Starting phenix.real_space_refine
on Tue Feb  3 12:38:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v45_64767/02_2026/9v45_64767_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v45_64767/02_2026/9v45_64767.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v45_64767/02_2026/9v45_64767_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v45_64767/02_2026/9v45_64767_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v45_64767/02_2026/9v45_64767.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v45_64767/02_2026/9v45_64767.map"
  }
  resolution = 3.41
  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=   1.000
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: 3
    Type Number    sf(0)   Gaussians
     C    1380      2.51       5
     N     350      2.21       5
     O     410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2140
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "B"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "C"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "D"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "E"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "F"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "G"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "H"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "I"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "J"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 214
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
  Time building chain proxies: 0.62, per 1000 atoms: 0.29
  Number of scatterers: 2140
  At special positions: 0
  Unit cell: (57.784, 94.132, 39.144, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     410      8.00
     N     350      7.00
     C    1380      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.16
  Conformation dependent library (CDL) restraints added in 78.7 milliseconds
  

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  540

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 46.3% 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 'A' and resid 166 through 171
    Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 176
      removed outlier: 6.745A  pdb=" N   PHE C 176 " --> pdb=" O   ASN A 175 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   PHE E 176 " --> pdb=" O   ASN C 175 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   PHE G 176 " --> pdb=" O   ASN E 175 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   PHE I 176 " --> pdb=" O   ASN G 175 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 182
      removed outlier: 6.626A  pdb=" N   ASP A 181 " --> pdb=" O   GLN C 182 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ASP C 181 " --> pdb=" O   GLN E 182 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ASP E 181 " --> pdb=" O   GLN G 182 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ASP G 181 " --> pdb=" O   GLN I 182 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 189
    Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 171
    Processing sheet with id=AA6, first strand: chain 'B' and resid 174 through 176
      removed outlier: 6.753A  pdb=" N   PHE D 176 " --> pdb=" O   ASN B 175 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   PHE F 176 " --> pdb=" O   ASN D 175 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   PHE H 176 " --> pdb=" O   ASN F 175 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   PHE J 176 " --> pdb=" O   ASN H 175 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 180 through 182
      removed outlier: 6.546A  pdb=" N   ASP B 181 " --> pdb=" O   GLN D 182 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ASP D 181 " --> pdb=" O   GLN F 182 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ASP F 181 " --> pdb=" O   GLN H 182 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ASP H 181 " --> pdb=" O   GLN J 182 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 188
      removed outlier: 6.330A  pdb=" N   ARG B 185 " --> pdb=" O   VAL D 186 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   TYR D 188 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   PHE B 187 " --> pdb=" O   TYR D 188 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ARG D 185 " --> pdb=" O   VAL F 186 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   TYR F 188 " --> pdb=" O   ARG D 185 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   PHE D 187 " --> pdb=" O   TYR F 188 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ARG F 185 " --> pdb=" O   VAL H 186 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   TYR H 188 " --> pdb=" O   ARG F 185 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   PHE F 187 " --> pdb=" O   TYR H 188 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ARG H 185 " --> pdb=" O   VAL J 186 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   TYR J 188 " --> pdb=" O   ARG H 185 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   PHE H 187 " --> pdb=" O   TYR J 188 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    64 hydrogen bonds defined for protein.
