Starting phenix.real_space_refine
on Wed Jun  4 23:35:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ua3_42049/06_2025/8ua3_42049.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ua3_42049/06_2025/8ua3_42049.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ua3_42049/06_2025/8ua3_42049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ua3_42049/06_2025/8ua3_42049.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ua3_42049/06_2025/8ua3_42049.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ua3_42049/06_2025/8ua3_42049.cif"
  }
  resolution = 3.8
  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=  -0.001 sd=   0.049
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      24      5.16       5
     C    2835      2.51       5
     N     746      2.21       5
     O     845      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4450
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 2517
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2517
          Classifications: {'peptide': 327}
          Link IDs: {'PTRANS': 13, 'TRANS': 313}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 972
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 2, 'TRANS': 119}
    Chain: "E"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 961
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
  Time building chain proxies: 4.15, per 1000 atoms: 0.93
  Number of scatterers: 4450
  At special positions: 0
  Unit cell: (80.64, 95.76, 80.64, 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      24     16.00
     O     845      8.00
     N     746      7.00
     C    2835      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 515.1 milliseconds
  

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1068

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 8 sheets defined
      31.8% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'C' and resid 72 through 76
      removed outlier: 3.898A  pdb=" N   GLU C  75 " --> pdb=" O   GLY C  72 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA C  76 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 72 through 76'
    Processing helix  chain 'C' and resid 82 through 92
    Processing helix  chain 'C' and resid 93 through 95
      No H-bonds generated for 'chain 'C' and resid 93 through 95'
    Processing helix  chain 'C' and resid 128 through 139
      removed outlier: 3.593A  pdb=" N   LEU C 135 " --> pdb=" O   THR C 131 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU C 138 " --> pdb=" O   ALA C 134 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   PHE C 139 " --> pdb=" O   LEU C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 209
    Processing helix  chain 'C' and resid 231 through 244
      removed outlier: 3.829A  pdb=" N   GLN C 237 " --> pdb=" O   SER C 233 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL C 240 " --> pdb=" O   LEU C 236 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   SER C 241 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   THR C 242 " --> pdb=" O   GLN C 238 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   PHE C 243 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 311
      removed outlier: 3.603A  pdb=" N   LEU C 309 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 349
      removed outlier: 3.521A  pdb=" N   PHE C 348 " --> pdb=" O   ALA C 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 15 through 30
      removed outlier: 3.622A  pdb=" N   VAL D  20 " --> pdb=" O   HIS D  16 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS D  30 " --> pdb=" O   ASP D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 56
      removed outlier: 3.610A  pdb=" N   ALA D  54 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER D  56 " --> pdb=" O   LEU D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 94
      removed outlier: 3.600A  pdb=" N   PHE D  84 " --> pdb=" O   THR D  80 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLU D  85 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
      Proline residue:  D  86  - end of helix
    Processing helix  chain 'D' and resid 101 through 112
      removed outlier: 4.574A  pdb=" N   GLU D 105 " --> pdb=" O   GLU D 101 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   VAL D 110 " --> pdb=" O   VAL D 106 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLU D 111 " --> pdb=" O   CYS D 107 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   PHE D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 15 through 29
    Processing helix  chain 'E' and resid 51 through 56
      removed outlier: 4.218A  pdb=" N   SER E  56 " --> pdb=" O   LEU E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 57 through 64
      removed outlier: 3.719A  pdb=" N   VAL E  64 " --> pdb=" O   HIS E  60 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 84 through 94
      removed outlier: 3.541A  pdb=" N   ILE E  88 " --> pdb=" O   PHE E  84 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLN E  89 " --> pdb=" O   GLU E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 114
    Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 71
      removed outlier: 3.693A  pdb=" N   TYR C 104 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE C 148 " --> pdb=" O   TYR C 104 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA C 106 " --> pdb=" O   ILE C 148 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL C 145 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LEU C 261 " --> pdb=" O   VAL C 145 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   GLY C 147 " --> pdb=" O   SER C 259 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN C 257 " --> pdb=" O   VAL C 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 166 through 168
      removed outlier: 5.977A  pdb=" N   GLY C 321 " --> pdb=" O   PHE C 355 " (cutoff:3.500A)
      removed outlier: 8.232A  pdb=" N   PHE C 357 " --> pdb=" O   GLY C 321 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   MET C 323 " --> pdb=" O   PHE C 357 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   GLY C 359 " --> pdb=" O   MET C 323 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ALA C 325 " --> pdb=" O   GLY C 359 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 193
      removed outlier: 3.768A  pdb=" N   GLY C 274 " --> pdb=" O   TYR C 225 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   GLY C 224 " --> pdb=" O   VAL C 255 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 217 through 220
      removed outlier: 3.780A  pdb=" N   VAL C 219 " --> pdb=" O   PHE C 280 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 362 through 363
      removed outlier: 3.667A  pdb=" N   GLU C 362 " --> pdb=" O   HIS C 388 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   HIS C 388 " --> pdb=" O   GLU C 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 373 through 374
    Processing sheet with id=AA7, first strand: chain 'D' and resid 45 through 47
      removed outlier: 3.702A  pdb=" N   VAL D  36 " --> pdb=" O   ALA D  47 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   THR D  37 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 8.287A  pdb=" N   LEU D  75 " --> pdb=" O   THR D  37 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   PHE D  39 " --> pdb=" O   LEU D  75 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 36 through 40

    135 hydrogen bonds defined for protein.
