Starting phenix.real_space_refine
on Wed Mar  4 12:01:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t9f_25756/03_2026/7t9f_25756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t9f_25756/03_2026/7t9f_25756.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t9f_25756/03_2026/7t9f_25756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t9f_25756/03_2026/7t9f_25756.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t9f_25756/03_2026/7t9f_25756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t9f_25756/03_2026/7t9f_25756.map"
  }
  resolution = 3.23
  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: 5
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4456      2.51       5
     N    1046      2.21       5
     O    1128      1.98       5
     H    6958      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13640
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 6820
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 15, 'TRANS': 429}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 6820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 6820
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 15, 'TRANS': 429}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.56, per 1000 atoms: 0.19
  Number of scatterers: 13640
  At special positions: 0
  Unit cell: (88.81, 100.43, 76.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     O    1128      8.00
     N    1046      7.00
     C    4456      6.00
     H    6958      1.00
    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: 1.24
  Conformation dependent library (CDL) restraints added in 372.8 milliseconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1656

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 0 sheets defined
      84.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 38
    Processing helix  chain 'A' and resid 42 through 62
    Processing helix  chain 'A' and resid 65 through 80
      Proline residue:  A  74  - end of helix
    Processing helix  chain 'A' and resid 84 through 90
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 94 through 114
      removed outlier: 3.718A  pdb=" N   PHE A  98 " --> pdb=" O   ASN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 127
    Processing helix  chain 'A' and resid 130 through 147
      removed outlier: 3.652A  pdb=" N   ALA A 134 " --> pdb=" O   LYS A 130 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL A 135 " --> pdb=" O   MET A 131 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   PHE A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 166
      removed outlier: 3.795A  pdb=" N   MET A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   MET A 158 " --> pdb=" O   THR A 154 " (cutoff:3.500A)
      Proline residue:  A 160  - end of helix
    Processing helix  chain 'A' and resid 175 through 193
      removed outlier: 4.400A  pdb=" N   VAL A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   SER A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 211
      removed outlier: 3.770A  pdb=" N   ALA A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 240
      Proline residue:  A 223  - end of helix
      Proline residue:  A 230  - end of helix
    Processing helix  chain 'A' and resid 260 through 277
    Processing helix  chain 'A' and resid 277 through 286
    Processing helix  chain 'A' and resid 290 through 306
    Processing helix  chain 'A' and resid 310 through 318
    Processing helix  chain 'A' and resid 319 through 339
      removed outlier: 3.633A  pdb=" N   LEU A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY A 327 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 356
      removed outlier: 5.025A  pdb=" N   ASP A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   MET A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 375
      removed outlier: 4.334A  pdb=" N   PHE A 375 " --> pdb=" O   PHE A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 397
      Proline residue:  A 387  - end of helix
      removed outlier: 3.765A  pdb=" N   THR A 391 " --> pdb=" O   PRO A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 4.066A  pdb=" N   LEU A 403 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 429
    Processing helix  chain 'A' and resid 434 through 460
    Processing helix  chain 'B' and resid 19 through 38
    Processing helix  chain 'B' and resid 42 through 62
    Processing helix  chain 'B' and resid 65 through 80
      Proline residue:  B  74  - end of helix
    Processing helix  chain 'B' and resid 84 through 90
    Processing helix  chain 'B' and resid 91 through 93
      No H-bonds generated for 'chain 'B' and resid 91 through 93'
    Processing helix  chain 'B' and resid 94 through 114
      removed outlier: 3.719A  pdb=" N   PHE B  98 " --> pdb=" O   ASN B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 127
    Processing helix  chain 'B' and resid 130 through 147
      removed outlier: 3.652A  pdb=" N   ALA B 134 " --> pdb=" O   LYS B 130 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL B 135 " --> pdb=" O   MET B 131 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   PHE B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 166
      removed outlier: 3.795A  pdb=" N   MET B 157 " --> pdb=" O   ALA B 153 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   MET B 158 " --> pdb=" O   THR B 154 " (cutoff:3.500A)
      Proline residue:  B 160  - end of helix
    Processing helix  chain 'B' and resid 175 through 193
      removed outlier: 4.400A  pdb=" N   VAL B 185 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER B 190 " --> pdb=" O   ALA B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 211
      removed outlier: 3.771A  pdb=" N   ALA B 204 " --> pdb=" O   SER B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 240
      Proline residue:  B 223  - end of helix
      Proline residue:  B 230  - end of helix
    Processing helix  chain 'B' and resid 260 through 277
    Processing helix  chain 'B' and resid 277 through 286
    Processing helix  chain 'B' and resid 290 through 306
    Processing helix  chain 'B' and resid 310 through 318
    Processing helix  chain 'B' and resid 319 through 339
      removed outlier: 3.632A  pdb=" N   LEU B 323 " --> pdb=" O   ASP B 319 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY B 327 " --> pdb=" O   LEU B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 356
      removed outlier: 5.026A  pdb=" N   ASP B 351 " --> pdb=" O   ASN B 347 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   MET B 352 " --> pdb=" O   ALA B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 375
      removed outlier: 4.334A  pdb=" N   PHE B 375 " --> pdb=" O   PHE B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 397
      Proline residue:  B 387  - end of helix
      removed outlier: 3.765A  pdb=" N   THR B 391 " --> pdb=" O   PRO B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 413
      removed outlier: 4.066A  pdb=" N   LEU B 403 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 429
    Processing helix  chain 'B' and resid 434 through 460

    512 hydrogen bonds defined for protein.
