Starting phenix.real_space_refine
on Tue Mar  3 11:29:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x84_33055/03_2026/7x84_33055.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x84_33055/03_2026/7x84_33055.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x84_33055/03_2026/7x84_33055.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x84_33055/03_2026/7x84_33055.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x84_33055/03_2026/7x84_33055.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x84_33055/03_2026/7x84_33055.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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 3 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: 0.45, per 1000 atoms: 0.14
  Number of scatterers: 3258
  At special positions: 0
  Unit cell: (99.6, 107.07, 33.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      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=2.02
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 121.7 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 15 sheets defined
      0.0% alpha, 28.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 125 through 126
    Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130
    Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134
      removed outlier: 6.992A  pdb=" N   VAL B 133 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   VAL A 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 139
      removed outlier: 6.438A  pdb=" N   GLN B 138 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   GLN A 138 " --> pdb=" O   LYS C 139 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 152
    Processing sheet with id=AA6, first strand: chain 'B' and resid 162 through 168
      removed outlier: 6.865A  pdb=" N   ALA B 167 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLN A 168 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ALA A 167 " --> pdb=" O   THR C 166 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   GLN C 168 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 177
      removed outlier: 6.377A  pdb=" N   ILE B 176 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE A 176 " --> pdb=" O   GLY C 177 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 180 through 186
      removed outlier: 6.429A  pdb=" N   LEU B 181 " --> pdb=" O   ASN A 182 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ILE A 184 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   ASN B 183 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 9.793A  pdb=" N   ILE A 186 " --> pdb=" O   ASN B 183 " (cutoff:3.500A)
      removed outlier: 9.027A  pdb=" N   THR B 185 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LEU A 181 " --> pdb=" O   ASN C 182 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE C 184 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   ASN A 183 " --> pdb=" O   ILE C 184 " (cutoff:3.500A)
      removed outlier: 9.807A  pdb=" N   ILE C 186 " --> pdb=" O   ASN A 183 " (cutoff:3.500A)
      removed outlier: 9.041A  pdb=" N   THR A 185 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 197 through 198
      removed outlier: 6.664A  pdb=" N   TYR B 197 " --> pdb=" O   THR A 198 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   TYR A 197 " --> pdb=" O   THR C 198 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203
    Processing sheet with id=AB2, first strand: chain 'B' and resid 215 through 221
      removed outlier: 6.645A  pdb=" N   THR B 215 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   SER A 218 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ILE B 217 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   LYS A 220 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   ILE B 219 " --> pdb=" O   LYS A 220 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   THR A 215 " --> pdb=" O   LEU C 216 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   SER C 218 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE A 217 " --> pdb=" O   SER C 218 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   LYS C 220 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 8.497A  pdb=" N   ILE A 219 " --> pdb=" O   LYS C 220 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 226 through 228
    Processing sheet with id=AB4, first strand: chain 'B' and resid 235 through 238
      removed outlier: 6.452A  pdb=" N   THR B 235 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   GLY A 238 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   PHE B 237 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   THR A 235 " --> pdb=" O   TYR C 236 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   GLY C 238 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   PHE A 237 " --> pdb=" O   GLY C 238 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 243 through 247
    Processing sheet with id=AB6, first strand: chain 'B' and resid 251 through 252

    32 hydrogen bonds defined for protein.