    366 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: 1.15

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 761
        1.29 -     1.42: 1138
        1.42 -     1.55: 2599
        1.55 -     1.68: 4
        1.68 -     1.81: 31
  Bond restraints: 4533
  Sorted by residual:
  bond pdb=" CG  PRO D  86 "
       pdb=" CD  PRO D  86 "
    ideal  model  delta    sigma   weight residual
    1.503  1.157  0.346 3.40e-02 8.65e+02 1.04e+02
  bond pdb=" N   PRO D  86 "
       pdb=" CD  PRO D  86 "
    ideal  model  delta    sigma   weight residual
    1.473  1.552 -0.079 1.40e-02 5.10e+03 3.18e+01
  bond pdb=" CB  PRO D  86 "
       pdb=" CG  PRO D  86 "
    ideal  model  delta    sigma   weight residual
    1.492  1.640 -0.148 5.00e-02 4.00e+02 8.82e+00
  bond pdb=" N   PRO D  86 "
       pdb=" CA  PRO D  86 "
    ideal  model  delta    sigma   weight residual
    1.472  1.438  0.034 1.34e-02 5.57e+03 6.31e+00
  bond pdb=" CA  ARG E  28 "
       pdb=" C   ARG E  28 "
    ideal  model  delta    sigma   weight residual
    1.523  1.498  0.025 1.30e-02 5.92e+03 3.72e+00
  ... (remaining 4528 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.59: 6088
        3.59 -     7.18: 38
        7.18 -    10.77: 2
       10.77 -    14.36: 1
       14.36 -    17.96: 2
  Bond angle restraints: 6131
  Sorted by residual:
  angle pdb=" CA  PRO D  86 "
        pdb=" N   PRO D  86 "
        pdb=" CD  PRO D  86 "
      ideal   model   delta    sigma   weight residual
     112.00   94.95   17.05 1.40e+00 5.10e-01 1.48e+02
  angle pdb=" N   PRO D  86 "
        pdb=" CD  PRO D  86 "
        pdb=" CG  PRO D  86 "
      ideal   model   delta    sigma   weight residual
     103.20   85.24   17.96 1.50e+00 4.44e-01 1.43e+02
  angle pdb=" CA  PRO D  86 "
        pdb=" CB  PRO D  86 "
        pdb=" CG  PRO D  86 "
      ideal   model   delta    sigma   weight residual
     104.50   92.33   12.17 1.90e+00 2.77e-01 4.10e+01
  angle pdb=" N   TYR D  58 "
        pdb=" CA  TYR D  58 "
        pdb=" C   TYR D  58 "
      ideal   model   delta    sigma   weight residual
     114.04  107.44    6.60 1.24e+00 6.50e-01 2.83e+01
  angle pdb=" N   PRO D  86 "
        pdb=" CA  PRO D  86 "
        pdb=" CB  PRO D  86 "
      ideal   model   delta    sigma   weight residual
     103.26   97.72    5.54 1.14e+00 7.69e-01 2.36e+01
  ... (remaining 6126 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 2230
       16.74 -    33.49: 361
       33.49 -    50.23: 89
       50.23 -    66.97: 23
       66.97 -    83.71: 7
  Dihedral angle restraints: 2710
    sinusoidal: 1064
      harmonic: 1646
  Sorted by residual:
  dihedral pdb=" CA  VAL C 381 "
           pdb=" C   VAL C 381 "
           pdb=" N   LYS C 382 "
           pdb=" CA  LYS C 382 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.68   25.32     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  GLU D  41 "
           pdb=" C   GLU D  41 "
           pdb=" N   GLY D  42 "
           pdb=" CA  GLY D  42 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.86   25.14     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" CA  ARG C 203 "
           pdb=" C   ARG C 203 "
           pdb=" N   HIS C 204 "
           pdb=" CA  HIS C 204 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.09  -22.91     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 2707 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 400
       0.031 -    0.062: 189
       0.062 -    0.092: 70
       0.092 -    0.123: 34
       0.123 -    0.154: 15
  Chirality restraints: 708
  Sorted by residual:
  chirality pdb=" CB  ILE E 118 "
            pdb=" CA  ILE E 118 "
            pdb=" CG1 ILE E 118 "
            pdb=" CG2 ILE E 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.92e-01
  chirality pdb=" CG  LEU E  33 "
            pdb=" CB  LEU E  33 "
            pdb=" CD1 LEU E  33 "
            pdb=" CD2 LEU E  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.75e-01
  chirality pdb=" CA  LEU C 201 "
            pdb=" N   LEU C 201 "
            pdb=" C   LEU C 201 "
            pdb=" CB  LEU C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.64e-01
  ... (remaining 705 not shown)

  Planarity restraints: 793
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D  85 "   -0.112 5.00e-02 4.00e+02   1.52e-01 3.68e+01
        pdb=" N   PRO D  86 "    0.261 5.00e-02 4.00e+02
        pdb=" CA  PRO D  86 "   -0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO D  86 "   -0.075 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D  75 "    0.034 5.00e-02 4.00e+02   5.20e-02 4.32e+00
        pdb=" N   PRO D  76 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO D  76 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D  76 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C  90 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.29e+00
        pdb=" CD  GLU C  90 "    0.031 2.00e-02 2.50e+03
        pdb=" OE1 GLU C  90 "   -0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU C  90 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 790 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 207