    192 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: 0.22

  Time building geometry restraints manager: 0.23 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 360
        1.29 -     1.35: 340
        1.35 -     1.41: 190
        1.41 -     1.48: 340
        1.48 -     1.54: 950
  Bond restraints: 2180
  Sorted by residual:
  bond pdb=" CA  VAL E 165 "
       pdb=" CB  VAL E 165 "
    ideal  model  delta    sigma   weight residual
    1.532  1.539 -0.007 1.47e-02 4.63e+03 2.23e-01
  bond pdb=" CA  VAL A 165 "
       pdb=" CB  VAL A 165 "
    ideal  model  delta    sigma   weight residual
    1.532  1.539 -0.007 1.47e-02 4.63e+03 2.22e-01
  bond pdb=" CG  PRO F 184 "
       pdb=" CD  PRO F 184 "
    ideal  model  delta    sigma   weight residual
    1.503  1.487  0.016 3.40e-02 8.65e+02 2.19e-01
  bond pdb=" CG  PRO D 184 "
       pdb=" CD  PRO D 184 "
    ideal  model  delta    sigma   weight residual
    1.503  1.487  0.016 3.40e-02 8.65e+02 2.13e-01
  bond pdb=" CG  PRO H 184 "
       pdb=" CD  PRO H 184 "
    ideal  model  delta    sigma   weight residual
    1.503  1.487  0.016 3.40e-02 8.65e+02 2.11e-01
  ... (remaining 2175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.78: 2613
        0.78 -     1.56: 277
        1.56 -     2.33: 54
        2.33 -     3.11: 21
        3.11 -     3.89: 15
  Bond angle restraints: 2980
  Sorted by residual:
  angle pdb=" N   VAL A 165 "
        pdb=" CA  VAL A 165 "
        pdb=" C   VAL A 165 "
      ideal   model   delta    sigma   weight residual
     108.93  111.42   -2.49 1.35e+00 5.49e-01 3.40e+00
  angle pdb=" N   VAL E 165 "
        pdb=" CA  VAL E 165 "
        pdb=" C   VAL E 165 "
      ideal   model   delta    sigma   weight residual
     108.93  111.40   -2.47 1.35e+00 5.49e-01 3.34e+00
  angle pdb=" N   VAL C 165 "
        pdb=" CA  VAL C 165 "
        pdb=" C   VAL C 165 "
      ideal   model   delta    sigma   weight residual
     108.93  111.36   -2.43 1.35e+00 5.49e-01 3.24e+00
  angle pdb=" N   VAL I 165 "
        pdb=" CA  VAL I 165 "
        pdb=" C   VAL I 165 "
      ideal   model   delta    sigma   weight residual
     108.93  111.35   -2.42 1.35e+00 5.49e-01 3.22e+00
  angle pdb=" N   VAL G 165 "
        pdb=" CA  VAL G 165 "
        pdb=" C   VAL G 165 "
      ideal   model   delta    sigma   weight residual
     108.93  111.35   -2.42 1.35e+00 5.49e-01 3.20e+00
  ... (remaining 2975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.76: 1040
        8.76 -    17.51: 155
       17.51 -    26.27: 85
       26.27 -    35.02: 15
       35.02 -    43.78: 15
  Dihedral angle restraints: 1310
    sinusoidal: 500
      harmonic: 810
  Sorted by residual:
  dihedral pdb=" CG  ARG C 185 "
           pdb=" CD  ARG C 185 "
           pdb=" NE  ARG C 185 "
           pdb=" CZ  ARG C 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.78  -43.78     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG I 185 "
           pdb=" CD  ARG I 185 "
           pdb=" NE  ARG I 185 "
           pdb=" CZ  ARG I 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.77  -43.77     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG A 185 "
           pdb=" CD  ARG A 185 "
           pdb=" NE  ARG A 185 "
           pdb=" CZ  ARG A 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.76  -43.76     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 1307 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 157
       0.025 -    0.050: 141
       0.050 -    0.075: 31
       0.075 -    0.100: 17
       0.100 -    0.125: 24
  Chirality restraints: 370
  Sorted by residual:
  chirality pdb=" CA  ILE E 168 "
            pdb=" N   ILE E 168 "
            pdb=" C   ILE E 168 "
            pdb=" CB  ILE E 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  ILE A 168 "
            pdb=" N   ILE A 168 "
            pdb=" C   ILE A 168 "
            pdb=" CB  ILE A 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  chirality pdb=" CA  ILE D 168 "
            pdb=" N   ILE D 168 "
            pdb=" C   ILE D 168 "
            pdb=" CB  ILE D 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 367 not shown)

  Planarity restraints: 380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 176 "   -0.005 2.00e-02 2.50e+03   5.25e-03 4.82e-01
        pdb=" CG  PHE C 176 "    0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 176 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 176 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 176 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 176 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 176 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 176 "   -0.005 2.00e-02 2.50e+03   5.20e-03 4.73e-01
        pdb=" CG  PHE A 176 "    0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 176 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 176 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 176 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 176 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 176 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G 176 "   -0.006 2.00e-02 2.50e+03   5.15e-03 4.64e-01