    96 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: 0.37

  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: 518
        1.45 -     1.57: 1732
        1.57 -     1.69: 0
        1.69 -     1.80: 36
  Bond restraints: 3312
  Sorted by residual:
  bond pdb=" CA  THR C 234 "
       pdb=" CB  THR C 234 "
    ideal  model  delta    sigma   weight residual
    1.523  1.549 -0.026 1.35e-02 5.49e+03 3.76e+00
  bond pdb=" CA  THR B 234 "
       pdb=" CB  THR B 234 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 1.35e-02 5.49e+03 3.40e+00
  bond pdb=" CA  THR A 234 "
       pdb=" CB  THR A 234 "
    ideal  model  delta    sigma   weight residual
    1.523  1.547 -0.024 1.35e-02 5.49e+03 3.21e+00
  bond pdb=" CG1 ILE B 146 "
       pdb=" CD1 ILE B 146 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.32e+00
  bond pdb=" CG1 ILE A 146 "
       pdb=" CD1 ILE A 146 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.30e+00
  ... (remaining 3307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 4370
        2.08 -     4.16: 121
        4.16 -     6.24: 9
        6.24 -     8.32: 0
        8.32 -    10.40: 3
  Bond angle restraints: 4503
  Sorted by residual:
  angle pdb=" N   THR C 234 "
        pdb=" CA  THR C 234 "
        pdb=" C   THR C 234 "
      ideal   model   delta    sigma   weight residual
     107.23  117.63  -10.40 1.67e+00 3.59e-01 3.87e+01
  angle pdb=" N   THR A 234 "
        pdb=" CA  THR A 234 "
        pdb=" C   THR A 234 "
      ideal   model   delta    sigma   weight residual
     107.23  117.58  -10.35 1.67e+00 3.59e-01 3.84e+01
  angle pdb=" N   THR B 234 "
        pdb=" CA  THR B 234 "
        pdb=" C   THR B 234 "
      ideal   model   delta    sigma   weight residual
     107.23  117.57  -10.34 1.67e+00 3.59e-01 3.83e+01
  angle pdb=" C   THR A 234 "
        pdb=" CA  THR A 234 "
        pdb=" CB  THR A 234 "
      ideal   model   delta    sigma   weight residual
     111.42  106.84    4.58 1.31e+00 5.83e-01 1.22e+01
  angle pdb=" C   THR C 234 "
        pdb=" CA  THR C 234 "
        pdb=" CB  THR C 234 "
      ideal   model   delta    sigma   weight residual
     111.42  106.84    4.58 1.31e+00 5.83e-01 1.22e+01
  ... (remaining 4498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.39: 1767
       15.39 -    30.77: 157
       30.77 -    46.16: 65
       46.16 -    61.54: 3
       61.54 -    76.93: 3
  Dihedral angle restraints: 1995
    sinusoidal: 777
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CA  TYR C 135 "
           pdb=" C   TYR C 135 "
           pdb=" N   ASP C 136 "
           pdb=" CA  ASP C 136 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.02  -17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  TYR B 135 "
           pdb=" C   TYR B 135 "
           pdb=" N   ASP B 136 "
           pdb=" CA  ASP B 136 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.03  -17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  TYR A 135 "
           pdb=" C   TYR A 135 "
           pdb=" N   ASP A 136 "
           pdb=" CA  ASP A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.05  -17.95     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 1992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 259
       0.031 -    0.063: 146
       0.063 -    0.094: 61
       0.094 -    0.125: 62
       0.125 -    0.156: 15
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CB  THR C 153 "
            pdb=" CA  THR C 153 "
            pdb=" OG1 THR C 153 "
            pdb=" CG2 THR C 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.16 2.00e-01 2.50e+01 6.08e-01
  chirality pdb=" CB  THR A 153 "
            pdb=" CA  THR A 153 "
            pdb=" OG1 THR A 153 "
            pdb=" CG2 THR A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.92e-01
  chirality pdb=" CB  THR B 153 "
            pdb=" CA  THR B 153 "
            pdb=" OG1 THR B 153 "
            pdb=" CG2 THR B 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.88e-01
  ... (remaining 540 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 143 "    0.022 2.00e-02 2.50e+03   1.93e-02 7.43e+00
        pdb=" CG  TYR C 143 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 143 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 143 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 143 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 143 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 143 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR C 143 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 143 "    0.022 2.00e-02 2.50e+03   1.92e-02 7.34e+00
