Starting phenix.real_space_refine
on Tue Mar  3 11:29:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x83_33054/03_2026/7x83_33054.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x83_33054/03_2026/7x83_33054.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x83_33054/03_2026/7x83_33054.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x83_33054/03_2026/7x83_33054.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x83_33054/03_2026/7x83_33054.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x83_33054/03_2026/7x83_33054.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.003
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      21      5.16       5
     C    2082      2.51       5
     N     519      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3258
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
  Restraints were copied for chains:
    A, C
  Time building chain proxies: 0.49, per 1000 atoms: 0.15
  Number of scatterers: 3258
  At special positions: 0
  Unit cell: (100.43, 100.43, 35.69, 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      21     16.00
     O     636      8.00
     N     519      7.00
     C    2082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 99.9 milliseconds
  

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 33.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130
      removed outlier: 6.705A  pdb=" N   LYS B 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137
      removed outlier: 6.653A  pdb=" N   SER B 134 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   VAL C 137 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ASP B 136 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144
      removed outlier: 6.553A  pdb=" N   TYR B 143 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151
      removed outlier: 6.958A  pdb=" N   LEU B 150 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 156
      removed outlier: 6.509A  pdb=" N   ASN B 155 " --> pdb=" O   ASN C 156 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 164
      removed outlier: 6.916A  pdb=" N   GLU B 163 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 169
      removed outlier: 6.584A  pdb=" N   GLN B 168 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 186
      removed outlier: 6.541A  pdb=" N   THR B 185 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 192
      removed outlier: 6.479A  pdb=" N   LEU B 190 " --> pdb=" O   ASP A 191 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 213
      removed outlier: 8.933A  pdb=" N   VAL B 202 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 9.746A  pdb=" N   GLU A 205 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   ALA B 204 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   MET A 207 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   GLU B 206 " --> pdb=" O   MET A 207 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   TYR A 209 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   SER B 208 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   TYR A 211 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   MET B 210 " --> pdb=" O   TYR A 211 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   PHE A 213 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ASP B 212 " --> pdb=" O   PHE A 213 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   VAL C 202 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   ILE B 203 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA C 204 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 216 through 219
      removed outlier: 5.914A  pdb=" N   LEU B 216 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   ILE C 219 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   SER B 218 " --> pdb=" O   ILE C 219 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 222 through 230
      removed outlier: 6.990A  pdb=" N   VAL B 230 " --> pdb=" O   GLN A 229 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   ASN B 223 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   LEU C 226 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   VAL B 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   MET C 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   MET B 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   VAL C 230 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   GLN B 229 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 240 through 244
      removed outlier: 6.646A  pdb=" N   SER B 240 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 8.319A  pdb=" N   ILE C 243 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   GLN B 242 " --> pdb=" O   ILE C 243 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 251 through 253
      removed outlier: 6.458A  pdb=" N   ASP B 252 " --> pdb=" O   CYS A 253 " (cutoff:3.500A)

    41 hydrogen bonds defined for protein.