        pdb=" CG  PHE G 176 "    0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHE G 176 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE G 176 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE G 176 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE G 176 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE G 176 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 377 not shown)

  Histogram of nonbonded interaction distances:
        2.63 -     3.08: 1481
        3.08 -     3.54: 1960
        3.54 -     3.99: 3358
        3.99 -     4.45: 4021
        4.45 -     4.90: 7252
  Nonbonded interactions: 18072
  Sorted by model distance:
  nonbonded pdb=" O   THR C 183 "
            pdb=" OG1 THR C 183 "
     model   vdw
     2.626 3.040
  nonbonded pdb=" O   THR I 183 "
            pdb=" OG1 THR I 183 "
     model   vdw
     2.627 3.040
  nonbonded pdb=" O   THR A 183 "
            pdb=" OG1 THR A 183 "
     model   vdw
     2.627 3.040
  nonbonded pdb=" O   THR E 183 "
            pdb=" OG1 THR E 183 "
     model   vdw
     2.627 3.040
  nonbonded pdb=" O   THR G 183 "
            pdb=" OG1 THR G 183 "
     model   vdw
     2.627 3.040
  ... (remaining 18067 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             3.280
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     3.840
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
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      :  0.003   0.016   2180  Z= 0.142
  Angle     :  0.609   3.889   2980  Z= 0.321
  Chirality :  0.047   0.125    370
  Planarity :  0.003   0.018    380
  Dihedral  : 12.200  43.776    770
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  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: -3.03 (0.56), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.43), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 185 
 TYR   0.002   0.001   TYR G 188 
 PHE   0.012   0.002   PHE C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 2180)
  covalent geometry    : angle       0.60908 ( 2980)
  hydrogen bonds       : bond        0.10535 (   64)
  hydrogen bonds       : angle       6.49846 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.081 
Fit side-chains
REVERT: B  178 ASN cc_start: 0.8453 (p0) cc_final: 0.8159 (p0)
REVERT: F  178 ASN cc_start: 0.8637 (p0) cc_final: 0.8176 (p0)
REVERT: H  172 ASP cc_start: 0.8239 (t70) cc_final: 0.7868 (t70)
REVERT: H  178 ASN cc_start: 0.8711 (p0) cc_final: 0.8433 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0328
  time to fit residues: 1.6523
Evaluate side-chains
  33 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.147609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.135398 restraints weight = 2630.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4378 rms_B_bonded: 2.53
r_work: 0.4234 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.4110 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   2180  Z= 0.147
  Angle     :  0.593   3.994   2980  Z= 0.319
  Chirality :  0.048   0.155    370
  Planarity :  0.002   0.009    380
  Dihedral  :  5.123  15.558    280
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  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: -3.21 (0.53), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 185 
 TYR   0.007   0.001   TYR I 188 
 PHE   0.009   0.002   PHE G 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 2180)
  covalent geometry    : angle       0.59347 ( 2980)
  hydrogen bonds       : bond        0.02582 (   64)
  hydrogen bonds       : angle       4.75266 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.051 
Fit side-chains
REVERT: A  177 ASN cc_start: 0.8013 (m110) cc_final: 0.7450 (m-40)
REVERT: A  179 GLN cc_start: 0.7842 (pt0) cc_final: 0.7467 (pt0)
REVERT: B  177 ASN cc_start: 0.7967 (m110) cc_final: 0.7623 (m110)
REVERT: C  179 GLN cc_start: 0.7776 (pt0) cc_final: 0.7350 (pt0)
REVERT: D  181 ASP cc_start: 0.7645 (m-30) cc_final: 0.6688 (t0)
REVERT: G  187 PHE cc_start: 0.8018 (m-80) cc_final: 0.7753 (m-80)
REVERT: H  185 ARG cc_start: 0.7311 (mtt90) cc_final: 0.6856 (ttm-80)
REVERT: I  185 ARG cc_start: 0.7491 (mtt180) cc_final: 0.6439 (mtm-85)
REVERT: J  175 ASN cc_start: 0.8400 (t0) cc_final: 0.8147 (t0)
REVERT: J  185 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7418 (mtt90)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0617
  time to fit residues: 3.3618
Evaluate side-chains
  35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
G 175 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.142410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.130994 restraints weight = 2777.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.4294 rms_B_bonded: 2.42
r_work: 0.4156 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.4029 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2180  Z= 0.147
  Angle     :  0.583   4.601   2980  Z= 0.311
  Chirality :  0.047   0.138    370
  Planarity :  0.002   0.011    380
  Dihedral  :  4.853  14.055    280
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 11.60 %