    1536 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: 2.91

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6952
        1.03 -     1.23: 6
        1.23 -     1.42: 2758
        1.42 -     1.62: 3984
        1.62 -     1.82: 98
  Bond restraints: 13798
  Sorted by residual:
  bond pdb=" CA  ASP A 251 "
       pdb=" HA  ASP A 251 "
    ideal  model  delta    sigma   weight residual
    0.970  0.930  0.040 2.00e-02 2.50e+03 3.91e+00
  bond pdb=" CB  PHE B 428 "
       pdb=" CG  PHE B 428 "
    ideal  model  delta    sigma   weight residual
    1.502  1.544 -0.042 2.30e-02 1.89e+03 3.27e+00
  bond pdb=" CB  PHE A 428 "
       pdb=" CG  PHE A 428 "
    ideal  model  delta    sigma   weight residual
    1.502  1.542 -0.040 2.30e-02 1.89e+03 2.97e+00
  bond pdb=" CB  ASP B 251 "
       pdb=" CG  ASP B 251 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.87e+00
  bond pdb=" CB  ASP A 251 "
       pdb=" CG  ASP A 251 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.80e+00
  ... (remaining 13793 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.16: 25043
        8.16 -    16.31: 6
       16.31 -    24.47: 12
       24.47 -    32.63: 18
       32.63 -    40.78: 5
  Bond angle restraints: 25084
  Sorted by residual:
  angle pdb=" N   ASP A 251 "
        pdb=" CA  ASP A 251 "
        pdb=" HA  ASP A 251 "
      ideal   model   delta    sigma   weight residual
     110.00   69.22   40.78 3.00e+00 1.11e-01 1.85e+02
  angle pdb=" C   ASP A 251 "
        pdb=" CA  ASP A 251 "
        pdb=" HA  ASP A 251 "
      ideal   model   delta    sigma   weight residual
     109.00   69.94   39.06 3.00e+00 1.11e-01 1.70e+02
  angle pdb=" C   SER A 213 "
        pdb=" CA  SER A 213 "
        pdb=" HA  SER A 213 "
      ideal   model   delta    sigma   weight residual
     109.00   70.70   38.30 3.00e+00 1.11e-01 1.63e+02
  angle pdb=" N   SER A 213 "
        pdb=" CA  SER A 213 "
        pdb=" HA  SER A 213 "
      ideal   model   delta    sigma   weight residual
     110.00   74.82   35.18 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" CB  SER A 213 "
        pdb=" CA  SER A 213 "
        pdb=" HA  SER A 213 "
      ideal   model   delta    sigma   weight residual
     109.00   74.29   34.71 3.00e+00 1.11e-01 1.34e+02
  ... (remaining 25079 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5715
       17.97 -    35.94: 515
       35.94 -    53.91: 174
       53.91 -    71.87: 50
       71.87 -    89.84: 16
  Dihedral angle restraints: 6470
    sinusoidal: 3394
      harmonic: 3076
  Sorted by residual:
  dihedral pdb=" CA  MET B 398 "
           pdb=" C   MET B 398 "
           pdb=" N   SER B 399 "
           pdb=" CA  SER B 399 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.99  -28.01     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  MET A 398 "
           pdb=" C   MET A 398 "
           pdb=" N   SER A 399 "
           pdb=" CA  SER A 399 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.04  -27.96     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  GLY B 397 "
           pdb=" C   GLY B 397 "
           pdb=" N   MET B 398 "
           pdb=" CA  MET B 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.91   23.09     0      5.00e+00 4.00e-02 2.13e+01
  ... (remaining 6467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.398: 1156
       0.398 -    0.795: 0
       0.795 -    1.193: 0
       1.193 -    1.590: 0
       1.590 -    1.988: 2
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" CG  LEU A 250 "
            pdb=" CB  LEU A 250 "
            pdb=" CD1 LEU A 250 "
            pdb=" CD2 LEU A 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.60   -1.99 2.00e-01 2.50e+01 9.88e+01
  chirality pdb=" CG  LEU B 250 "
            pdb=" CB  LEU B 250 "
            pdb=" CD1 LEU B 250 "
            pdb=" CD2 LEU B 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.60   -1.99 2.00e-01 2.50e+01 9.86e+01
  chirality pdb=" CA  ASP B 251 "
            pdb=" N   ASP B 251 "
            pdb=" C   ASP B 251 "
            pdb=" CB  ASP B 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.41e-01
  ... (remaining 1155 not shown)

  Planarity restraints: 1986
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B  28 "    0.015 2.00e-02 2.50e+03   3.00e-02 9.00e+00
        pdb=" CG  ASP B  28 "   -0.052 2.00e-02 2.50e+03
        pdb=" OD1 ASP B  28 "    0.019 2.00e-02 2.50e+03
        pdb=" OD2 ASP B  28 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A  28 "    0.015 2.00e-02 2.50e+03   3.00e-02 9.00e+00
        pdb=" CG  ASP A  28 "   -0.052 2.00e-02 2.50e+03
        pdb=" OD1 ASP A  28 "    0.019 2.00e-02 2.50e+03