    123 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.30

  Time building geometry restraints manager: 0.32 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: 1026
        1.34 -     1.45: 538
        1.45 -     1.57: 1712
        1.57 -     1.69: 0
        1.69 -     1.80: 36
  Bond restraints: 3312
  Sorted by residual:
  bond pdb=" CA  VAL B 230 "
       pdb=" C   VAL B 230 "
    ideal  model  delta    sigma   weight residual
    1.527  1.513  0.014 8.50e-03 1.38e+04 2.73e+00
  bond pdb=" CA  ARG B 247 "
       pdb=" C   ARG B 247 "
    ideal  model  delta    sigma   weight residual
    1.531  1.514  0.017 1.08e-02 8.57e+03 2.46e+00
  bond pdb=" CA  ARG A 247 "
       pdb=" C   ARG A 247 "
    ideal  model  delta    sigma   weight residual
    1.531  1.515  0.017 1.08e-02 8.57e+03 2.34e+00
  bond pdb=" CA  VAL C 230 "
       pdb=" C   VAL C 230 "
    ideal  model  delta    sigma   weight residual
    1.527  1.514  0.013 8.50e-03 1.38e+04 2.34e+00
  bond pdb=" CA  ARG C 247 "
       pdb=" C   ARG C 247 "
    ideal  model  delta    sigma   weight residual
    1.531  1.515  0.016 1.08e-02 8.57e+03 2.33e+00
  ... (remaining 3307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 3790
        1.03 -     2.06: 559
        2.06 -     3.09: 121
        3.09 -     4.12: 21
        4.12 -     5.16: 12
  Bond angle restraints: 4503
  Sorted by residual:
  angle pdb=" C   GLN C 245 "
        pdb=" N   GLU C 246 "
        pdb=" CA  GLU C 246 "
      ideal   model   delta    sigma   weight residual
     122.11  117.17    4.94 1.59e+00 3.96e-01 9.66e+00
  angle pdb=" C   GLN B 245 "
        pdb=" N   GLU B 246 "
        pdb=" CA  GLU B 246 "
      ideal   model   delta    sigma   weight residual
     122.11  117.17    4.94 1.59e+00 3.96e-01 9.66e+00
  angle pdb=" C   GLN A 245 "
        pdb=" N   GLU A 246 "
        pdb=" CA  GLU A 246 "
      ideal   model   delta    sigma   weight residual
     122.11  117.21    4.90 1.59e+00 3.96e-01 9.50e+00
  angle pdb=" C   LEU A 144 "
        pdb=" N   ASN A 145 "
        pdb=" CA  ASN A 145 "
      ideal   model   delta    sigma   weight residual
     121.54  126.70   -5.16 1.91e+00 2.74e-01 7.28e+00
  angle pdb=" CA  TYR C 143 "
        pdb=" CB  TYR C 143 "
        pdb=" CG  TYR C 143 "
      ideal   model   delta    sigma   weight residual
     113.90  118.75   -4.85 1.80e+00 3.09e-01 7.27e+00
  ... (remaining 4498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 1794
       16.36 -    32.72: 175
       32.72 -    49.08: 17
       49.08 -    65.43: 6
       65.43 -    81.79: 3
  Dihedral angle restraints: 1995
    sinusoidal: 777
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CA  GLN C 138 "
           pdb=" C   GLN C 138 "
           pdb=" N   LYS C 139 "
           pdb=" CA  LYS C 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.93   22.07     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  GLN A 138 "
           pdb=" C   GLN A 138 "
           pdb=" N   LYS A 139 "
           pdb=" CA  LYS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.99   22.01     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  GLN B 138 "
           pdb=" C   GLN B 138 "
           pdb=" N   LYS B 139 "
           pdb=" CA  LYS B 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.00   22.00     0      5.00e+00 4.00e-02 1.94e+01
  ... (remaining 1992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 255
       0.035 -    0.071: 156
       0.071 -    0.106: 88
       0.106 -    0.142: 35
       0.142 -    0.177: 9
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CA  ASN A 145 "
            pdb=" N   ASN A 145 "
            pdb=" C   ASN A 145 "
            pdb=" CB  ASN A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.86e-01
  chirality pdb=" CA  ASN C 145 "
            pdb=" N   ASN C 145 "
            pdb=" C   ASN C 145 "
            pdb=" CB  ASN C 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.81e-01
  chirality pdb=" CA  ASN B 145 "
            pdb=" N   ASN B 145 "
            pdb=" C   ASN B 145 "
            pdb=" CB  ASN B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.53e-01
  ... (remaining 540 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 143 "    0.018 2.00e-02 2.50e+03   1.14e-02 2.60e+00