    Favored  : 87.20 %
  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: -3.09 (0.53), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 185 
 TYR   0.004   0.001   TYR B 188 
 PHE   0.010   0.002   PHE B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 2180)
  covalent geometry    : angle       0.58295 ( 2980)
  hydrogen bonds       : bond        0.02157 (   64)
  hydrogen bonds       : angle       4.34872 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  179 GLN cc_start: 0.8142 (pt0) cc_final: 0.7746 (pt0)
REVERT: B  177 ASN cc_start: 0.8330 (m110) cc_final: 0.7940 (m-40)
REVERT: C  179 GLN cc_start: 0.8060 (pt0) cc_final: 0.7548 (pt0)
REVERT: D  181 ASP cc_start: 0.7964 (m-30) cc_final: 0.6985 (t0)
REVERT: H  185 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7272 (ttm-80)
  outliers start: 3
  outliers final: 2
  residues processed: 29
  average time/residue: 0.0398
  time to fit residues: 1.5363
Evaluate side-chains
  27 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  174 SER
Chi-restraints excluded: chain H residue  174 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.156830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.145482 restraints weight = 2573.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.4341 rms_B_bonded: 2.34
r_work: 0.4208 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.4082 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.4082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2180  Z= 0.142
  Angle     :  0.562   4.028   2980  Z= 0.299
  Chirality :  0.046   0.140    370
  Planarity :  0.002   0.009    380
  Dihedral  :  4.851  14.433    280
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 13.60 %
    Favored  : 86.00 %
  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: -2.98 (0.54), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 185 
 TYR   0.003   0.001   TYR E 188 
 PHE   0.008   0.002   PHE C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 2180)
  covalent geometry    : angle       0.56206 ( 2980)
  hydrogen bonds       : bond        0.01863 (   64)
  hydrogen bonds       : angle       4.20568 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.050 
Fit side-chains
REVERT: A  179 GLN cc_start: 0.8007 (pt0) cc_final: 0.7636 (pt0)
REVERT: B  177 ASN cc_start: 0.8250 (m110) cc_final: 0.7912 (m110)
REVERT: C  179 GLN cc_start: 0.8081 (pt0) cc_final: 0.7537 (pt0)
REVERT: D  181 ASP cc_start: 0.7796 (m-30) cc_final: 0.6865 (t0)
REVERT: H  185 ARG cc_start: 0.7577 (mtt90) cc_final: 0.7132 (mtt90)
REVERT: I  180 LEU cc_start: 0.8006 (mt) cc_final: 0.7796 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0387
  time to fit residues: 1.3097
Evaluate side-chains
  21 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    1.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.149665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.138068 restraints weight = 2650.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.4373 rms_B_bonded: 2.47
r_work: 0.4232 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.4105 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.5030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2180  Z= 0.121
  Angle     :  0.540   3.944   2980  Z= 0.287
  Chirality :  0.046   0.131    370
  Planarity :  0.002   0.010    380
  Dihedral  :  4.590  13.667    280
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 15.60 %
    Favored  : 83.60 %
  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: -2.90 (0.54), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 185 
 TYR   0.003   0.001   TYR E 188 
 PHE   0.008   0.002   PHE F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 2180)
  covalent geometry    : angle       0.53972 ( 2980)
  hydrogen bonds       : bond        0.01834 (   64)
  hydrogen bonds       : angle       4.15065 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  177 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7797 (m-40)
REVERT: A  179 GLN cc_start: 0.8043 (pt0) cc_final: 0.7704 (pt0)
REVERT: B  177 ASN cc_start: 0.8275 (m110) cc_final: 0.7942 (m110)
REVERT: C  179 GLN cc_start: 0.8213 (pt0) cc_final: 0.7716 (pt0)
REVERT: H  185 ARG cc_start: 0.7601 (mtt90) cc_final: 0.7168 (mtt90)
REVERT: I  180 LEU cc_start: 0.8115 (mt) cc_final: 0.7908 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 25
  average time/residue: 0.0435
  time to fit residues: 1.4507
Evaluate side-chains
  24 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain E residue  174 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.138651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.126994 restraints weight = 2722.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.4234 rms_B_bonded: 2.65
r_work: 0.4098 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.5119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2180  Z= 0.187
  Angle     :  0.585   4.087   2980  Z= 0.316
  Chirality :  0.047   0.135    370
  Planarity :  0.002   0.013    380
  Dihedral  :  5.136  18.021    280
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.00 %
    Favored  : 83.60 %
