Starting phenix.real_space_refine
on Tue Feb  3 15:43:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ght_40050/02_2026/8ght_40050.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ght_40050/02_2026/8ght_40050.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ght_40050/02_2026/8ght_40050.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ght_40050/02_2026/8ght_40050.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ght_40050/02_2026/8ght_40050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ght_40050/02_2026/8ght_40050.map"
  }
  resolution = 3.05
  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=   0.014 sd=   0.091
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: 6
    Type Number    sf(0)   Gaussians
     Cd      6      9.23       5
     P       2      5.49       5
     S      24      5.16       5
     C    2818      2.51       5
     N     740      2.21       5
     O     776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  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: 4366
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 2139
          Classifications: {'peptide': 304}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 290}
    Chain: "B"
      Number of atoms: 2139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 2139
          Classifications: {'peptide': 304}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 290}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 41
          Ad-hoc single atom residues: {' CD': 3}
          Unusual residues: {'PTY': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 41
          Ad-hoc single atom residues: {' CD': 3}
          Unusual residues: {'PTY': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb="CD    CD B 503 " occ=0.60
  Time building chain proxies: 1.27, per 1000 atoms: 0.29
  Number of scatterers: 4366
  At special positions: 0
  Unit cell: (71.928, 83.916, 65.268, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cd      6     47.96
     S      24     16.00
     P       2     15.00
     O     776      8.00
     N     740      7.00
     C    2818      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: 0.44
  Conformation dependent library (CDL) restraints added in 441.6 milliseconds
  

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 2 sheets defined
      88.7% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 22
      removed outlier: 3.519A  pdb=" N   SER A  21 " --> pdb=" O   ALA A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 50
    Processing helix  chain 'A' and resid 52 through 76
      removed outlier: 3.677A  pdb=" N   VAL A  56 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 81
      removed outlier: 3.933A  pdb=" N   LEU A  80 " --> pdb=" O   MET A  76 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ARG A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 76 through 81'
    Processing helix  chain 'A' and resid 84 through 120
      removed outlier: 3.569A  pdb=" N   GLN A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 122 through 146
      removed outlier: 4.194A  pdb=" N   ALA A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 189
      removed outlier: 3.651A  pdb=" N   LEU A 169 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      Proline residue:  A 180  - end of helix
    Processing helix  chain 'A' and resid 190 through 192
      No H-bonds generated for 'chain 'A' and resid 190 through 192'
    Processing helix  chain 'A' and resid 193 through 223
      removed outlier: 4.193A  pdb=" N   GLY A 197 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
      Proline residue:  A 199  - end of helix
      Proline residue:  A 210  - end of helix
    Processing helix  chain 'A' and resid 228 through 252
      Proline residue:  A 241  - end of helix
      removed outlier: 3.543A  pdb=" N   SER A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 278
      removed outlier: 3.593A  pdb=" N   ILE A 260 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ALA A 266 " --> pdb=" O   MET A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 309
      removed outlier: 3.656A  pdb=" N   ALA A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLY A 309 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 22
      removed outlier: 3.519A  pdb=" N   SER B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 50
    Processing helix  chain 'B' and resid 52 through 76
      removed outlier: 3.677A  pdb=" N   VAL B  56 " --> pdb=" O   ASN B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 81
      removed outlier: 3.932A  pdb=" N   LEU B  80 " --> pdb=" O   MET B  76 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ARG B  81 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 76 through 81'
    Processing helix  chain 'B' and resid 84 through 120
      removed outlier: 3.569A  pdb=" N   GLN B  88 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
      Proline residue:  B 110  - end of helix
    Processing helix  chain 'B' and resid 122 through 146
      removed outlier: 4.194A  pdb=" N   ALA B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 189
      removed outlier: 3.652A  pdb=" N   LEU B 169 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      Proline residue:  B 180  - end of helix
    Processing helix  chain 'B' and resid 190 through 192
      No H-bonds generated for 'chain 'B' and resid 190 through 192'
    Processing helix  chain 'B' and resid 193 through 223
      removed outlier: 4.193A  pdb=" N   GLY B 197 " --> pdb=" O   ASP B 193 " (cutoff:3.500A)
      Proline residue:  B 199  - end of helix
      Proline residue:  B 210  - end of helix
    Processing helix  chain 'B' and resid 228 through 252
      Proline residue:  B 241  - end of helix
      removed outlier: 3.542A  pdb=" N   SER B 252 " --> pdb=" O   VAL B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 278
      removed outlier: 3.593A  pdb=" N   ILE B 260 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ALA B 266 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 309
      removed outlier: 3.655A  pdb=" N   ALA B 290 " --> pdb=" O   HIS B 286 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLY B 309 " --> pdb=" O   ASP B 305 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150
    Processing sheet with id=AA2, first strand: chain 'B' and resid 149 through 150

    393 hydrogen bonds defined for protein.