        pdb=" CG  TYR A 143 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 143 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 143 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 143 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 143 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 143 "    0.018 2.00e-02 2.50e+03   1.13e-02 2.56e+00
        pdb=" CG  TYR C 143 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 143 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 143 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 143 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 143 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 143 "    0.018 2.00e-02 2.50e+03   1.12e-02 2.51e+00
        pdb=" CG  TYR B 143 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 143 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 143 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 143 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 143 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 143 "    0.004 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 385
        2.75 -     3.29: 3104
        3.29 -     3.83: 5256
        3.83 -     4.36: 5810
        4.36 -     4.90: 11622
  Nonbonded interactions: 26177
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 236 "
            pdb=" OG  SER B 240 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OH  TYR A 236 "
            pdb=" OG  SER A 240 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OH  TYR C 236 "
            pdb=" OG  SER C 240 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OE2 GLU B 246 "
            pdb=" NH2 ARG B 247 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" OE2 GLU A 246 "
            pdb=" NH2 ARG A 247 "
     model   vdw
     2.300 3.120
  ... (remaining 26172 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 'B'
  selection = chain 'A'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.530
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.270
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.058   3315  Z= 0.395
  Angle     :  0.827   5.155   4509  Z= 0.495
  Chirality :  0.060   0.177    543
  Planarity :  0.003   0.011    558
  Dihedral  : 13.347  81.792   1206
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.79 %
    Favored  : 84.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.71 (0.28), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.35 (0.22), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 247 
 TYR   0.026   0.003   TYR A 143 
 PHE   0.010   0.003   PHE A 213 
 HIS   0.005   0.003   HIS C 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00890 ( 3312)
  covalent geometry    : angle       0.82450 ( 4503)
  SS BOND              : bond        0.00377 (    3)
  SS BOND              : angle       1.80250 (    6)
  hydrogen bonds       : bond        0.12708 (   41)
  hydrogen bonds       : angle       7.06288 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B  140 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7232 (ttm110)
REVERT: B  178 LYS cc_start: 0.7339 (mttt) cc_final: 0.6399 (tptt)
REVERT: B  215 THR cc_start: 0.7671 (t) cc_final: 0.7398 (t)
REVERT: A  140 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7490 (ttm110)
REVERT: A  178 LYS cc_start: 0.7850 (mttt) cc_final: 0.6991 (tptt)
REVERT: C  140 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7510 (ttm110)
REVERT: C  178 LYS cc_start: 0.7310 (mttt) cc_final: 0.6485 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0986
  time to fit residues: 5.6572
Evaluate side-chains
  37 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 223 ASN
A 223 ASN
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 155 ASN
C 223 ASN
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.271828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.228145 restraints weight = 4014.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.4617 rms_B_bonded: 0.87
r_work: 0.4889 rms_B_bonded: 0.41 restraints_weight: 0.5000
r_work: 0.4860 rms_B_bonded: 0.72 restraints_weight: 0.2500
r_work: 0.4710 rms_B_bonded: 2.65 restraints_weight: 0.1250
r_work (final): 0.4710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3315  Z= 0.147
  Angle     :  0.583   5.442   4509  Z= 0.323
  Chirality :  0.053   0.178    543
  Planarity :  0.002   0.020    558
  Dihedral  :  6.446  18.812    447
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 11.90 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.36 (0.30), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.08 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 247 