        pdb=" OD2 ASP A  28 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 428 "    0.004 2.00e-02 2.50e+03   1.02e-02 3.11e+00
        pdb=" CG  PHE A 428 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 428 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 428 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 428 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 428 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 428 "    0.002 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 428 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 428 "    0.007 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 428 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 428 "    0.005 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 428 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1983 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.16: 456
        2.16 -     2.77: 26456
        2.77 -     3.38: 40023
        3.38 -     3.99: 48857
        3.99 -     4.60: 77944
  Nonbonded interactions: 193736
  Sorted by model distance:
  nonbonded pdb=" H   ASP A 251 "
            pdb=" HA  ASP A 251 "
     model   vdw
     1.556 1.816
  nonbonded pdb=" H   SER A 213 "
            pdb=" HA  SER A 213 "
     model   vdw
     1.612 1.816
  nonbonded pdb=" OE1 GLU B 313 "
            pdb=" H   GLU B 313 "
     model   vdw
     1.639 2.450
  nonbonded pdb=" OE1 GLU A 313 "
            pdb=" H   GLU A 313 "
     model   vdw
     1.639 2.450
  nonbonded pdb=" HB3 ARG A 252 "
            pdb=" HG2 ARG A 252 "
     model   vdw
     1.692 1.952
  ... (remaining 193731 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'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  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:             0.050
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     13.830
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
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   0.052   6840  Z= 0.194
  Angle     :  0.841  13.513   9326  Z= 0.428
  Chirality :  0.092   1.988   1158
  Planarity :  0.004   0.043   1128
  Dihedral  : 13.184  88.850   2300
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  1.42 %
    Favored  : 98.30 %
  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:  0.16 (0.29), residues: 886
  helix:  0.92 (0.19), residues: 720
  sheet:  None (None), residues: 0
  loop : -3.50 (0.41), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 252 
 TYR   0.011   0.002   TYR B 187 
 PHE   0.026   0.002   PHE B 428 
 TRP   0.019   0.002   TRP A 217 
 HIS   0.004   0.001   HIS A  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 6840)
  covalent geometry    : angle       0.84077 ( 9326)
  hydrogen bonds       : bond        0.11774 (  512)
  hydrogen bonds       : angle       5.24326 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  127 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.6506 (mpp) cc_final: 0.6298 (mpp)
REVERT: A  313 GLU cc_start: 0.7787 (mp0) cc_final: 0.7512 (mp0)
  outliers start: 2
  outliers final: 2
  residues processed: 125
  average time/residue: 0.1343
  time to fit residues: 24.0464
Evaluate side-chains
  110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain B residue  247 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.133347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.102752 restraints weight = 38372.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.64
r_work: 0.3290 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6840  Z= 0.173
  Angle     :  0.639  11.617   9326  Z= 0.327
  Chirality :  0.084   1.822   1158
  Planarity :  0.004   0.037   1128
  Dihedral  :  5.508  54.966    914
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  5.97 %
    Favored  : 93.32 %
  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:  0.44 (0.29), residues: 886
  helix:  1.10 (0.20), residues: 722
  sheet:  None (None), residues: 0
  loop : -3.38 (0.40), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 252 
 TYR   0.010   0.002   TYR B 178 
 PHE   0.012   0.001   PHE A 371 
 TRP   0.012   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6840)
  covalent geometry    : angle       0.63865 ( 9326)
  hydrogen bonds       : bond        0.05285 (  512)
  hydrogen bonds       : angle       4.47148 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  118 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.7138 (mpp) cc_final: 0.6809 (mpp)
REVERT: A  313 GLU cc_start: 0.8543 (mp0) cc_final: 0.8272 (mp0)
REVERT: A  367 THR cc_start: 0.9158 (m) cc_final: 0.8947 (p)
REVERT: B  247 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7162 (mmm)