    1173 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: 0.69

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 702
        1.31 -     1.43: 1056
        1.43 -     1.56: 2626
        1.56 -     1.68: 4
        1.68 -     1.81: 48
  Bond restraints: 4436
  Sorted by residual:
  bond pdb=" C8  PTY B 501 "
       pdb=" O7  PTY B 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.400 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" C8  PTY A 404 "
       pdb=" O7  PTY A 404 "
    ideal  model  delta    sigma   weight residual
    1.331  1.399 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C30 PTY A 404 "
       pdb=" O4  PTY A 404 "
    ideal  model  delta    sigma   weight residual
    1.331  1.399 -0.068 2.00e-02 2.50e+03 1.14e+01
  bond pdb=" C30 PTY B 501 "
       pdb=" O4  PTY B 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.398 -0.067 2.00e-02 2.50e+03 1.12e+01
  bond pdb=" C6  PTY B 501 "
       pdb=" O7  PTY B 501 "
    ideal  model  delta    sigma   weight residual
    1.432  1.398  0.034 2.00e-02 2.50e+03 2.94e+00
  ... (remaining 4431 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 5948
        3.30 -     6.61: 78
        6.61 -     9.91: 6
        9.91 -    13.22: 0
       13.22 -    16.52: 2
  Bond angle restraints: 6034
  Sorted by residual:
  angle pdb=" O11 PTY A 404 "
        pdb=" P1  PTY A 404 "
        pdb=" O14 PTY A 404 "
      ideal   model   delta    sigma   weight residual
      92.90  109.42  -16.52 3.00e+00 1.11e-01 3.03e+01
  angle pdb=" O11 PTY B 501 "
        pdb=" P1  PTY B 501 "
        pdb=" O14 PTY B 501 "
      ideal   model   delta    sigma   weight residual
      92.90  109.40  -16.50 3.00e+00 1.11e-01 3.02e+01
  angle pdb=" N   THR A 281 "
        pdb=" CA  THR A 281 "
        pdb=" C   THR A 281 "
      ideal   model   delta    sigma   weight residual
     114.56  110.19    4.37 1.27e+00 6.20e-01 1.19e+01
  angle pdb=" N   THR B 281 "
        pdb=" CA  THR B 281 "
        pdb=" C   THR B 281 "
      ideal   model   delta    sigma   weight residual
     114.56  110.19    4.37 1.27e+00 6.20e-01 1.18e+01
  angle pdb=" O12 PTY A 404 "
        pdb=" P1  PTY A 404 "
        pdb=" O13 PTY A 404 "
      ideal   model   delta    sigma   weight residual
     119.61  110.02    9.59 3.00e+00 1.11e-01 1.02e+01
  ... (remaining 6029 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.09: 2522
       33.09 -    66.18: 62
       66.18 -    99.27: 6
       99.27 -   132.36: 0
      132.36 -   165.45: 2
  Dihedral angle restraints: 2592
    sinusoidal: 928
      harmonic: 1664
  Sorted by residual:
  dihedral pdb=" CA  ILE A 278 "
           pdb=" C   ILE A 278 "
           pdb=" N   PRO A 279 "
           pdb=" CA  PRO A 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.54   24.46     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  ILE B 278 "
           pdb=" C   ILE B 278 "
           pdb=" N   PRO B 279 "
           pdb=" CA  PRO B 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.60   24.40     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" C3  PTY B 501 "
           pdb=" O11 PTY B 501 "
           pdb=" P1  PTY B 501 "
           pdb=" O12 PTY B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.23  134.78  165.45     1      3.00e+01 1.11e-03 2.10e+01
  ... (remaining 2589 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 412
       0.023 -    0.047: 185
       0.047 -    0.070: 80
       0.070 -    0.094: 39
       0.094 -    0.117: 22
  Chirality restraints: 738
  Sorted by residual:
  chirality pdb=" CA  PRO B 180 "
            pdb=" N   PRO B 180 "
            pdb=" C   PRO B 180 "
            pdb=" CB  PRO B 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.42e-01
  chirality pdb=" CA  PRO A 180 "
            pdb=" N   PRO A 180 "
            pdb=" C   PRO A 180 "
            pdb=" CB  PRO A 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.32e-01
  chirality pdb=" CA  ASN A 178 "
            pdb=" N   ASN A 178 "
            pdb=" C   ASN A 178 "
            pdb=" CB  ASN A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.20e-01
  ... (remaining 735 not shown)