        pdb=" CG  TYR A 143 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 143 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 143 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 143 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 143 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 143 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 143 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 143 "    0.021 2.00e-02 2.50e+03   1.91e-02 7.33e+00
        pdb=" CG  TYR B 143 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 143 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 143 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 143 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 143 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 143 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B 143 "    0.002 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 685
        2.79 -     3.32: 2939
        3.32 -     3.84: 5161
        3.84 -     4.37: 5887
        4.37 -     4.90: 11776
  Nonbonded interactions: 26448
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 148 "
            pdb=" OG1 THR A 149 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ASN C 148 "
            pdb=" OG1 THR C 149 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ASN B 148 "
            pdb=" OG1 THR B 149 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OH  TYR C 236 "
            pdb=" O   HIS C 239 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OH  TYR A 236 "
            pdb=" O   HIS A 239 "
     model   vdw
     2.263 3.040
  ... (remaining 26443 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:             6.100
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.860
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:9.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
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      :  0.008   0.045   3315  Z= 0.346
  Angle     :  0.832  10.395   4509  Z= 0.490
  Chirality :  0.056   0.156    543
  Planarity :  0.003   0.020    558
  Dihedral  : 13.867  76.927   1206
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -5.69 (0.26), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.33 (0.20), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.047   0.004   TYR C 143 
 PHE   0.005   0.002   PHE B 213 
 HIS   0.004   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00785 ( 3312)
  covalent geometry    : angle       0.83231 ( 4503)
  SS BOND              : bond        0.00745 (    3)
  SS BOND              : angle       0.46240 (    6)
  hydrogen bonds       : bond        0.19690 (   32)
  hydrogen bonds       : angle       8.94400 (   96)

*********************** 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
  95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B  124 LYS cc_start: 0.8599 (mtmt) cc_final: 0.7078 (mmpt)
REVERT: B  140 ARG cc_start: 0.5415 (mtt180) cc_final: 0.4596 (ppt170)
REVERT: B  178 LYS cc_start: 0.7132 (mttm) cc_final: 0.5841 (pptt)
REVERT: B  180 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6598 (pmt170)
REVERT: B  249 GLN cc_start: 0.7762 (tt0) cc_final: 0.7515 (tm-30)
REVERT: B  252 ASP cc_start: 0.7813 (t0) cc_final: 0.7387 (t0)
REVERT: A  178 LYS cc_start: 0.6966 (mttm) cc_final: 0.6549 (mtpt)
REVERT: A  180 ARG cc_start: 0.7487 (mtt180) cc_final: 0.6897 (ttt180)
REVERT: A  249 GLN cc_start: 0.7659 (tt0) cc_final: 0.7428 (tp40)
REVERT: C  165 ILE cc_start: 0.8882 (mt) cc_final: 0.8650 (mt)
REVERT: C  178 LYS cc_start: 0.7352 (mttm) cc_final: 0.6292 (mmpt)
REVERT: C  180 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6563 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.5897
  time to fit residues: 57.3419
Evaluate side-chains
  75 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
B 245 GLN
A 148 ASN
A 156 ASN
A 245 GLN
C 148 ASN
C 156 ASN
C 229 GLN
C 245 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.141995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.126777 restraints weight = 4925.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 2.04
r_work: 0.3982 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3888 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3315  Z= 0.122
  Angle     :  0.616   5.924   4509  Z= 0.348
  Chirality :  0.052   0.142    543
  Planarity :  0.002   0.020    558
  Dihedral  :  5.952  19.274    447
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.11 %
    Favored  : 77.51 %
  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: -4.72 (0.30), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.019   0.002   TYR A 143 
 PHE   0.005   0.001   PHE A 237 
 HIS   0.002   0.001   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3312)
  covalent geometry    : angle       0.61622 ( 4503)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.29292 (    6)