 TYR   0.016   0.002   TYR B 143 
 PHE   0.008   0.002   PHE A 237 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3312)
  covalent geometry    : angle       0.58299 ( 4503)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       0.50782 (    6)
  hydrogen bonds       : bond        0.01757 (   41)
  hydrogen bonds       : angle       4.92871 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.150 
Fit side-chains
REVERT: B  140 ARG cc_start: 0.8335 (mtt180) cc_final: 0.8119 (ttm110)
REVERT: B  145 ASN cc_start: 0.8331 (p0) cc_final: 0.8021 (p0)
REVERT: B  146 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8226 (pt)
REVERT: B  178 LYS cc_start: 0.8262 (mttt) cc_final: 0.7739 (tptt)
REVERT: B  215 THR cc_start: 0.7716 (t) cc_final: 0.7501 (t)
REVERT: A  178 LYS cc_start: 0.8087 (mttt) cc_final: 0.7664 (tptt)
REVERT: C  145 ASN cc_start: 0.8159 (p0) cc_final: 0.7840 (p0)
REVERT: C  146 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7656 (pt)
REVERT: C  178 LYS cc_start: 0.7958 (mttt) cc_final: 0.7530 (tptt)
REVERT: C  215 THR cc_start: 0.7710 (t) cc_final: 0.7495 (t)
  outliers start: 13
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0743
  time to fit residues: 4.7594
Evaluate side-chains
  45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  175 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 29 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
B 156 ASN
A 156 ASN
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** 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 = 0.4672 r_free = 0.4672 target = 0.272769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4838 r_free = 0.4838 target = 0.228182 restraints weight = 3977.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.4614 rms_B_bonded: 1.06
r_work: 0.4883 rms_B_bonded: 0.49 restraints_weight: 0.5000
r_work: 0.4857 rms_B_bonded: 0.86 restraints_weight: 0.2500
r_work: 0.4666 rms_B_bonded: 3.46 restraints_weight: 0.1250
r_work (final): 0.4666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3315  Z= 0.149
  Angle     :  0.579   6.056   4509  Z= 0.320
  Chirality :  0.053   0.181    543
  Planarity :  0.002   0.030    558
  Dihedral  :  6.102  16.259    447
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 13.23 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.25 (0.30), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.99 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 140 
 TYR   0.016   0.002   TYR B 143 
 PHE   0.010   0.002   PHE A 237 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3312)
  covalent geometry    : angle       0.57890 ( 4503)
  SS BOND              : bond        0.00525 (    3)
  SS BOND              : angle       0.47201 (    6)
  hydrogen bonds       : bond        0.01637 (   41)
  hydrogen bonds       : angle       4.55031 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.146 
Fit side-chains
REVERT: B  145 ASN cc_start: 0.8325 (p0) cc_final: 0.7977 (p0)
REVERT: B  146 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8230 (pt)
REVERT: B  178 LYS cc_start: 0.8283 (mttt) cc_final: 0.7726 (tptt)
REVERT: B  215 THR cc_start: 0.7894 (t) cc_final: 0.7684 (t)
REVERT: A  178 LYS cc_start: 0.7967 (mttt) cc_final: 0.7518 (tptt)
REVERT: A  226 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7391 (tt)
REVERT: C  145 ASN cc_start: 0.8177 (p0) cc_final: 0.7660 (p0)
REVERT: C  146 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7691 (pt)
REVERT: C  178 LYS cc_start: 0.7993 (mttt) cc_final: 0.7503 (tptt)
REVERT: C  215 THR cc_start: 0.7771 (t) cc_final: 0.7566 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0574
  time to fit residues: 3.9574
Evaluate side-chains
  49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** 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 = 0.4660 r_free = 0.4660 target = 0.306627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 126)---------------|
| r_work = 0.4950 r_free = 0.4950 target = 0.252310 restraints weight = 4396.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.4530 rms_B_bonded: 0.89
r_work: 0.4799 rms_B_bonded: 0.39 restraints_weight: 0.5000
r_work: 0.4780 rms_B_bonded: 0.65 restraints_weight: 0.2500
r_work: 0.4630 rms_B_bonded: 2.48 restraints_weight: 0.1250