REVERT: B  367 THR cc_start: 0.9178 (m) cc_final: 0.8947 (p)
  outliers start: 5
  outliers final: 3
  residues processed: 113
  average time/residue: 0.1274
  time to fit residues: 21.3460
Evaluate side-chains
  109 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  247 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.129880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.096907 restraints weight = 39785.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.72
r_work: 0.3244 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6840  Z= 0.184
  Angle     :  0.626  11.021   9326  Z= 0.320
  Chirality :  0.082   1.733   1158
  Planarity :  0.004   0.034   1128
  Dihedral  :  5.154  45.176    914
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.09 %
    Favored  : 90.34 %
  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:  0.55 (0.28), residues: 886
  helix:  1.18 (0.19), residues: 724
  sheet:  None (None), residues: 0
  loop : -3.41 (0.37), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  20 
 TYR   0.010   0.002   TYR A 187 
 PHE   0.014   0.001   PHE B 371 
 TRP   0.013   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 6840)
  covalent geometry    : angle       0.62611 ( 9326)
  hydrogen bonds       : bond        0.04562 (  512)
  hydrogen bonds       : angle       4.26609 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  118 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.7307 (mpp) cc_final: 0.6968 (mpp)
REVERT: B  131 MET cc_start: 0.7753 (mpp) cc_final: 0.7476 (mpp)
  outliers start: 4
  outliers final: 2
  residues processed: 114
  average time/residue: 0.1325
  time to fit residues: 22.2081
Evaluate side-chains
  106 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain B residue  144 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.135695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.104148 restraints weight = 39455.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.68
r_work: 0.3415 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6840  Z= 0.149
  Angle     :  0.580  11.056   9326  Z= 0.297
  Chirality :  0.081   1.723   1158
  Planarity :  0.004   0.036   1128
  Dihedral  :  4.377  24.717    908
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.94 %
    Favored  : 89.35 %
  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:  0.69 (0.28), residues: 886
  helix:  1.28 (0.19), residues: 724
  sheet:  None (None), residues: 0
  loop : -3.34 (0.38), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 252 
 TYR   0.006   0.001   TYR B 178 
 PHE   0.013   0.001   PHE B 100 
 TRP   0.013   0.001   TRP A 311 
 HIS   0.003   0.001   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6840)
  covalent geometry    : angle       0.58027 ( 9326)
  hydrogen bonds       : bond        0.04092 (  512)
  hydrogen bonds       : angle       4.11198 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.7320 (mpp) cc_final: 0.7044 (mpp)
REVERT: B  131 MET cc_start: 0.7585 (mpp) cc_final: 0.7363 (mpp)
  outliers start: 5
  outliers final: 3
  residues processed: 104
  average time/residue: 0.1268
  time to fit residues: 19.6419
Evaluate side-chains
  104 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain B residue  144 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 13 optimal weight:    8.9990
   chunk 46 optimal weight:    0.0000
   chunk 43 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.4788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.135310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.103843 restraints weight = 39903.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.67
r_work: 0.3410 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6840  Z= 0.142
  Angle     :  0.570  11.143   9326  Z= 0.290
  Chirality :  0.081   1.717   1158
  Planarity :  0.004   0.036   1128
  Dihedral  :  4.308  24.399    908
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.23 %
    Favored  : 89.20 %
  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:  0.80 (0.29), residues: 886
  helix:  1.37 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -3.52 (0.38), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 252 
 TYR   0.005   0.001   TYR A 178 
 PHE   0.011   0.001   PHE A 100 
 TRP   0.013   0.001   TRP A 311 
 HIS   0.002   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6840)
  covalent geometry    : angle       0.56987 ( 9326)
  hydrogen bonds       : bond        0.03874 (  512)
  hydrogen bonds       : angle       3.99848 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.7350 (mpp) cc_final: 0.7116 (mpp)
REVERT: B  131 MET cc_start: 0.7567 (mpp) cc_final: 0.7300 (mpp)