  hydrogen bonds       : bond        0.03460 (   32)
  hydrogen bonds       : angle       6.55117 (   96)

*********************** 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
  99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.124 
Fit side-chains
REVERT: B  124 LYS cc_start: 0.8719 (mtmt) cc_final: 0.7129 (mmpt)
REVERT: B  140 ARG cc_start: 0.5282 (mtt180) cc_final: 0.4374 (ptm-80)
REVERT: B  148 ASN cc_start: 0.7419 (m-40) cc_final: 0.7007 (t0)
REVERT: B  178 LYS cc_start: 0.7084 (mttm) cc_final: 0.5620 (pptt)
REVERT: B  180 ARG cc_start: 0.7823 (mtt180) cc_final: 0.6459 (pmt170)
REVERT: B  190 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7894 (tt)
REVERT: B  205 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7897 (tt0)
REVERT: B  249 GLN cc_start: 0.8282 (tt0) cc_final: 0.7956 (tm-30)
REVERT: B  252 ASP cc_start: 0.7964 (t0) cc_final: 0.7446 (t0)
REVERT: A  148 ASN cc_start: 0.7343 (m-40) cc_final: 0.7133 (t0)
REVERT: A  178 LYS cc_start: 0.6855 (mttm) cc_final: 0.6452 (mtpt)
REVERT: A  180 ARG cc_start: 0.7802 (mtt180) cc_final: 0.6858 (ttt90)
REVERT: A  205 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7620 (tt0)
REVERT: C  178 LYS cc_start: 0.7314 (mttm) cc_final: 0.6142 (mmpt)
REVERT: C  180 ARG cc_start: 0.7708 (mtt180) cc_final: 0.6684 (tpm170)
  outliers start: 9
  outliers final: 1
  residues processed: 92
  average time/residue: 0.6524
  time to fit residues: 61.2389
Evaluate side-chains
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  205 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 20 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 9 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 182 ASN
C 229 GLN
C 239 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.138882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.123763 restraints weight = 4965.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 2.05
r_work: 0.3948 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3851 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3315  Z= 0.211
  Angle     :  0.686   6.811   4509  Z= 0.382
  Chirality :  0.053   0.150    543
  Planarity :  0.003   0.022    558
  Dihedral  :  6.063  20.063    447
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.84 %
    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: -4.32 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.016   0.002   TYR A 132 
 PHE   0.006   0.001   PHE A 213 
 HIS   0.006   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 3312)
  covalent geometry    : angle       0.68628 ( 4503)
  SS BOND              : bond        0.00521 (    3)
  SS BOND              : angle       0.38369 (    6)
  hydrogen bonds       : bond        0.03638 (   32)
  hydrogen bonds       : angle       6.32258 (   96)

*********************** 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
  97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.078 
Fit side-chains
REVERT: B  124 LYS cc_start: 0.8676 (mtmt) cc_final: 0.7055 (mmpt)
REVERT: B  140 ARG cc_start: 0.5311 (mtt180) cc_final: 0.4394 (ptm-80)
REVERT: B  178 LYS cc_start: 0.7063 (mttm) cc_final: 0.5637 (pptt)
REVERT: B  180 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6444 (pmt170)
REVERT: B  206 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8330 (tm-30)
REVERT: B  249 GLN cc_start: 0.8193 (tt0) cc_final: 0.7901 (tm-30)
REVERT: B  252 ASP cc_start: 0.7968 (t0) cc_final: 0.7461 (t0)
REVERT: A  178 LYS cc_start: 0.6817 (mttm) cc_final: 0.6417 (mtpt)
REVERT: A  180 ARG cc_start: 0.7790 (mtt180) cc_final: 0.6865 (ttt180)
REVERT: A  205 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7590 (tt0)
REVERT: C  178 LYS cc_start: 0.7323 (mttm) cc_final: 0.6106 (mmpt)
REVERT: C  180 ARG cc_start: 0.7707 (mtt180) cc_final: 0.6604 (tpm170)
  outliers start: 15
  outliers final: 4
  residues processed: 88
  average time/residue: 0.6323
  time to fit residues: 56.7740
Evaluate side-chains
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain C residue  153 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
B 182 ASN
A 148 ASN
A 182 ASN
C 229 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.138742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.123581 restraints weight = 5010.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.4042 rms_B_bonded: 2.03
r_work: 0.3960 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3863 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3315  Z= 0.199
  Angle     :  0.678  10.251   4509  Z= 0.377
  Chirality :  0.052   0.149    543
  Planarity :  0.003   0.023    558
  Dihedral  :  6.038  21.410    447
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 21.96 %