r_work (final): 0.4630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.049   3315  Z= 0.343
  Angle     :  0.741   6.444   4509  Z= 0.413
  Chirality :  0.059   0.195    543
  Planarity :  0.003   0.028    558
  Dihedral  :  6.829  20.184    447
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.79 %
    Favored  : 83.21 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 14.02 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.48 (0.30), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.17 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 140 
 TYR   0.027   0.003   TYR B 143 
 PHE   0.016   0.003   PHE A 237 
 HIS   0.007   0.004   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00808 ( 3312)
  covalent geometry    : angle       0.74073 ( 4503)
  SS BOND              : bond        0.00738 (    3)
  SS BOND              : angle       0.92731 (    6)
  hydrogen bonds       : bond        0.02140 (   41)
  hydrogen bonds       : angle       4.53376 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.124 
Fit side-chains
REVERT: B  145 ASN cc_start: 0.8361 (p0) cc_final: 0.7812 (p0)
REVERT: B  178 LYS cc_start: 0.8526 (mttt) cc_final: 0.7907 (tptt)
REVERT: A  145 ASN cc_start: 0.8213 (p0) cc_final: 0.7989 (p0)
REVERT: A  178 LYS cc_start: 0.8139 (mttt) cc_final: 0.7690 (tptt)
REVERT: C  145 ASN cc_start: 0.8281 (p0) cc_final: 0.7791 (p0)
REVERT: C  178 LYS cc_start: 0.8188 (mttt) cc_final: 0.7670 (tptt)
  outliers start: 19
  outliers final: 15
  residues processed: 58
  average time/residue: 0.0465
  time to fit residues: 3.4914
Evaluate side-chains
  52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  180 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0770
   overall best weight:    1.3944

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** 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 = 0.4692 r_free = 0.4692 target = 0.275794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.231719 restraints weight = 3950.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.4649 rms_B_bonded: 0.84
r_work: 0.4926 rms_B_bonded: 0.38 restraints_weight: 0.5000
r_work: 0.4908 rms_B_bonded: 0.64 restraints_weight: 0.2500
r_work: 0.4762 rms_B_bonded: 2.46 restraints_weight: 0.1250
r_work (final): 0.4762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3315  Z= 0.115
  Angle     :  0.560   6.324   4509  Z= 0.307
  Chirality :  0.052   0.167    543
  Planarity :  0.002   0.021    558
  Dihedral  :  5.957  15.937    447
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 14.81 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.10 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.88 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 140 
 TYR   0.014   0.001   TYR B 143 
 PHE   0.006   0.001   PHE A 237 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 3312)
  covalent geometry    : angle       0.55976 ( 4503)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.30524 (    6)
  hydrogen bonds       : bond        0.01338 (   41)
  hydrogen bonds       : angle       4.33732 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.120 
Fit side-chains
REVERT: B  141 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8587 (t)
REVERT: B  145 ASN cc_start: 0.8305 (p0) cc_final: 0.7959 (p0)
REVERT: B  146 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8209 (pt)
REVERT: B  178 LYS cc_start: 0.8298 (mttt) cc_final: 0.7817 (tptt)
REVERT: A  138 GLN cc_start: 0.8289 (pt0) cc_final: 0.7969 (pt0)
REVERT: A  178 LYS cc_start: 0.7947 (mttt) cc_final: 0.7598 (tptt)
REVERT: C  145 ASN cc_start: 0.8169 (p0) cc_final: 0.7654 (p0)
REVERT: C  146 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7730 (pt)
REVERT: C  178 LYS cc_start: 0.8000 (mttt) cc_final: 0.7545 (tptt)
  outliers start: 19
  outliers final: 12
  residues processed: 58
  average time/residue: 0.0543
  time to fit residues: 4.0437
Evaluate side-chains
  53 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0870
   overall best weight:    2.6166

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** 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 = 0.4665 r_free = 0.4665 target = 0.268961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.4882 r_free = 0.4882 target = 0.223824 restraints weight = 3991.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.4619 rms_B_bonded: 0.84
r_work: 0.4893 rms_B_bonded: 0.38 restraints_weight: 0.5000