  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: -3.09 (0.53), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 185 
 TYR   0.003   0.001   TYR E 188 
 PHE   0.009   0.002   PHE C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 2180)
  covalent geometry    : angle       0.58515 ( 2980)
  hydrogen bonds       : bond        0.01818 (   64)
  hydrogen bonds       : angle       4.18004 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 18
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  177 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7757 (m110)
REVERT: A  179 GLN cc_start: 0.7919 (pt0) cc_final: 0.7477 (pt0)
REVERT: B  177 ASN cc_start: 0.8204 (m110) cc_final: 0.7815 (m110)
REVERT: C  179 GLN cc_start: 0.7846 (pt0) cc_final: 0.7284 (pt0)
REVERT: D  181 ASP cc_start: 0.7576 (m-30) cc_final: 0.7284 (m-30)
REVERT: H  185 ARG cc_start: 0.7170 (mtt90) cc_final: 0.6726 (mtt90)
REVERT: I  180 LEU cc_start: 0.7872 (mt) cc_final: 0.7657 (mt)
  outliers start: 6
  outliers final: 4
  residues processed: 23
  average time/residue: 0.0462
  time to fit residues: 1.4056
Evaluate side-chains
  23 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain E residue  174 SER
Chi-restraints excluded: chain G residue  174 SER
Chi-restraints excluded: chain I residue  174 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
G 175 ASN
I 175 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.143260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.130431 restraints weight = 2616.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.4296 rms_B_bonded: 2.76
r_work: 0.4153 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2180  Z= 0.130
  Angle     :  0.542   3.994   2980  Z= 0.289
  Chirality :  0.046   0.132    370
  Planarity :  0.002   0.013    380
  Dihedral  :  4.672  13.878    280
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.60 %
    Favored  : 84.40 %
  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: -2.94 (0.54), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 185 
 TYR   0.003   0.001   TYR E 188 
 PHE   0.008   0.002   PHE F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 2180)
  covalent geometry    : angle       0.54207 ( 2980)
  hydrogen bonds       : bond        0.01786 (   64)
  hydrogen bonds       : angle       4.09773 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  177 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7750 (m110)
REVERT: A  179 GLN cc_start: 0.7924 (pt0) cc_final: 0.7516 (pt0)
REVERT: B  177 ASN cc_start: 0.8146 (m110) cc_final: 0.7767 (m110)
REVERT: C  179 GLN cc_start: 0.7913 (pt0) cc_final: 0.7385 (pt0)
REVERT: H  185 ARG cc_start: 0.7154 (mtt90) cc_final: 0.6713 (mtt90)
REVERT: I  180 LEU cc_start: 0.8027 (mt) cc_final: 0.7825 (mt)
  outliers start: 5
  outliers final: 4
  residues processed: 24
  average time/residue: 0.0448
  time to fit residues: 1.4249
Evaluate side-chains
  24 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain E residue  174 SER
Chi-restraints excluded: chain G residue  174 SER
Chi-restraints excluded: chain I residue  174 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0770
   chunk 18 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.0940

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.143346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.130924 restraints weight = 2663.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.4341 rms_B_bonded: 2.71
r_work: 0.4198 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.5320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2180  Z= 0.126
  Angle     :  0.535   3.952   2980  Z= 0.285
  Chirality :  0.046   0.131    370
  Planarity :  0.002   0.014    380
  Dihedral  :  4.576  13.523    280
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.60 %
    Favored  : 84.00 %
  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: -2.87 (0.54), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 185 
 TYR   0.003   0.001   TYR E 188 
 PHE   0.008   0.002   PHE F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2180)
  covalent geometry    : angle       0.53473 ( 2980)
  hydrogen bonds       : bond        0.01745 (   64)
  hydrogen bonds       : angle       4.06198 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A  177 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7691 (m110)
REVERT: A  179 GLN cc_start: 0.7882 (pt0) cc_final: 0.7481 (pt0)
REVERT: B  177 ASN cc_start: 0.8132 (m110) cc_final: 0.7754 (m110)
REVERT: C  179 GLN cc_start: 0.7910 (pt0) cc_final: 0.7399 (pt0)
REVERT: H  185 ARG cc_start: 0.7104 (mtt90) cc_final: 0.6659 (mtt90)
  outliers start: 6
  outliers final: 4
  residues processed: 27
  average time/residue: 0.0441
  time to fit residues: 1.5840
Evaluate side-chains
  26 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain E residue  174 SER
Chi-restraints excluded: chain G residue  174 SER
Chi-restraints excluded: chain I residue  174 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 15 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