  Planarity restraints: 764
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 274 "    0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   SER B 274 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   SER B 274 "    0.021 2.00e-02 2.50e+03
        pdb=" N   HIS B 275 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 274 "   -0.016 2.00e-02 2.50e+03   3.20e-02 1.03e+01
        pdb=" C   SER A 274 "    0.055 2.00e-02 2.50e+03
        pdb=" O   SER A 274 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   HIS A 275 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 272 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   VAL B 272 "    0.055 2.00e-02 2.50e+03
        pdb=" O   VAL B 272 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   VAL B 273 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 761 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1084
        2.80 -     3.32: 4614
        3.32 -     3.85: 7333
        3.85 -     4.37: 7859
        4.37 -     4.90: 14047
  Nonbonded interactions: 34937
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 208 "
            pdb=" OE2 GLU B 240 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD2 ASP A 208 "
            pdb=" OE2 GLU A 240 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" CE1 HIS B 151 "
            pdb=" OE1 GLU B 276 "
     model   vdw
     2.282 3.260
  nonbonded pdb=" CE1 HIS A 151 "
            pdb=" OE1 GLU A 276 "
     model   vdw
     2.282 3.260
  nonbonded pdb=" OD1 ASP A 144 "
            pdb=" CE1 HIS A 149 "
     model   vdw
     2.285 3.260
  ... (remaining 34932 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' and (resid 6 through 309 or resid 402 through 403))
  selection = (chain 'B' and (resid 6 through 309 or resid 502 through 503))
}

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=0.60 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:             0.120
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.790
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4436  Z= 0.223
  Angle     :  0.871  16.520   6034  Z= 0.418
  Chirality :  0.038   0.117    738
  Planarity :  0.006   0.041    764
  Dihedral  : 15.440 165.450   1540
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.62 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  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:  1.91 (0.35), residues: 604
  helix:  2.27 (0.24), residues: 482
  sheet:  None (None), residues: 0
  loop : -3.12 (0.47), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 163 
 TYR   0.016   0.002   TYR B 145 
 PHE   0.010   0.002   PHE A  94 
 TRP   0.014   0.002   TRP B 168 
 HIS   0.006   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 4436)
  covalent geometry    : angle       0.87112 ( 6034)
  hydrogen bonds       : bond        0.12833 (  393)
  hydrogen bonds       : angle       5.48685 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: B   89 ASP cc_start: 0.8787 (m-30) cc_final: 0.8524 (m-30)
REVERT: B  157 GLN cc_start: 0.7995 (mm110) cc_final: 0.7716 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0530
  time to fit residues: 7.4957
Evaluate side-chains
  76 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.087546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.071346 restraints weight = 6776.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.41
r_work: 0.2937 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4436  Z= 0.160
  Angle     :  0.647   7.020   6034  Z= 0.321
  Chirality :  0.036   0.115    738
  Planarity :  0.005   0.038    764
  Dihedral  : 10.148 109.557    702
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.13 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.35 %
    Favored  : 84.47 %
  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:  2.76 (0.36), residues: 604
  helix:  2.87 (0.24), residues: 486
  sheet:  None (None), residues: 0
  loop : -3.03 (0.51), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 195 
 TYR   0.012   0.001   TYR B 145 
 PHE   0.009   0.001   PHE A  94 
 TRP   0.006   0.001   TRP B 168 
 HIS   0.006   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4436)