r_work: 0.4866 rms_B_bonded: 0.66 restraints_weight: 0.2500
r_work: 0.4714 rms_B_bonded: 2.55 restraints_weight: 0.1250
r_work (final): 0.4714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3315  Z= 0.167
  Angle     :  0.597   6.893   4509  Z= 0.329
  Chirality :  0.053   0.182    543
  Planarity :  0.002   0.012    558
  Dihedral  :  5.993  16.284    447
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.03 %
    Favored  : 86.97 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 15.61 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.04 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 140 
 TYR   0.018   0.002   TYR B 143 
 PHE   0.010   0.002   PHE A 237 
 HIS   0.006   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 3312)
  covalent geometry    : angle       0.59740 ( 4503)
  SS BOND              : bond        0.00410 (    3)
  SS BOND              : angle       0.49173 (    6)
  hydrogen bonds       : bond        0.01515 (   41)
  hydrogen bonds       : angle       4.17517 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.123 
Fit side-chains
REVERT: B  141 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8654 (t)
REVERT: B  145 ASN cc_start: 0.8283 (p0) cc_final: 0.7933 (p0)
REVERT: B  146 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8217 (pt)
REVERT: B  178 LYS cc_start: 0.8357 (mttt) cc_final: 0.7865 (tptt)
REVERT: A  178 LYS cc_start: 0.7991 (mttt) cc_final: 0.7585 (tptt)
REVERT: C  145 ASN cc_start: 0.8218 (p0) cc_final: 0.7717 (p0)
REVERT: C  146 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7677 (pt)
REVERT: C  178 LYS cc_start: 0.8023 (mttt) cc_final: 0.7508 (tptt)
  outliers start: 20
  outliers final: 14
  residues processed: 61
  average time/residue: 0.0500
  time to fit residues: 3.8561
Evaluate side-chains
  57 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  180 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
B 138 GLN
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 GLN
** C 239 HIS ** 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 = 0.4653 r_free = 0.4653 target = 0.267455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.221918 restraints weight = 4102.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.4597 rms_B_bonded: 1.07
r_work: 0.4860 rms_B_bonded: 0.49 restraints_weight: 0.5000
r_work: 0.4832 rms_B_bonded: 0.87 restraints_weight: 0.2500
r_work: 0.4646 rms_B_bonded: 3.43 restraints_weight: 0.1250
r_work (final): 0.4646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3315  Z= 0.190
  Angle     :  0.614   6.732   4509  Z= 0.340
  Chirality :  0.054   0.183    543
  Planarity :  0.002   0.009    558
  Dihedral  :  6.137  17.005    447
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.53 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 17.46 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.04 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 140 
 TYR   0.020   0.002   TYR A 143 
 PHE   0.015   0.002   PHE A 213 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 3312)
  covalent geometry    : angle       0.61439 ( 4503)
  SS BOND              : bond        0.00437 (    3)
  SS BOND              : angle       0.59188 (    6)
  hydrogen bonds       : bond        0.01574 (   41)
  hydrogen bonds       : angle       4.19343 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 38
  time to evaluate  : 0.126 
Fit side-chains
REVERT: B  141 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8687 (t)
REVERT: B  145 ASN cc_start: 0.8291 (p0) cc_final: 0.7933 (p0)
REVERT: B  146 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8244 (pt)
REVERT: B  178 LYS cc_start: 0.8423 (mttt) cc_final: 0.7880 (tptt)
REVERT: B  235 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7682 (m)
REVERT: A  178 LYS cc_start: 0.8034 (mttt) cc_final: 0.7615 (tptt)
REVERT: C  145 ASN cc_start: 0.8201 (p0) cc_final: 0.7722 (p0)
REVERT: C  146 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7735 (pt)
REVERT: C  178 LYS cc_start: 0.8174 (mttt) cc_final: 0.7573 (tptt)
  outliers start: 21
  outliers final: 14
  residues processed: 57
  average time/residue: 0.0486
  time to fit residues: 3.5785
Evaluate side-chains
  56 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 38