    Favored  : 73.54 %
  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: -4.10 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.015   0.002   TYR C 211 
 PHE   0.005   0.001   PHE B 171 
 HIS   0.005   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 3312)
  covalent geometry    : angle       0.67836 ( 4503)
  SS BOND              : bond        0.00475 (    3)
  SS BOND              : angle       0.39157 (    6)
  hydrogen bonds       : bond        0.03399 (   32)
  hydrogen bonds       : angle       6.31708 (   96)

*********************** 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
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.108 
Fit side-chains
REVERT: B  124 LYS cc_start: 0.8631 (mtmt) cc_final: 0.6998 (mmpt)
REVERT: B  140 ARG cc_start: 0.5268 (mtt180) cc_final: 0.4387 (ptm-80)
REVERT: B  178 LYS cc_start: 0.7036 (mttm) cc_final: 0.5593 (pptt)
REVERT: B  180 ARG cc_start: 0.7883 (mtt180) cc_final: 0.6437 (pmt170)
REVERT: B  249 GLN cc_start: 0.8160 (tt0) cc_final: 0.7901 (tm-30)
REVERT: B  252 ASP cc_start: 0.8011 (t0) cc_final: 0.7486 (t0)
REVERT: A  178 LYS cc_start: 0.6812 (mttm) cc_final: 0.6413 (mtpt)
REVERT: A  180 ARG cc_start: 0.7807 (mtt180) cc_final: 0.6842 (ttt180)
REVERT: A  205 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7522 (tt0)
REVERT: C  148 ASN cc_start: 0.7582 (m-40) cc_final: 0.7307 (t0)
REVERT: C  163 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7340 (mt-10)
REVERT: C  178 LYS cc_start: 0.7302 (mttm) cc_final: 0.6120 (mmpt)
REVERT: C  180 ARG cc_start: 0.7651 (mtt180) cc_final: 0.6524 (tpm170)
  outliers start: 17
  outliers final: 7
  residues processed: 87
  average time/residue: 0.6669
  time to fit residues: 59.2054
Evaluate side-chains
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  153 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 182 ASN
A 182 ASN
C 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.140627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.125504 restraints weight = 4899.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 2.03
r_work: 0.3987 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3892 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3315  Z= 0.164
  Angle     :  0.642   9.290   4509  Z= 0.358
  Chirality :  0.052   0.147    543
  Planarity :  0.002   0.022    558
  Dihedral  :  5.902  21.570    447
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.81 %
    Favored  : 71.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.97 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.014   0.002   TYR C 211 
 PHE   0.005   0.001   PHE A 213 
 HIS   0.004   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3312)
  covalent geometry    : angle       0.64258 ( 4503)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       0.34465 (    6)
  hydrogen bonds       : bond        0.03078 (   32)
  hydrogen bonds       : angle       6.22271 (   96)

*********************** 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
  96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: B  124 LYS cc_start: 0.8653 (mtmt) cc_final: 0.7066 (mmpt)
REVERT: B  140 ARG cc_start: 0.5274 (mtt180) cc_final: 0.4362 (ptm-80)
REVERT: B  180 ARG cc_start: 0.7861 (mtt180) cc_final: 0.6422 (pmt170)
REVERT: B  249 GLN cc_start: 0.8157 (tt0) cc_final: 0.7909 (tm-30)
REVERT: B  251 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.8706 (t)
REVERT: B  252 ASP cc_start: 0.8017 (t0) cc_final: 0.7484 (t0)
REVERT: A  180 ARG cc_start: 0.7799 (mtt180) cc_final: 0.6872 (ttt180)
REVERT: A  205 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7461 (tt0)
REVERT: C  163 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7284 (mt-10)
REVERT: C  178 LYS cc_start: 0.7280 (mttm) cc_final: 0.6175 (mmpt)
REVERT: C  180 ARG cc_start: 0.7662 (mtt180) cc_final: 0.6542 (tpm170)
REVERT: C  249 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8288 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 89
  average time/residue: 0.6092
  time to fit residues: 55.4127
Evaluate side-chains
  84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  143 TYR
Chi-restraints excluded: chain C residue  153 THR
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:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
B 182 ASN
A 148 ASN
A 156 ASN
A 182 ASN
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 229 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.137512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.122366 restraints weight = 5002.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 2.06
r_work: 0.3941 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3845 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3315  Z= 0.257