  covalent geometry    : angle       0.64658 ( 6034)
  hydrogen bonds       : bond        0.04676 (  393)
  hydrogen bonds       : angle       4.40336 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7226 (t80)
REVERT: A  152 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8547 (tm-30)
REVERT: A  160 GLU cc_start: 0.8463 (pp20) cc_final: 0.8235 (pp20)
REVERT: A  193 ASP cc_start: 0.8443 (t0) cc_final: 0.7942 (t0)
REVERT: B   67 PHE cc_start: 0.8699 (t80) cc_final: 0.8465 (t80)
REVERT: B   75 LEU cc_start: 0.9458 (mm) cc_final: 0.9193 (mm)
REVERT: B   89 ASP cc_start: 0.9067 (m-30) cc_final: 0.8615 (m-30)
REVERT: B  157 GLN cc_start: 0.7868 (mm110) cc_final: 0.7620 (mm110)
REVERT: B  170 PHE cc_start: 0.8695 (m-80) cc_final: 0.8495 (m-80)
REVERT: B  262 MET cc_start: 0.9141 (mmm) cc_final: 0.8208 (mmm)
REVERT: B  295 MET cc_start: 0.9323 (mmm) cc_final: 0.9008 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 92
  average time/residue: 0.0447
  time to fit residues: 5.9183
Evaluate side-chains
  82 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  145 TYR
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  298 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 = 0.3345 r_free = 0.3345 target = 0.085667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.069090 restraints weight = 6012.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.21
r_work: 0.2889 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4436  Z= 0.154
  Angle     :  0.624   8.569   6034  Z= 0.306
  Chirality :  0.036   0.120    738
  Planarity :  0.004   0.040    764
  Dihedral  :  8.051  57.498    702
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.79 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.02 %
    Favored  : 82.52 %
  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:  3.10 (0.36), residues: 604
  helix:  3.18 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -3.21 (0.48), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 195 
 TYR   0.007   0.001   TYR B 145 
 PHE   0.009   0.001   PHE A  94 
 TRP   0.007   0.001   TRP B 168 
 HIS   0.004   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4436)
  covalent geometry    : angle       0.62425 ( 6034)
  hydrogen bonds       : bond        0.05028 (  393)
  hydrogen bonds       : angle       4.31940 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8734 (tm-30)
REVERT: A  160 GLU cc_start: 0.8734 (pp20) cc_final: 0.8469 (pp20)
REVERT: A  193 ASP cc_start: 0.8472 (t0) cc_final: 0.8086 (t0)
REVERT: A  280 GLU cc_start: 0.8554 (mp0) cc_final: 0.8097 (mp0)
REVERT: B   67 PHE cc_start: 0.8749 (t80) cc_final: 0.8049 (t80)
REVERT: B   75 LEU cc_start: 0.9490 (mm) cc_final: 0.9141 (mm)
REVERT: B   89 ASP cc_start: 0.9144 (m-30) cc_final: 0.8606 (m-30)
REVERT: B  157 GLN cc_start: 0.8164 (mm110) cc_final: 0.7924 (mm110)
REVERT: B  170 PHE cc_start: 0.8737 (m-80) cc_final: 0.8444 (m-80)
REVERT: B  287 GLU cc_start: 0.8885 (mp0) cc_final: 0.8684 (mp0)
REVERT: B  295 MET cc_start: 0.9320 (mmm) cc_final: 0.9105 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 90
  average time/residue: 0.0439
  time to fit residues: 5.6622
Evaluate side-chains
  79 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain B residue   61 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 41 optimal weight:    8.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3392 r_free = 0.3392 target = 0.088388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.071743 restraints weight = 5890.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.22
r_work: 0.2943 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4436  Z= 0.130
  Angle     :  0.592   6.195   6034  Z= 0.291
  Chirality :  0.035   0.116    738
  Planarity :  0.004   0.042    764
  Dihedral  :  7.279  56.871    702
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.30 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.20 %
    Favored  : 79.85 %
  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:  3.30 (0.36), residues: 604
  helix:  3.35 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -3.28 (0.47), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 195 