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  180 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 21 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** 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 = 0.4699 r_free = 0.4699 target = 0.309761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.256348 restraints weight = 4457.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.4569 rms_B_bonded: 0.87
r_work: 0.4839 rms_B_bonded: 0.47 restraints_weight: 0.5000
r_work: 0.4815 rms_B_bonded: 0.78 restraints_weight: 0.2500
r_work: 0.4668 rms_B_bonded: 2.74 restraints_weight: 0.1250
r_work (final): 0.4668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3315  Z= 0.260
  Angle     :  0.673   6.721   4509  Z= 0.375
  Chirality :  0.057   0.192    543
  Planarity :  0.002   0.011    558
  Dihedral  :  6.452  19.138    447
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.79 %
    Favored  : 83.21 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 17.72 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.13 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.91 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 140 
 TYR   0.025   0.002   TYR A 143 
 PHE   0.014   0.002   PHE A 237 
 HIS   0.006   0.003   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 ( 3312)
  covalent geometry    : angle       0.67329 ( 4503)
  SS BOND              : bond        0.00595 (    3)
  SS BOND              : angle       0.75664 (    6)
  hydrogen bonds       : bond        0.01799 (   41)
  hydrogen bonds       : angle       4.24120 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 37
  time to evaluate  : 0.130 
Fit side-chains
REVERT: B  141 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8709 (t)
REVERT: B  145 ASN cc_start: 0.8281 (p0) cc_final: 0.8007 (p0)
REVERT: B  178 LYS cc_start: 0.8367 (mttt) cc_final: 0.7713 (tptt)
REVERT: B  235 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7821 (m)
REVERT: A  178 LYS cc_start: 0.8054 (mttt) cc_final: 0.7588 (tptt)
REVERT: C  145 ASN cc_start: 0.8276 (p0) cc_final: 0.7767 (p0)
REVERT: C  178 LYS cc_start: 0.8136 (mttt) cc_final: 0.7478 (tptt)
  outliers start: 20
  outliers final: 17
  residues processed: 55
  average time/residue: 0.0541
  time to fit residues: 3.8055
Evaluate side-chains
  54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 35
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  180 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0980
   chunk 12 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** 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 = 0.4648 r_free = 0.4648 target = 0.267003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 112)---------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.220504 restraints weight = 4123.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.4600 rms_B_bonded: 0.87
r_work: 0.4863 rms_B_bonded: 0.39 restraints_weight: 0.5000
r_work: 0.4843 rms_B_bonded: 0.65 restraints_weight: 0.2500
r_work: 0.4696 rms_B_bonded: 2.48 restraints_weight: 0.1250
r_work (final): 0.4696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3315  Z= 0.194
  Angle     :  0.628   7.538   4509  Z= 0.349
  Chirality :  0.055   0.175    543
  Planarity :  0.002   0.009    558
  Dihedral  :  6.242  17.936    447
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.53 %
    Favored  : 86.47 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 18.78 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.07 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.86 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 140 
 TYR   0.020   0.002   TYR A 143 
 PHE   0.013   0.002   PHE A 213 
 HIS   0.006   0.003   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 3312)
  covalent geometry    : angle       0.62772 ( 4503)
  SS BOND              : bond        0.00457 (    3)
  SS BOND              : angle       0.56626 (    6)
  hydrogen bonds       : bond        0.01625 (   41)
  hydrogen bonds       : angle       4.22621 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B  141 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8661 (t)
REVERT: B  145 ASN cc_start: 0.8322 (p0) cc_final: 0.7826 (p0)
REVERT: B  146 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8248 (pt)
REVERT: B  178 LYS cc_start: 0.8387 (mttt) cc_final: 0.7917 (tptt)
REVERT: B  235 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7678 (m)
REVERT: A  178 LYS cc_start: 0.8052 (mttt) cc_final: 0.7646 (tptt)
REVERT: C  145 ASN cc_start: 0.8172 (p0) cc_final: 0.7707 (p0)