  Angle     :  0.719   8.835   4509  Z= 0.403
  Chirality :  0.053   0.152    543
  Planarity :  0.003   0.024    558
  Dihedral  :  6.172  22.298    447
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 24.34 %
    Favored  : 71.16 %
  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: -3.94 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.019   0.003   TYR B 143 
 PHE   0.006   0.001   PHE B 171 
 HIS   0.006   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 3312)
  covalent geometry    : angle       0.71914 ( 4503)
  SS BOND              : bond        0.00678 (    3)
  SS BOND              : angle       0.43626 (    6)
  hydrogen bonds       : bond        0.03607 (   32)
  hydrogen bonds       : angle       6.25873 (   96)

*********************** 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
  91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.137 
Fit side-chains
REVERT: B  124 LYS cc_start: 0.8630 (mtmt) cc_final: 0.7014 (mmpt)
REVERT: B  140 ARG cc_start: 0.5371 (mtt180) cc_final: 0.4530 (ptm-80)
REVERT: B  178 LYS cc_start: 0.7067 (mttm) cc_final: 0.5619 (pptt)
REVERT: B  180 ARG cc_start: 0.7905 (mtt180) cc_final: 0.6460 (pmt170)
REVERT: B  249 GLN cc_start: 0.8235 (tt0) cc_final: 0.7901 (tm-30)
REVERT: B  251 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.8726 (t)
REVERT: B  252 ASP cc_start: 0.8029 (t0) cc_final: 0.7523 (t0)
REVERT: A  178 LYS cc_start: 0.6817 (mttm) cc_final: 0.6417 (mtpt)
REVERT: A  180 ARG cc_start: 0.7806 (mtt180) cc_final: 0.6873 (ttt180)
REVERT: A  205 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7555 (tt0)
REVERT: C  163 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7289 (mt-10)
REVERT: C  178 LYS cc_start: 0.7298 (mttm) cc_final: 0.6103 (mmpt)
REVERT: C  180 ARG cc_start: 0.7679 (mtt180) cc_final: 0.6492 (tpm170)
REVERT: C  249 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8365 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 84
  average time/residue: 0.6747
  time to fit residues: 57.8729
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  143 TYR
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  143 TYR
Chi-restraints excluded: chain C residue  153 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 182 ASN
A 182 ASN
C 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.140300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.125037 restraints weight = 5030.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 2.08
r_work: 0.3972 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3874 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3315  Z= 0.177
  Angle     :  0.662   8.381   4509  Z= 0.371
  Chirality :  0.052   0.146    543
  Planarity :  0.002   0.024    558
  Dihedral  :  5.996  22.344    447
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 24.60 %
    Favored  : 70.90 %
  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: -3.82 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.013   0.002   TYR B 143 
 PHE   0.005   0.001   PHE A 213 
 HIS   0.005   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 3312)
  covalent geometry    : angle       0.66195 ( 4503)
  SS BOND              : bond        0.00392 (    3)
  SS BOND              : angle       0.34798 (    6)
  hydrogen bonds       : bond        0.03121 (   32)
  hydrogen bonds       : angle       6.24745 (   96)

*********************** 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
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: B  124 LYS cc_start: 0.8612 (mtmt) cc_final: 0.7000 (mmpt)
REVERT: B  140 ARG cc_start: 0.5269 (mtt180) cc_final: 0.4390 (ptm-80)
REVERT: B  180 ARG cc_start: 0.7845 (mtt180) cc_final: 0.6400 (pmt170)
REVERT: B  249 GLN cc_start: 0.8167 (tt0) cc_final: 0.7756 (tm-30)
REVERT: B  251 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.8693 (t)
REVERT: B  252 ASP cc_start: 0.8047 (t0) cc_final: 0.7534 (t0)
REVERT: A  180 ARG cc_start: 0.7770 (mtt180) cc_final: 0.6828 (ttt180)
REVERT: A  205 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7548 (tt0)
REVERT: C  163 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7281 (mt-10)
REVERT: C  178 LYS cc_start: 0.7249 (mttm) cc_final: 0.6132 (mmpt)
REVERT: C  180 ARG cc_start: 0.7653 (mtt180) cc_final: 0.6497 (tpm170)
REVERT: C  247 ARG cc_start: 0.8946 (ttt-90) cc_final: 0.8706 (ttt90)
REVERT: C  249 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8250 (tm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 87
  average time/residue: 0.6088
  time to fit residues: 54.1242
Evaluate side-chains
  87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  143 TYR