        2.71 -     3.26: 4460
        3.26 -     3.81: 6817
        3.81 -     4.35: 8407
        4.35 -     4.90: 13987
  Nonbonded interactions: 33878
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 107 "
            pdb=" N   SER C 108 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" OG  SER C 263 "
            pdb=" OD1 ASN C 266 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OD1 ASP C 298 "
            pdb=" OG1 THR C 301 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   VAL C 240 "
            pdb=" OG  SER C 244 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" NH2 ARG C 346 "
            pdb=" O   PRO C 350 "
     model   vdw
     2.214 3.120
  ... (remaining 33873 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 'D' and resid 7 through 127)
  selection = chain 'E'
}

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:             3.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.330
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
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      :  0.007   0.346   4533  Z= 0.254
  Angle     :  0.923  17.956   6131  Z= 0.577
  Chirality :  0.047   0.154    708
  Planarity :  0.007   0.152    793
  Dihedral  : 18.048  83.712   1642
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  7.65 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 30.52 %
    Favored  : 68.88 %
  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: -2.26 (0.35), residues: 562
  helix: -1.21 (0.40), residues: 172
  sheet: -0.08 (0.55), residues: 106
  loop : -2.29 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  68 
 HIS   0.004   0.001   HIS E  16 
 PHE   0.026   0.002   PHE C 373 
 TYR   0.026   0.001   TYR C 334 
 ARG   0.015   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27900 (  135)
  hydrogen bonds       : angle      10.13075 (  366)
  covalent geometry    : bond        0.00672 ( 4533)
  covalent geometry    : angle       0.92299 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 114
  time to evaluate  : 0.478 
Fit side-chains
REVERT: C   94 ASN cc_start: 0.4771 (OUTLIER) cc_final: 0.4458 (m-40)
REVERT: C  247 ASN cc_start: 0.7839 (p0) cc_final: 0.7585 (p0)
REVERT: D   14 SER cc_start: 0.8678 (p) cc_final: 0.8356 (t)
REVERT: E   77 GLU cc_start: 0.7206 (pm20) cc_final: 0.6786 (pm20)
REVERT: E  104 ASP cc_start: 0.8158 (t0) cc_final: 0.7706 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 117
  average time/residue: 0.1747
  time to fit residues: 26.0715
Evaluate side-chains
  80 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   94 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    0.1980
   chunk 16 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C  82 HIS
** D  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 117 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 = 0.4285 r_free = 0.4285 target = 0.197585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.159944 restraints weight = 5492.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.161318 restraints weight = 4248.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.163929 restraints weight = 3535.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4533  Z= 0.160
  Angle     :  0.686  10.082   6131  Z= 0.367
  Chirality :  0.049   0.151    708
  Planarity :  0.005   0.065    793
  Dihedral  :  5.924  46.652    603
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.19 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 29.12 %
    Favored  : 66.87 %
  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: -2.22 (0.35), residues: 562
  helix: -1.12 (0.39), residues: 185
  sheet:  0.27 (0.54), residues: 109
  loop : -2.54 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C  68 
 HIS   0.006   0.001   HIS C 398 
 PHE   0.012   0.002   PHE D 112 
 TYR   0.009   0.001   TYR E  11 
 ARG   0.007   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04630 (  135)
  hydrogen bonds       : angle       6.95850 (  366)
  covalent geometry    : bond        0.00363 ( 4533)
  covalent geometry    : angle       0.68613 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: C  129 MET cc_start: 0.6467 (mpp) cc_final: 0.5428 (ttm)
REVERT: C  347 LYS cc_start: 0.7361 (tptm) cc_final: 0.6822 (tttp)
REVERT: E   44 ARG cc_start: 0.8272 (mtp85) cc_final: 0.8048 (mtp85)
  outliers start: 20
  outliers final: 12
  residues processed: 102
  average time/residue: 0.2406
  time to fit residues: 32.2006
Evaluate side-chains
  88 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  384 ASP
Chi-restraints excluded: chain C residue  388 HIS
Chi-restraints excluded: chain C residue  399 LEU
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue  104 ASP
Chi-restraints excluded: chain D residue  124 GLN
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   50 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue   81 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  94 ASN
C 163 ASN
