6619.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.151988 restraints weight = 4142.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.154615 restraints weight = 3035.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4754  Z= 0.138
  Angle     :  0.790   9.708   6444  Z= 0.382
  Chirality :  0.043   0.229    753
  Planarity :  0.004   0.036    791
  Dihedral  :  5.012  37.570    637
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.73 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  8.80 %
    Allowed  : 37.09 %
    Favored  : 54.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.36), residues: 571
  helix:  3.62 (0.31), residues: 222
  sheet: -2.66 (0.56), residues: 80
  loop : -3.13 (0.29), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP d  43 
 HIS   0.005   0.001   HIS g  29 
 PHE   0.008   0.001   PHE g  56 
 TYR   0.031   0.001   TYR f  99 
 ARG   0.002   0.000   ARG e 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03835 (  222)
  hydrogen bonds       : angle       3.45806 (  639)
  SS BOND              : bond        0.00364 (    8)
  SS BOND              : angle       1.55558 (   16)
  covalent geometry    : bond        0.00300 ( 4746)
  covalent geometry    : angle       0.78687 ( 6428)

*********************** 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
  194 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 148
  time to evaluate  : 0.547 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7415 (tm)
REVERT: b   54 LYS cc_start: 0.7774 (tptp) cc_final: 0.7329 (tptp)
REVERT: e   61 HIS cc_start: 0.7204 (OUTLIER) cc_final: 0.6155 (p90)
REVERT: e  128 MET cc_start: 0.6396 (tmm) cc_final: 0.6059 (tmm)
REVERT: f   36 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.5037 (t80)
REVERT: f  137 ASP cc_start: 0.8706 (t70) cc_final: 0.8226 (t0)
REVERT: g  110 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8070 (mt)
REVERT: n  284 MET cc_start: 0.9078 (tpp) cc_final: 0.8873 (tpp)
  outliers start: 46
  outliers final: 32
  residues processed: 175
  average time/residue: 0.1388
  time to fit residues: 31.2810
Evaluate side-chains
  177 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 141
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   34 LEU
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   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  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   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   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  135 PHE
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  300 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.176250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.143951 restraints weight = 6613.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.147782 restraints weight = 4195.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.150449 restraints weight = 3096.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4754  Z= 0.149
  Angle     :  0.796   9.830   6444  Z= 0.387
  Chirality :  0.043   0.229    753
  Planarity :  0.004   0.038    791
  Dihedral  :  5.032  38.553    637
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.38 %
    Favored  : 87.74 %
  Rotamer:
    Outliers :  9.18 %
    Allowed  : 35.76 %
    Favored  : 55.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.36), residues: 571
  helix:  3.67 (0.31), residues: 221
  sheet: -2.59 (0.56), residues: 80
  loop : -3.16 (0.29), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP d  43 
 HIS   0.003   0.001   HIS g  29 
 PHE   0.010   0.001   PHE g  56 
 TYR   0.029   0.001   TYR f  99 
 ARG   0.002   0.000   ARG d  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04125 (  222)
  hydrogen bonds       : angle       3.49037 (  639)
  SS BOND              : bond        0.00301 (    8)
  SS BOND              : angle       1.50932 (   16)
  covalent geometry    : bond        0.00342 ( 4746)
  covalent geometry    : angle       0.79367 ( 6428)

*********************** 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: 48
    poor density    : 147
  time to evaluate  : 0.537 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7501 (tm)
REVERT: b   54 LYS cc_start: 0.7900 (tptp) cc_final: 0.7476 (tptp)
REVERT: e   61 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.6496 (p90)
REVERT: e   81 HIS cc_start: 0.8649 (p-80) cc_final: 0.8384 (p-80)
REVERT: e  128 MET cc_start: 0.6393 (tmm) cc_final: 0.6043 (tmm)
REVERT: f   36 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.4928 (t80)
REVERT: f   37 LYS cc_start: 0.6876 (tppt) cc_final: 0.6063 (ttmm)
REVERT: f  137 ASP cc_start: 0.8720 (t70) cc_final: 0.8222 (t0)
REVERT: g  110 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8145 (mt)
  outliers start: 48
  outliers final: 37
  residues processed: 177
  average time/residue: 0.1467
  time to fit residues: 33.9641
Evaluate side-chains
  185 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   34 LEU
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   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  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   29 HIS
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   76 SER
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  135 PHE
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  300 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 35 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0470
   chunk 42 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.4169 r_free = 0.4169 target = 0.177968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.145479 restraints weight = 6580.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.149301 restraints weight = 4143.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.151855 restraints weight = 3053.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4754  Z= 0.145
  Angle     :  0.811   9.654   6444  Z= 0.395
  Chirality :  0.043   0.218    753
  Planarity :  0.004   0.039    791
  Dihedral  :  5.022  38.073    637
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.73 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 38.24 %
    Favored  : 54.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.36), residues: 571
  helix:  3.68 (0.31), residues: 221
  sheet: -2.47 (0.57), residues: 80
  loop : -3.14 (0.30), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP d  43 
 HIS   0.005   0.001   HIS g  29 
 PHE   0.006   0.001   PHE g  56 
 TYR   0.032   0.001   TYR f  99 
 ARG   0.003   0.000   ARG d  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  222)
  hydrogen bonds       : angle       3.49038 (  639)
  SS BOND              : bond        0.00309 (    8)
  SS BOND              : angle       1.50539 (   16)
  covalent geometry    : bond        0.00332 ( 4746)
  covalent geometry    : angle       0.80897 ( 6428)