 TYR   0.006   0.001   TYR B 145 
 PHE   0.010   0.001   PHE A  94 
 TRP   0.005   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4436)
  covalent geometry    : angle       0.59212 ( 6034)
  hydrogen bonds       : bond        0.04336 (  393)
  hydrogen bonds       : angle       4.19274 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.9427 (mm) cc_final: 0.9226 (tp)
REVERT: A  160 GLU cc_start: 0.8754 (pp20) cc_final: 0.8431 (pp20)
REVERT: A  193 ASP cc_start: 0.8536 (t0) cc_final: 0.8125 (t0)
REVERT: A  207 GLN cc_start: 0.8561 (pp30) cc_final: 0.7667 (pp30)
REVERT: A  280 GLU cc_start: 0.8573 (mp0) cc_final: 0.8092 (mp0)
REVERT: B   67 PHE cc_start: 0.8778 (t80) cc_final: 0.8161 (t80)
REVERT: B   89 ASP cc_start: 0.9100 (m-30) cc_final: 0.8586 (m-30)
REVERT: B  150 GLU cc_start: 0.8910 (tt0) cc_final: 0.8653 (tt0)
REVERT: B  157 GLN cc_start: 0.8092 (mm110) cc_final: 0.7867 (mm110)
REVERT: B  262 MET cc_start: 0.9225 (mmm) cc_final: 0.8926 (mtp)
REVERT: B  280 GLU cc_start: 0.8650 (mp0) cc_final: 0.8330 (mp0)
REVERT: B  287 GLU cc_start: 0.8835 (mp0) cc_final: 0.8528 (mp0)
REVERT: B  295 MET cc_start: 0.9311 (mmm) cc_final: 0.9068 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 92
  average time/residue: 0.0443
  time to fit residues: 5.7983
Evaluate side-chains
  91 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  238 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3412 r_free = 0.3412 target = 0.090224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.073937 restraints weight = 5937.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.20
r_work: 0.2972 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2973
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.4021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4436  Z= 0.125
  Angle     :  0.583   6.198   6034  Z= 0.288
  Chirality :  0.035   0.129    738
  Planarity :  0.004   0.043    764
  Dihedral  :  6.753  54.642    702
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.30 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 19.66 %
    Favored  : 78.64 %
  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:  3.39 (0.36), residues: 604
  helix:  3.43 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -3.34 (0.47), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 195 
 TYR   0.004   0.001   TYR B 145 
 PHE   0.010   0.001   PHE B  94 
 TRP   0.004   0.000   TRP B 168 
 HIS   0.004   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4436)
  covalent geometry    : angle       0.58344 ( 6034)
  hydrogen bonds       : bond        0.04089 (  393)
  hydrogen bonds       : angle       4.13436 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   67 PHE cc_start: 0.8945 (t80) cc_final: 0.8443 (t80)
REVERT: A  160 GLU cc_start: 0.8759 (pp20) cc_final: 0.8429 (pp20)
REVERT: A  193 ASP cc_start: 0.8547 (t0) cc_final: 0.8156 (t0)
REVERT: A  207 GLN cc_start: 0.9190 (pp30) cc_final: 0.8887 (pp30)
REVERT: A  280 GLU cc_start: 0.8559 (mp0) cc_final: 0.8151 (mp0)
REVERT: A  295 MET cc_start: 0.9346 (mmp) cc_final: 0.9104 (mmm)
REVERT: B   67 PHE cc_start: 0.8769 (t80) cc_final: 0.8271 (t80)
REVERT: B   89 ASP cc_start: 0.9054 (m-30) cc_final: 0.8541 (m-30)
REVERT: B  157 GLN cc_start: 0.8201 (mm110) cc_final: 0.7937 (mm110)
REVERT: B  170 PHE cc_start: 0.8758 (m-80) cc_final: 0.8465 (m-80)
REVERT: B  207 GLN cc_start: 0.8665 (pp30) cc_final: 0.7746 (pp30)
REVERT: B  262 MET cc_start: 0.9280 (mmm) cc_final: 0.8954 (mtp)
REVERT: B  280 GLU cc_start: 0.8628 (mp0) cc_final: 0.8282 (mp0)
REVERT: B  287 GLU cc_start: 0.8828 (mp0) cc_final: 0.8490 (mp0)
REVERT: B  295 MET cc_start: 0.9333 (mmm) cc_final: 0.9069 (mmm)
REVERT: B  306 THR cc_start: 0.8264 (t) cc_final: 0.7999 (t)
  outliers start: 7
  outliers final: 6
  residues processed: 102
  average time/residue: 0.0325
  time to fit residues: 4.7732
Evaluate side-chains
  97 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  183 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:   20.0000