** D  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  27 GLN
** E 117 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 = 0.3926 r_free = 0.3926 target = 0.169014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.137549 restraints weight = 5410.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.137935 restraints weight = 5176.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.139683 restraints weight = 4955.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4533  Z= 0.187
  Angle     :  0.690   9.845   6131  Z= 0.364
  Chirality :  0.049   0.146    708
  Planarity :  0.004   0.039    793
  Dihedral  :  5.528  23.255    600
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.72 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 29.52 %
    Favored  : 65.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.12 (0.35), residues: 562
  helix: -0.92 (0.39), residues: 183
  sheet:  0.08 (0.54), residues: 113
  loop : -2.47 (0.35), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP C  68 
 HIS   0.006   0.002   HIS E  16 
 PHE   0.016   0.002   PHE D  84 
 TYR   0.011   0.002   TYR E  11 
 ARG   0.007   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04215 (  135)
  hydrogen bonds       : angle       6.31702 (  366)
  covalent geometry    : bond        0.00438 ( 4533)
  covalent geometry    : angle       0.69049 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
REVERT: C   94 ASN cc_start: 0.4956 (OUTLIER) cc_final: 0.4751 (m110)
REVERT: C  129 MET cc_start: 0.6156 (mpp) cc_final: 0.5306 (ttm)
REVERT: C  347 LYS cc_start: 0.7314 (tptm) cc_final: 0.6951 (tttp)
REVERT: E   44 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7846 (mtp85)
  outliers start: 26
  outliers final: 16
  residues processed: 97
  average time/residue: 0.1963
  time to fit residues: 24.4454
Evaluate side-chains
  92 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   94 ASN
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  388 HIS
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue  104 ASP
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   50 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  106 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 1 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** D  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.169460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.134992 restraints weight = 5392.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.135536 restraints weight = 4856.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.136605 restraints weight = 4703.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4533  Z= 0.160
  Angle     :  0.654  11.279   6131  Z= 0.343
  Chirality :  0.048   0.144    708
  Planarity :  0.004   0.036    793
  Dihedral  :  5.415  23.364    600
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.30 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 29.72 %
    Favored  : 64.66 %
  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: -2.05 (0.35), residues: 562
  helix: -0.76 (0.40), residues: 179
  sheet: -0.18 (0.52), residues: 115
  loop : -2.35 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  68 
 HIS   0.005   0.001   HIS C 398 
 PHE   0.012   0.002   PHE D  84 
 TYR   0.010   0.001   TYR E  11 
 ARG   0.008   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03573 (  135)
  hydrogen bonds       : angle       6.11007 (  366)
  covalent geometry    : bond        0.00380 ( 4533)
  covalent geometry    : angle       0.65352 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.523 
Fit side-chains
REVERT: C  347 LYS cc_start: 0.7592 (tptm) cc_final: 0.7303 (tttp)
REVERT: E   44 ARG cc_start: 0.8335 (mtp85) cc_final: 0.7972 (mtp85)
  outliers start: 28
  outliers final: 20
  residues processed: 99
  average time/residue: 0.2183
  time to fit residues: 26.8799
Evaluate side-chains
  93 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  144 GLN
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  388 HIS
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain D residue  104 ASP
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  106 VAL
Chi-restraints excluded: chain E residue  123 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 40 optimal weight:    0.3980
   chunk 2 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C  94 ASN
C 388 HIS
** D  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  48 HIS
** E 117 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 = 0.4237 r_free = 0.4237 target = 0.191661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.153925 restraints weight = 5617.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.153841 restraints weight = 4308.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.158024 restraints weight = 3817.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4533  Z= 0.160
  Angle     :  0.665  11.984   6131  Z= 0.344
  Chirality :  0.048   0.154    708
  Planarity :  0.004   0.041    793
  Dihedral  :  5.376  23.062    600
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.19 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  6.22 %
    Allowed  : 29.52 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.99 (0.35), residues: 562
  helix: -0.78 (0.40), residues: 183