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  143 TYR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  163 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    0.1980
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0870
   overall best weight:    1.8564

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
B 182 ASN
A 148 ASN
A 182 ASN
C 229 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.140786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.125292 restraints weight = 5054.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 2.10
r_work: 0.3996 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3896 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3315  Z= 0.157
  Angle     :  0.648   8.478   4509  Z= 0.360
  Chirality :  0.051   0.144    543
  Planarity :  0.002   0.026    558
  Dihedral  :  5.898  21.921    447
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 25.40 %
    Favored  : 70.63 %
  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: -3.70 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.013   0.002   TYR C 211 
 PHE   0.005   0.001   PHE A 237 
 HIS   0.004   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3312)
  covalent geometry    : angle       0.64874 ( 4503)
  SS BOND              : bond        0.00306 (    3)
  SS BOND              : angle       0.33385 (    6)
  hydrogen bonds       : bond        0.02973 (   32)
  hydrogen bonds       : angle       6.23994 (   96)

*********************** 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
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: B  124 LYS cc_start: 0.8628 (mtmt) cc_final: 0.6990 (mmpt)
REVERT: B  140 ARG cc_start: 0.5254 (mtt180) cc_final: 0.4342 (ptm-80)
REVERT: B  180 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6429 (pmt170)
REVERT: B  249 GLN cc_start: 0.8129 (tt0) cc_final: 0.7794 (tm-30)
REVERT: B  251 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8712 (t)
REVERT: B  252 ASP cc_start: 0.8056 (t0) cc_final: 0.7532 (t0)
REVERT: A  180 ARG cc_start: 0.7779 (mtt180) cc_final: 0.6838 (ttt180)
REVERT: A  205 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7498 (tt0)
REVERT: C  163 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7198 (mt-10)
REVERT: C  178 LYS cc_start: 0.7236 (mttm) cc_final: 0.6127 (mmpt)
REVERT: C  180 ARG cc_start: 0.7643 (mtt180) cc_final: 0.6488 (tpm170)
REVERT: C  247 ARG cc_start: 0.8955 (ttt-90) cc_final: 0.8708 (ttt90)
REVERT: C  249 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8236 (tm-30)
  outliers start: 15
  outliers final: 10
  residues processed: 87
  average time/residue: 0.6387
  time to fit residues: 56.7977
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  143 TYR
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  143 TYR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  163 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 182 ASN
A 182 ASN
C 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.139853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.124608 restraints weight = 5048.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.4056 rms_B_bonded: 2.07
r_work: 0.3973 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3873 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3315  Z= 0.194
  Angle     :  0.696   8.931   4509  Z= 0.385
  Chirality :  0.052   0.147    543
  Planarity :  0.003   0.026    558
  Dihedral  :  5.977  21.976    447
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 26.19 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.68 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.27), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.017   0.002   TYR B 143 
 PHE   0.005   0.001   PHE B 171 
 HIS   0.004   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 3312)
  covalent geometry    : angle       0.69655 ( 4503)
  SS BOND              : bond        0.00436 (    3)
  SS BOND              : angle       0.37560 (    6)
  hydrogen bonds       : bond        0.03197 (   32)
  hydrogen bonds       : angle       6.21826 (   96)

*********************** 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
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: B  124 LYS cc_start: 0.8628 (mtmt) cc_final: 0.7019 (mmpt)
REVERT: B  140 ARG cc_start: 0.5306 (mtt180) cc_final: 0.4420 (ptm-80)
REVERT: B  180 ARG cc_start: 0.7890 (mtt180) cc_final: 0.6444 (pmt170)
REVERT: B  249 GLN cc_start: 0.8149 (tt0) cc_final: 0.7898 (tm-30)
REVERT: B  251 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.8722 (t)
REVERT: B  252 ASP cc_start: 0.8076 (t0) cc_final: 0.7527 (t0)
REVERT: A  180 ARG cc_start: 0.7783 (mtt180) cc_final: 0.6847 (ttt180)
REVERT: C  163 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7227 (mt-10)