   chunk 32 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.3258 r_free = 0.3258 target = 0.080182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.063900 restraints weight = 5880.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 2.13
r_work: 0.2795 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   4436  Z= 0.225
  Angle     :  0.677   6.171   6034  Z= 0.343
  Chirality :  0.038   0.117    738
  Planarity :  0.004   0.038    764
  Dihedral  :  7.520  55.279    702
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.79 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.93 %
    Favored  : 78.16 %
  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:  3.28 (0.36), residues: 604
  helix:  3.28 (0.23), residues: 486
  sheet:  None (None), residues: 0
  loop : -3.09 (0.51), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 283 
 TYR   0.007   0.001   TYR A 258 
 PHE   0.013   0.001   PHE A  94 
 TRP   0.006   0.001   TRP B 168 
 HIS   0.006   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 4436)
  covalent geometry    : angle       0.67670 ( 6034)
  hydrogen bonds       : bond        0.06154 (  393)
  hydrogen bonds       : angle       4.51788 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  160 GLU cc_start: 0.8977 (pp20) cc_final: 0.8703 (pp20)
REVERT: A  193 ASP cc_start: 0.8638 (t0) cc_final: 0.8259 (t0)
REVERT: A  280 GLU cc_start: 0.8777 (mp0) cc_final: 0.8385 (mp0)
REVERT: B   89 ASP cc_start: 0.9278 (m-30) cc_final: 0.8672 (m-30)
REVERT: B  157 GLN cc_start: 0.8185 (mm110) cc_final: 0.7894 (mm110)
REVERT: B  262 MET cc_start: 0.9507 (mmm) cc_final: 0.9231 (tpp)
REVERT: B  280 GLU cc_start: 0.8808 (mp0) cc_final: 0.8453 (mp0)
REVERT: B  287 GLU cc_start: 0.9052 (mp0) cc_final: 0.8677 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 82
  average time/residue: 0.0408
  time to fit residues: 4.6916
Evaluate side-chains
  78 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  278 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3347 r_free = 0.3347 target = 0.086114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.069719 restraints weight = 5796.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.14
r_work: 0.2891 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4436  Z= 0.146
  Angle     :  0.623   7.190   6034  Z= 0.312
  Chirality :  0.036   0.118    738
  Planarity :  0.004   0.040    764
  Dihedral  :  7.068  56.056    702
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.30 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.15 %
    Favored  : 76.94 %
  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:  3.29 (0.36), residues: 604
  helix:  3.34 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -3.28 (0.48), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 195 
 TYR   0.007   0.001   TYR B 145 
 PHE   0.012   0.001   PHE B  94 
 TRP   0.005   0.001   TRP B 168 
 HIS   0.005   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4436)
  covalent geometry    : angle       0.62335 ( 6034)
  hydrogen bonds       : bond        0.04801 (  393)
  hydrogen bonds       : angle       4.31837 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  160 GLU cc_start: 0.8960 (pp20) cc_final: 0.8660 (pp20)
REVERT: A  193 ASP cc_start: 0.8694 (t0) cc_final: 0.8337 (t0)
REVERT: A  262 MET cc_start: 0.9396 (mmm) cc_final: 0.9172 (mtp)
REVERT: A  280 GLU cc_start: 0.8736 (mp0) cc_final: 0.8344 (mp0)
REVERT: B   38 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9256 (tp)
REVERT: B   67 PHE cc_start: 0.8937 (t80) cc_final: 0.8338 (t80)
REVERT: B   89 ASP cc_start: 0.9219 (m-30) cc_final: 0.8643 (m-30)
REVERT: B  157 GLN cc_start: 0.8066 (mm110) cc_final: 0.7812 (mm110)
REVERT: B  170 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8799 (m-80)
REVERT: B  280 GLU cc_start: 0.8765 (mp0) cc_final: 0.8370 (mp0)
REVERT: B  287 GLU cc_start: 0.8998 (mp0) cc_final: 0.8610 (mp0)
REVERT: B  306 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8205 (t)
  outliers start: 12
  outliers final: 6
  residues processed: 86
  average time/residue: 0.0391
  time to fit residues: 4.8179
Evaluate side-chains
  86 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3364 r_free = 0.3364 target = 0.086517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.069762 restraints weight = 5606.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 2.12