  sheet: -0.19 (0.53), residues: 115
  loop : -2.26 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  68 
 HIS   0.005   0.001   HIS C 398 
 PHE   0.010   0.001   PHE D  84 
 TYR   0.017   0.002   TYR C 225 
 ARG   0.007   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  135)
  hydrogen bonds       : angle       6.03218 (  366)
  covalent geometry    : bond        0.00380 ( 4533)
  covalent geometry    : angle       0.66507 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.488 
Fit side-chains
REVERT: C  226 ASN cc_start: 0.8011 (m-40) cc_final: 0.7082 (t0)
REVERT: E   44 ARG cc_start: 0.8319 (mtp85) cc_final: 0.8076 (mtp85)
  outliers start: 31
  outliers final: 24
  residues processed: 103
  average time/residue: 0.1517
  time to fit residues: 20.3026
Evaluate side-chains
  98 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  144 GLN
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  388 HIS
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain D residue  104 ASP
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   81 VAL
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain E residue  106 VAL
Chi-restraints excluded: chain E residue  123 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    0.0670
   chunk 34 optimal weight:    0.0020
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.4926

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

Flipped N/Q/H residues before XYZ refinement:
C 379 ASN
** D  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 117 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 = 0.4254 r_free = 0.4254 target = 0.193152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.154409 restraints weight = 5490.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.158022 restraints weight = 4781.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.159308 restraints weight = 3370.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.4150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4533  Z= 0.137
  Angle     :  0.662  12.836   6131  Z= 0.337
  Chirality :  0.047   0.144    708
  Planarity :  0.004   0.046    793
  Dihedral  :  5.238  24.305    600
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.47 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 30.72 %
    Favored  : 64.06 %
  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: -1.92 (0.35), residues: 562
  helix: -0.63 (0.40), residues: 182
  sheet: -0.17 (0.53), residues: 115
  loop : -2.27 (0.35), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  68 
 HIS   0.004   0.001   HIS C 398 
 PHE   0.013   0.001   PHE C 357 
 TYR   0.020   0.002   TYR C 225 
 ARG   0.010   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  135)
  hydrogen bonds       : angle       6.00120 (  366)
  covalent geometry    : bond        0.00324 ( 4533)
  covalent geometry    : angle       0.66195 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.498 
Fit side-chains
REVERT: C  226 ASN cc_start: 0.7945 (m-40) cc_final: 0.7063 (t0)
REVERT: C  375 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8090 (tt)
  outliers start: 26
  outliers final: 21
  residues processed: 106
  average time/residue: 0.1473
  time to fit residues: 20.2333
Evaluate side-chains
  101 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  144 GLN
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain D residue  104 ASP
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain E residue  106 VAL
Chi-restraints excluded: chain E residue  123 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0980
   chunk 14 optimal weight:    0.0060
   chunk 16 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
** D  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.194259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.154683 restraints weight = 5526.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.158072 restraints weight = 4872.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.159656 restraints weight = 3475.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.4403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4533  Z= 0.127
  Angle     :  0.655  13.455   6131  Z= 0.331
  Chirality :  0.047   0.157    708
  Planarity :  0.004   0.043    793
  Dihedral  :  5.106  23.898    600
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.47 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 31.53 %
    Favored  : 63.65 %
  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: -1.82 (0.35), residues: 562
  helix: -0.52 (0.40), residues: 182
  sheet:  0.05 (0.54), residues: 112
  loop : -2.30 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C  68 
 HIS   0.003   0.001   HIS C 398 
 PHE   0.016   0.001   PHE D   9 
 TYR   0.019   0.002   TYR C 225 
 ARG   0.010   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03211 (  135)
  hydrogen bonds       : angle       5.86133 (  366)
  covalent geometry    : bond        0.00298 ( 4533)
  covalent geometry    : angle       0.65455 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.499 
Fit side-chains
REVERT: C  226 ASN cc_start: 0.7954 (m-40) cc_final: 0.6994 (t0)