REVERT: C  146 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7739 (pt)
REVERT: C  178 LYS cc_start: 0.8157 (mttt) cc_final: 0.7565 (tptt)
  outliers start: 18
  outliers final: 14
  residues processed: 53
  average time/residue: 0.0493
  time to fit residues: 3.3331
Evaluate side-chains
  54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  180 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0070
   chunk 13 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    2.0604

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** 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 = 0.4681 r_free = 0.4681 target = 0.271497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 113)---------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.226058 restraints weight = 4093.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.4637 rms_B_bonded: 0.88
r_work: 0.4905 rms_B_bonded: 0.39 restraints_weight: 0.5000
r_work: 0.4887 rms_B_bonded: 0.66 restraints_weight: 0.2500
r_work: 0.4735 rms_B_bonded: 2.58 restraints_weight: 0.1250
r_work (final): 0.4735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3315  Z= 0.140
  Angle     :  0.582   7.424   4509  Z= 0.322
  Chirality :  0.053   0.168    543
  Planarity :  0.002   0.008    558
  Dihedral  :  5.915  16.784    447
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 19.58 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.97 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 140 
 TYR   0.016   0.002   TYR B 143 
 PHE   0.013   0.002   PHE A 213 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3312)
  covalent geometry    : angle       0.58207 ( 4503)
  SS BOND              : bond        0.00383 (    3)
  SS BOND              : angle       0.41327 (    6)
  hydrogen bonds       : bond        0.01463 (   41)
  hydrogen bonds       : angle       4.16375 (  123)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.117 
Fit side-chains
REVERT: B  141 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8678 (t)
REVERT: B  145 ASN cc_start: 0.8302 (p0) cc_final: 0.7861 (p0)
REVERT: B  146 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8204 (pt)
REVERT: B  178 LYS cc_start: 0.8313 (mttt) cc_final: 0.7818 (tptt)
REVERT: A  178 LYS cc_start: 0.7991 (mttt) cc_final: 0.7579 (tptt)
REVERT: C  145 ASN cc_start: 0.8230 (p0) cc_final: 0.7711 (p0)
REVERT: C  146 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7685 (pt)
REVERT: C  178 LYS cc_start: 0.8072 (mttt) cc_final: 0.7532 (tptt)
  outliers start: 17
  outliers final: 13
  residues processed: 62
  average time/residue: 0.0517
  time to fit residues: 4.1035
Evaluate side-chains
  55 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  160 VAL
Chi-restraints excluded: chain C residue  175 VAL
Chi-restraints excluded: chain C residue  180 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** 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 = 0.4665 r_free = 0.4665 target = 0.268766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.4883 r_free = 0.4883 target = 0.222636 restraints weight = 4124.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.4617 rms_B_bonded: 0.86
r_work: 0.4895 rms_B_bonded: 0.46 restraints_weight: 0.5000
r_work: 0.4869 rms_B_bonded: 0.78 restraints_weight: 0.2500
r_work: 0.4724 rms_B_bonded: 2.74 restraints_weight: 0.1250
r_work (final): 0.4724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3315  Z= 0.178
  Angle     :  0.612   7.561   4509  Z= 0.340
  Chirality :  0.055   0.176    543
  Planarity :  0.002   0.008    558
  Dihedral  :  6.028  17.651    447
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.04 %
    Favored  : 85.96 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 19.31 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.96 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 140 
 TYR   0.018   0.002   TYR A 143 
 PHE   0.009   0.002   PHE A 237 
 HIS   0.005   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 3312)
  covalent geometry    : angle       0.61249 ( 4503)
  SS BOND              : bond        0.00435 (    3)
  SS BOND              : angle       0.47497 (    6)
  hydrogen bonds       : bond        0.01539 (   41)
  hydrogen bonds       : angle       4.14746 (  123)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1065.05 seconds
wall clock time: 18 minutes 50.96 seconds (1130.96 seconds total)