r_work: 0.2906 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.4390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4436  Z= 0.142
  Angle     :  0.629   6.836   6034  Z= 0.313
  Chirality :  0.036   0.133    738
  Planarity :  0.004   0.040    764
  Dihedral  :  6.763  54.292    702
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.13 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.60 %
    Favored  : 76.21 %
  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:  3.27 (0.36), residues: 604
  helix:  3.33 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -3.32 (0.48), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 195 
 TYR   0.005   0.001   TYR B 145 
 PHE   0.012   0.001   PHE B  94 
 TRP   0.004   0.001   TRP B 168 
 HIS   0.004   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4436)
  covalent geometry    : angle       0.62851 ( 6034)
  hydrogen bonds       : bond        0.04602 (  393)
  hydrogen bonds       : angle       4.23378 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  160 GLU cc_start: 0.8966 (pp20) cc_final: 0.8661 (pp20)
REVERT: A  193 ASP cc_start: 0.8697 (t0) cc_final: 0.8338 (t0)
REVERT: A  262 MET cc_start: 0.9405 (mmm) cc_final: 0.9177 (mtp)
REVERT: B   38 LEU cc_start: 0.9475 (mm) cc_final: 0.9262 (tp)
REVERT: B   67 PHE cc_start: 0.8916 (t80) cc_final: 0.8250 (t80)
REVERT: B   89 ASP cc_start: 0.9217 (m-30) cc_final: 0.8678 (m-30)
REVERT: B  157 GLN cc_start: 0.8142 (mm110) cc_final: 0.7922 (mm110)
REVERT: B  170 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8778 (m-80)
REVERT: B  262 MET cc_start: 0.9388 (mmm) cc_final: 0.9097 (mtp)
REVERT: B  280 GLU cc_start: 0.8722 (mp0) cc_final: 0.8314 (mp0)
REVERT: B  287 GLU cc_start: 0.8988 (mp0) cc_final: 0.8611 (mp0)
REVERT: B  306 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8178 (t)
  outliers start: 9
  outliers final: 7
  residues processed: 85
  average time/residue: 0.0358
  time to fit residues: 4.2992
Evaluate side-chains
  89 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.089103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.072116 restraints weight = 5379.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.09
r_work: 0.2955 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.4554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4436  Z= 0.134
  Angle     :  0.625   6.872   6034  Z= 0.310
  Chirality :  0.036   0.141    738
  Planarity :  0.004   0.040    764
  Dihedral  :  6.335  51.875    702
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.13 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.09 %
    Favored  : 75.00 %
  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:  3.25 (0.36), residues: 604
  helix:  3.34 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -3.42 (0.47), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 195 
 TYR   0.005   0.001   TYR B 145 
 PHE   0.011   0.001   PHE B  94 
 TRP   0.003   0.000   TRP B 168 
 HIS   0.004   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4436)
  covalent geometry    : angle       0.62477 ( 6034)
  hydrogen bonds       : bond        0.04210 (  393)
  hydrogen bonds       : angle       4.17924 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   67 PHE cc_start: 0.8976 (t80) cc_final: 0.8421 (t80)
REVERT: A  160 GLU cc_start: 0.9056 (pp20) cc_final: 0.8781 (pp20)
REVERT: A  193 ASP cc_start: 0.8686 (t0) cc_final: 0.8334 (t0)
REVERT: A  262 MET cc_start: 0.9381 (mmm) cc_final: 0.9145 (mtp)
REVERT: A  295 MET cc_start: 0.9389 (mmm) cc_final: 0.9152 (mmm)
REVERT: B   67 PHE cc_start: 0.8899 (t80) cc_final: 0.8259 (t80)
REVERT: B   89 ASP cc_start: 0.9153 (m-30) cc_final: 0.8624 (m-30)
REVERT: B  170 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8783 (m-80)
REVERT: B  208 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6818 (t0)
REVERT: B  280 GLU cc_start: 0.8697 (mp0) cc_final: 0.8279 (mp0)
REVERT: B  287 GLU cc_start: 0.8939 (mp0) cc_final: 0.8544 (mp0)
REVERT: B  306 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7939 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0422