REVERT: C  375 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8023 (tt)
REVERT: C  394 MET cc_start: 0.8217 (mmm) cc_final: 0.8013 (mmm)
REVERT: D   19 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7435 (t0)
REVERT: D  105 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7523 (mm-30)
REVERT: E   33 LEU cc_start: 0.8780 (mm) cc_final: 0.8475 (mm)
REVERT: E   62 ARG cc_start: 0.8496 (mmt180) cc_final: 0.8218 (mmt90)
  outliers start: 24
  outliers final: 21
  residues processed: 104
  average time/residue: 0.1498
  time to fit residues: 20.1749
Evaluate side-chains
  103 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  240 VAL
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain C residue  388 HIS
Chi-restraints excluded: chain D residue   19 ASN
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain D residue  104 ASP
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  106 VAL
Chi-restraints excluded: chain E residue  123 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0970
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 39 optimal weight:    0.1980
   chunk 41 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0970
   chunk 55 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
** D  19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.186778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.149017 restraints weight = 5513.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.150653 restraints weight = 5441.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.153058 restraints weight = 4681.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.4572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4533  Z= 0.123
  Angle     :  0.661  12.685   6131  Z= 0.335
  Chirality :  0.047   0.162    708
  Planarity :  0.003   0.039    793
  Dihedral  :  5.003  24.146    600
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.01 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 32.13 %
    Favored  : 63.05 %
  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: -1.63 (0.35), residues: 562
  helix: -0.25 (0.40), residues: 179
  sheet:  0.09 (0.54), residues: 112
  loop : -2.23 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C  68 
 HIS   0.003   0.001   HIS C 398 
 PHE   0.016   0.001   PHE D   9 
 TYR   0.020   0.002   TYR C 225 
 ARG   0.009   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03144 (  135)
  hydrogen bonds       : angle       5.80433 (  366)
  covalent geometry    : bond        0.00289 ( 4533)
  covalent geometry    : angle       0.66122 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
REVERT: C  226 ASN cc_start: 0.7930 (m-40) cc_final: 0.7027 (t0)
REVERT: C  249 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8271 (mp)
REVERT: C  375 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7917 (tt)
REVERT: C  394 MET cc_start: 0.8205 (mmm) cc_final: 0.7857 (mtp)
REVERT: D   19 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7492 (t0)
REVERT: E   68 ASP cc_start: 0.8081 (t70) cc_final: 0.7807 (t0)
  outliers start: 24
  outliers final: 19
  residues processed: 102
  average time/residue: 0.1555
  time to fit residues: 20.4928
Evaluate side-chains
  110 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  249 ILE
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain C residue  388 HIS
Chi-restraints excluded: chain D residue   19 ASN
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain D residue  104 ASP
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  106 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0000
   chunk 46 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0670
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0970
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    0.1980
   overall best weight:    0.2120

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

Flipped N/Q/H residues before XYZ refinement:
D  19 ASN
E 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.177088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.141364 restraints weight = 5354.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.144608 restraints weight = 4815.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.145490 restraints weight = 3458.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.4834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4533  Z= 0.110
  Angle     :  0.656  12.430   6131  Z= 0.332
  Chirality :  0.047   0.192    708
  Planarity :  0.003   0.035    793
  Dihedral  :  4.928  24.103    600
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.30 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 33.13 %
    Favored  : 63.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.45 (0.36), residues: 562
  helix: -0.05 (0.41), residues: 178
  sheet:  0.25 (0.54), residues: 112
  loop : -2.18 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C  68 
 HIS   0.003   0.001   HIS C 398 
 PHE   0.015   0.001   PHE D   9 
 TYR   0.020   0.001   TYR C 225 
 ARG   0.008   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03073 (  135)
  hydrogen bonds       : angle       5.67025 (  366)