REVERT: C  178 LYS cc_start: 0.7229 (mttm) cc_final: 0.6116 (mmpt)
REVERT: C  180 ARG cc_start: 0.7682 (mtt180) cc_final: 0.6516 (tpm170)
REVERT: C  247 ARG cc_start: 0.8942 (ttt-90) cc_final: 0.8701 (ttt90)
REVERT: C  249 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8281 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 80
  average time/residue: 0.6668
  time to fit residues: 54.4543
Evaluate side-chains
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  143 TYR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  163 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:    0.6980
   chunk 18 optimal weight:    8.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
B 182 ASN
A 148 ASN
A 182 ASN
C 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.140269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.125007 restraints weight = 5037.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 2.09
r_work: 0.3977 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3878 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3315  Z= 0.188
  Angle     :  0.693   9.165   4509  Z= 0.384
  Chirality :  0.052   0.147    543
  Planarity :  0.003   0.026    558
  Dihedral  :  5.985  21.641    447
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 26.72 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.66 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.27), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.026   0.002   TYR B 143 
 PHE   0.005   0.001   PHE B 171 
 HIS   0.004   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 3312)
  covalent geometry    : angle       0.69373 ( 4503)
  SS BOND              : bond        0.00407 (    3)
  SS BOND              : angle       0.35219 (    6)
  hydrogen bonds       : bond        0.03145 (   32)
  hydrogen bonds       : angle       6.23285 (   96)

********************** 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
  84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: B  124 LYS cc_start: 0.8636 (mtmt) cc_final: 0.7033 (mmpt)
REVERT: B  140 ARG cc_start: 0.5278 (mtt180) cc_final: 0.4398 (ptm-80)
REVERT: B  180 ARG cc_start: 0.7888 (mtt180) cc_final: 0.6445 (pmt170)
REVERT: B  249 GLN cc_start: 0.8207 (tt0) cc_final: 0.7828 (tm-30)
REVERT: B  251 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8681 (t)
REVERT: B  252 ASP cc_start: 0.8064 (t0) cc_final: 0.7562 (t0)
REVERT: A  180 ARG cc_start: 0.7787 (mtt180) cc_final: 0.6855 (ttt180)
REVERT: C  163 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7202 (mt-10)
REVERT: C  178 LYS cc_start: 0.7210 (mttm) cc_final: 0.6117 (mmpt)
REVERT: C  180 ARG cc_start: 0.7688 (mtt180) cc_final: 0.6523 (tpm170)
REVERT: C  247 ARG cc_start: 0.8949 (ttt-90) cc_final: 0.8707 (ttt90)
REVERT: C  249 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8211 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 79
  average time/residue: 0.6952
  time to fit residues: 56.0959
Evaluate side-chains
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  172 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  143 TYR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  163 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0470
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0670
   chunk 34 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    0.2980
   overall best weight:    1.2820

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
B 182 ASN
A 182 ASN
C 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.143585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.127790 restraints weight = 4883.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 2.09
r_work: 0.4014 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3919 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3315  Z= 0.130
  Angle     :  0.639   9.188   4509  Z= 0.353
  Chirality :  0.051   0.140    543
  Planarity :  0.002   0.025    558
  Dihedral  :  5.739  20.876    447
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 26.46 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.55 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.27), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 247 
 TYR   0.024   0.002   TYR B 143 
 PHE   0.005   0.001   PHE C 237 
 HIS   0.003   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3312)
  covalent geometry    : angle       0.63968 ( 4503)
  SS BOND              : bond        0.00135 (    3)
  SS BOND              : angle       0.30679 (    6)
  hydrogen bonds       : bond        0.02681 (   32)
  hydrogen bonds       : angle       6.17069 (   96)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1656.20 seconds
wall clock time: 28 minutes 57.36 seconds (1737.36 seconds total)