*********************** 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
  184 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 0.574 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7469 (tm)
REVERT: b   54 LYS cc_start: 0.7950 (tptp) cc_final: 0.7530 (tptp)
REVERT: e   61 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6472 (p90)
REVERT: e   85 LYS cc_start: 0.8206 (pttp) cc_final: 0.7919 (mtpp)
REVERT: e  128 MET cc_start: 0.6334 (tmm) cc_final: 0.5998 (tmm)
REVERT: f   37 LYS cc_start: 0.6920 (tppt) cc_final: 0.6089 (ttmm)
REVERT: f  128 MET cc_start: 0.7162 (tmm) cc_final: 0.5777 (tpt)
REVERT: f  137 ASP cc_start: 0.8705 (t70) cc_final: 0.8223 (t0)
REVERT: g  110 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8155 (mt)
  outliers start: 40
  outliers final: 33
  residues processed: 168
  average time/residue: 0.1442
  time to fit residues: 31.2319
Evaluate side-chains
  174 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 138
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   34 LEU
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   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  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 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   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  133 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  271 LEU
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 4 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0670
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0570
   chunk 35 optimal weight:    0.1980
   chunk 54 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0370
   overall best weight:    0.2114

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

Flipped N/Q/H residues before XYZ refinement:
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.182744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.151265 restraints weight = 6595.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.155107 restraints weight = 4184.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.157725 restraints weight = 3076.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4754  Z= 0.141
  Angle     :  0.812  10.931   6444  Z= 0.389
  Chirality :  0.043   0.208    753
  Planarity :  0.004   0.040    791
  Dihedral  :  4.942  37.312    637
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.03 %
    Favored  : 88.09 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 39.96 %
    Favored  : 53.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.36), residues: 571
  helix:  3.73 (0.31), residues: 221
  sheet: -2.29 (0.58), residues: 80
  loop : -3.13 (0.30), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP d  43 
 HIS   0.005   0.001   HIS g  29 
 PHE   0.007   0.001   PHE f  87 
 TYR   0.031   0.001   TYR f  99 
 ARG   0.004   0.000   ARG e 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03597 (  222)
  hydrogen bonds       : angle       3.39636 (  639)
  SS BOND              : bond        0.00313 (    8)
  SS BOND              : angle       1.45983 (   16)
  covalent geometry    : bond        0.00318 ( 4746)
  covalent geometry    : angle       0.80935 ( 6428)

********************** 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
  173 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 0.491 
Fit side-chains
REVERT: b   34 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7388 (tm)
REVERT: b   54 LYS cc_start: 0.7781 (tptp) cc_final: 0.7381 (tptp)
REVERT: e   85 LYS cc_start: 0.8059 (pttp) cc_final: 0.7738 (mtpp)
REVERT: e  128 MET cc_start: 0.6337 (tmm) cc_final: 0.5970 (tmm)
REVERT: f   37 LYS cc_start: 0.6814 (tppt) cc_final: 0.6034 (ttmm)
REVERT: f  128 MET cc_start: 0.6901 (tmm) cc_final: 0.5637 (tpt)
REVERT: f  137 ASP cc_start: 0.8690 (t70) cc_final: 0.8209 (t0)
REVERT: g  110 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8066 (mt)
REVERT: m  290 TRP cc_start: 0.5649 (m100) cc_final: 0.5393 (m100)
  outliers start: 33
  outliers final: 25
  residues processed: 162
  average time/residue: 0.1388
  time to fit residues: 29.2316
Evaluate side-chains
  162 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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   64 ILE
Chi-restraints excluded: chain d residue   73 CYS
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   66 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 g residue   29 HIS
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  271 LEU
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 24 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 32 optimal weight:    0.3980
   chunk 47 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 43 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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  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 = 0.4126 r_free = 0.4126 target = 0.173321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.139590 restraints weight = 6646.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.143505 restraints weight = 4192.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.146147 restraints weight = 3092.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.4643

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= 0.182
  Angle     :  0.843  10.725   6444  Z= 0.410
  Chirality :  0.044   0.208    753
  Planarity :  0.005   0.040    791
  Dihedral  :  4.991  35.140    637
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 12.61 %
    Favored  : 86.51 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 40.15 %
    Favored  : 53.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.36), residues: 571
  helix:  3.68 (0.31), residues: 222
  sheet: -2.14 (0.61), residues: 80
  loop : -3.15 (0.30), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP d  43 
 HIS   0.003   0.001   HIS g  29 
 PHE   0.008   0.001   PHE n 296 
 TYR   0.038   0.002   TYR g  34 
 ARG   0.005   0.001   ARG e 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  222)
  hydrogen bonds       : angle       3.55351 (  639)
  SS BOND              : bond        0.00262 (    8)
  SS BOND              : angle       1.54955 (   16)
  covalent geometry    : bond        0.00423 ( 4746)
  covalent geometry    : angle       0.84096 ( 6428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1919.76 seconds
wall clock time: 34 minutes 11.52 seconds (2051.52 seconds total)