  covalent geometry    : bond        0.00249 ( 4533)
  covalent geometry    : angle       0.65569 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: C  226 ASN cc_start: 0.8003 (m-40) cc_final: 0.6997 (t0)
REVERT: C  249 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8253 (mp)
REVERT: C  343 ASP cc_start: 0.7309 (m-30) cc_final: 0.6884 (m-30)
REVERT: D   30 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7529 (pttt)
REVERT: D   44 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7321 (mtp85)
  outliers start: 17
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1651
  time to fit residues: 21.9658
Evaluate side-chains
  99 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  249 ILE
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  339 ASN
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   30 LYS
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain E residue   24 LEU
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  106 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
D 116 HIS
E  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.180285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.145709 restraints weight = 5552.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.145593 restraints weight = 4795.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.148496 restraints weight = 4254.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.4987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4533  Z= 0.216
  Angle     :  0.749  11.666   6131  Z= 0.385
  Chirality :  0.051   0.201    708
  Planarity :  0.004   0.051    793
  Dihedral  :  5.363  22.642    600
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  8.72 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 32.33 %
    Favored  : 63.86 %
  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: -1.66 (0.35), residues: 562
  helix: -0.35 (0.40), residues: 175
  sheet:  0.14 (0.54), residues: 110
  loop : -2.18 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP C  68 
 HIS   0.006   0.002   HIS E  16 
 PHE   0.022   0.002   PHE C 357 
 TYR   0.024   0.002   TYR C 225 
 ARG   0.009   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03747 (  135)
  hydrogen bonds       : angle       5.95015 (  366)
  covalent geometry    : bond        0.00511 ( 4533)
  covalent geometry    : angle       0.74875 ( 6131)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
REVERT: C  226 ASN cc_start: 0.7994 (m-40) cc_final: 0.7234 (t0)
REVERT: C  306 MET cc_start: 0.7867 (mtm) cc_final: 0.7630 (mtm)
REVERT: C  375 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8037 (tt)
REVERT: C  394 MET cc_start: 0.8207 (mmm) cc_final: 0.7744 (mtm)
REVERT: D   30 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7657 (pttt)
REVERT: D   44 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7367 (mtp85)
  outliers start: 19
  outliers final: 14
  residues processed: 94
  average time/residue: 0.1972
  time to fit residues: 22.9419
Evaluate side-chains
  93 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  158 MET
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  375 LEU
Chi-restraints excluded: chain C residue  388 HIS
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   30 LYS
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue  104 ASP
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain D residue  126 LEU
Chi-restraints excluded: chain E residue   34 CYS
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  106 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0470
   chunk 9 optimal weight:    0.9990
   chunk 40 optimal weight:    0.2980
   chunk 52 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
E  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.190099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.151085 restraints weight = 5514.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.151229 restraints weight = 4440.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.153080 restraints weight = 4362.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.5126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4533  Z= 0.139
  Angle     :  0.689  11.738   6131  Z= 0.352
  Chirality :  0.048   0.181    708
  Planarity :  0.004   0.039    793
  Dihedral  :  5.137  23.075    600
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.65 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 32.53 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.57 (0.35), residues: 562
  helix: -0.17 (0.40), residues: 175
  sheet: -0.21 (0.51), residues: 118
  loop : -2.06 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  68 
 HIS   0.004   0.001   HIS C 398 
 PHE   0.014   0.001   PHE D   9 
 TYR   0.023   0.002   TYR C 225 
 ARG   0.010   0.001   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 (  135)
  hydrogen bonds       : angle       5.88522 (  366)
  covalent geometry    : bond        0.00327 ( 4533)
  covalent geometry    : angle       0.68878 ( 6131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2033.46 seconds
wall clock time: 36 minutes 51.69 seconds (2211.69 seconds total)