  time to fit residues: 5.8763
Evaluate side-chains
  97 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  170 PHE
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.089587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.072893 restraints weight = 5158.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 2.00
r_work: 0.2949 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2810
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2810
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.4585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4436  Z= 0.149
  Angle     :  0.650   7.310   6034  Z= 0.323
  Chirality :  0.037   0.166    738
  Planarity :  0.004   0.039    764
  Dihedral  :  6.272  49.916    702
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.63 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.60 %
    Favored  : 75.00 %
  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:  3.22 (0.36), residues: 604
  helix:  3.32 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -3.46 (0.48), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 195 
 TYR   0.004   0.001   TYR B 145 
 PHE   0.013   0.001   PHE B  94 
 TRP   0.003   0.000   TRP A 168 
 HIS   0.004   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4436)
  covalent geometry    : angle       0.64981 ( 6034)
  hydrogen bonds       : bond        0.04598 (  393)
  hydrogen bonds       : angle       4.21388 ( 1173)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   67 PHE cc_start: 0.8941 (t80) cc_final: 0.8341 (t80)
REVERT: A   99 MET cc_start: 0.8343 (mtt) cc_final: 0.7903 (mtt)
REVERT: A  160 GLU cc_start: 0.9050 (pp20) cc_final: 0.8779 (pp20)
REVERT: A  193 ASP cc_start: 0.8675 (t0) cc_final: 0.8312 (t0)
REVERT: B   67 PHE cc_start: 0.8865 (t80) cc_final: 0.8133 (t80)
REVERT: B   89 ASP cc_start: 0.9165 (m-30) cc_final: 0.8620 (m-30)
REVERT: B  208 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6562 (t0)
REVERT: B  262 MET cc_start: 0.9392 (mmm) cc_final: 0.9072 (mtp)
REVERT: B  280 GLU cc_start: 0.8698 (mp0) cc_final: 0.8242 (mp0)
REVERT: B  287 GLU cc_start: 0.8934 (mp0) cc_final: 0.8529 (mp0)
REVERT: B  306 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8049 (t)
  outliers start: 14
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0458
  time to fit residues: 5.8318
Evaluate side-chains
  93 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  306 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0020
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:   20.0000
   chunk 46 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0170
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0570
   overall best weight:    0.4148

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

Flipped N/Q/H residues before XYZ refinement:
B  22 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.095275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.078053 restraints weight = 5356.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.08
r_work: 0.3060 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4436  Z= 0.131
  Angle     :  0.635   6.867   6034  Z= 0.311
  Chirality :  0.036   0.161    738
  Planarity :  0.004   0.040    764
  Dihedral  :  5.794  46.589    702
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.30 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.84 %
    Favored  : 75.00 %
  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:  3.20 (0.36), residues: 604
  helix:  3.34 (0.23), residues: 484
  sheet:  None (None), residues: 0
  loop : -3.61 (0.47), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 153 
 TYR   0.005   0.001   TYR B 145 
 PHE   0.012   0.001   PHE B  94 
 TRP   0.002   0.000   TRP A 168 
 HIS   0.006   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4436)
  covalent geometry    : angle       0.63497 ( 6034)
  hydrogen bonds       : bond        0.03695 (  393)
  hydrogen bonds       : angle       4.10204 ( 1173)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 985.66 seconds
wall clock time: 17 minutes 36.44 seconds (1056.44 seconds total)