I 175 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.147136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.134588 restraints weight = 2643.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.4379 rms_B_bonded: 2.70
r_work: 0.4237 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.5425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   2180  Z= 0.109
  Angle     :  0.523   3.883   2980  Z= 0.279
  Chirality :  0.046   0.131    370
  Planarity :  0.002   0.015    380
  Dihedral  :  4.352  13.250    280
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.60 %
    Favored  : 82.40 %
  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: -2.75 (0.54), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 185 
 TYR   0.003   0.001   TYR E 188 
 PHE   0.008   0.001   PHE G 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 2180)
  covalent geometry    : angle       0.52341 ( 2980)
  hydrogen bonds       : bond        0.01771 (   64)
  hydrogen bonds       : angle       4.01706 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A  177 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7586 (m-40)
REVERT: A  179 GLN cc_start: 0.7857 (pt0) cc_final: 0.7478 (pt0)
REVERT: B  177 ASN cc_start: 0.8088 (m110) cc_final: 0.7704 (m110)
REVERT: C  179 GLN cc_start: 0.7912 (pt0) cc_final: 0.7407 (pt0)
REVERT: D  181 ASP cc_start: 0.7614 (m-30) cc_final: 0.6698 (t0)
REVERT: H  185 ARG cc_start: 0.7092 (mtt90) cc_final: 0.6647 (mtt90)
  outliers start: 5
  outliers final: 4
  residues processed: 27
  average time/residue: 0.0330
  time to fit residues: 1.2105
Evaluate side-chains
  28 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain E residue  174 SER
Chi-restraints excluded: chain G residue  174 SER
Chi-restraints excluded: chain I residue  174 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    1.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.141549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.129335 restraints weight = 2721.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.4343 rms_B_bonded: 2.73
r_work: 0.4201 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.5406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2180  Z= 0.158
  Angle     :  0.560   3.996   2980  Z= 0.302
  Chirality :  0.047   0.132    370
  Planarity :  0.002   0.015    380
  Dihedral  :  4.696  14.332    280
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.60 %
    Favored  : 82.40 %
  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: -2.89 (0.54), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 185 
 TYR   0.003   0.001   TYR E 188 
 PHE   0.008   0.002   PHE C 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 2180)
  covalent geometry    : angle       0.56010 ( 2980)
  hydrogen bonds       : bond        0.01752 (   64)
  hydrogen bonds       : angle       4.09209 (  192)

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

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

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  500 Ramachandran restraints generated.
    250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  177 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7800 (m110)
REVERT: A  179 GLN cc_start: 0.7958 (pt0) cc_final: 0.7539 (pt0)
REVERT: B  177 ASN cc_start: 0.8213 (m110) cc_final: 0.7869 (m110)
REVERT: C  179 GLN cc_start: 0.7962 (pt0) cc_final: 0.7480 (pt0)
REVERT: H  185 ARG cc_start: 0.7212 (mtt90) cc_final: 0.6772 (mtt90)
  outliers start: 5
  outliers final: 4
  residues processed: 22
  average time/residue: 0.0478
  time to fit residues: 1.3736
Evaluate side-chains
  24 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ASN
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain E residue  174 SER
Chi-restraints excluded: chain G residue  174 SER
Chi-restraints excluded: chain I residue  174 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0170
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 18 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.6220

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.149518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.136369 restraints weight = 2624.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.4400 rms_B_bonded: 2.78
r_work: 0.4254 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.5520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2180  Z= 0.097
  Angle     :  0.513   3.831   2980  Z= 0.273
  Chirality :  0.046   0.130    370
  Planarity :  0.002   0.016    380
  Dihedral  :  4.256  13.177    280
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.00 %
    Favored  : 82.00 %
  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: -2.72 (0.54), residues: 250
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 185 
 TYR   0.003   0.001   TYR E 188 
 PHE   0.009   0.002   PHE F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 2180)
  covalent geometry    : angle       0.51343 ( 2980)
  hydrogen bonds       : bond        0.01775 (   64)
  hydrogen bonds       : angle       3.97326 (  192)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 734.06 seconds
wall clock time: 13 minutes 16.50 seconds (796.50 seconds total)