  outliers start: 4
  outliers final: 3
  residues processed: 109
  average time/residue: 0.1179
  time to fit residues: 18.9625
Evaluate side-chains
  105 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  144 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.136038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.104687 restraints weight = 39635.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.71
r_work: 0.3420 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6840  Z= 0.125
  Angle     :  0.559  11.036   9326  Z= 0.283
  Chirality :  0.080   1.710   1158
  Planarity :  0.004   0.036   1128
  Dihedral  :  4.284  24.633    908
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.51 %
    Favored  : 88.49 %
  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:  0.96 (0.29), residues: 886
  helix:  1.47 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -3.46 (0.38), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 252 
 TYR   0.004   0.001   TYR B 178 
 PHE   0.008   0.001   PHE A 396 
 TRP   0.013   0.001   TRP B 311 
 HIS   0.002   0.001   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6840)
  covalent geometry    : angle       0.55882 ( 9326)
  hydrogen bonds       : bond        0.03725 (  512)
  hydrogen bonds       : angle       3.92346 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  112 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.7355 (mpp) cc_final: 0.7135 (mpp)
REVERT: B  131 MET cc_start: 0.7564 (mpp) cc_final: 0.7303 (mpp)
REVERT: B  157 MET cc_start: 0.8142 (pmm) cc_final: 0.7721 (pmm)
REVERT: B  427 VAL cc_start: 0.6648 (OUTLIER) cc_final: 0.6333 (p)
  outliers start: 7
  outliers final: 6
  residues processed: 109
  average time/residue: 0.1345
  time to fit residues: 21.5908
Evaluate side-chains
  110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  427 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.130255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.097430 restraints weight = 39587.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.73
r_work: 0.3244 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6840  Z= 0.124
  Angle     :  0.556  11.093   9326  Z= 0.280
  Chirality :  0.081   1.713   1158
  Planarity :  0.004   0.037   1128
  Dihedral  :  4.250  24.504    908
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 11.08 %
    Favored  : 88.07 %
  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:  1.02 (0.29), residues: 886
  helix:  1.53 (0.20), residues: 728
  sheet:  None (None), residues: 0
  loop : -3.48 (0.37), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 252 
 TYR   0.005   0.001   TYR A 187 
 PHE   0.009   0.001   PHE A 100 
 TRP   0.013   0.001   TRP B 311 
 HIS   0.003   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6840)
  covalent geometry    : angle       0.55579 ( 9326)
  hydrogen bonds       : bond        0.03650 (  512)
  hydrogen bonds       : angle       3.87856 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.7478 (mpp) cc_final: 0.7202 (mpp)
REVERT: A  247 MET cc_start: 0.7675 (mmm) cc_final: 0.7361 (mmm)
REVERT: B  131 MET cc_start: 0.7568 (mpp) cc_final: 0.7282 (mpp)
REVERT: B  427 VAL cc_start: 0.6611 (OUTLIER) cc_final: 0.6301 (p)
  outliers start: 6
  outliers final: 5
  residues processed: 111
  average time/residue: 0.1290
  time to fit residues: 20.9768
Evaluate side-chains
  113 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  427 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.129818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.096569 restraints weight = 39936.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.80
r_work: 0.3224 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6840  Z= 0.138
  Angle     :  0.560  11.029   9326  Z= 0.284
  Chirality :  0.081   1.721   1158
  Planarity :  0.004   0.037   1128
  Dihedral  :  4.242  24.748    908
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.51 %
    Favored  : 88.49 %
  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:  1.09 (0.29), residues: 886
  helix:  1.57 (0.20), residues: 728
  sheet:  None (None), residues: 0
  loop : -3.45 (0.38), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 252 
 TYR   0.014   0.002   TYR A 187 
 PHE   0.009   0.001   PHE A 100 
 TRP   0.012   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6840)
  covalent geometry    : angle       0.55971 ( 9326)
  hydrogen bonds       : bond        0.03646 (  512)
  hydrogen bonds       : angle       3.87776 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  116 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.7491 (mpp) cc_final: 0.7205 (mpp)
REVERT: A  247 MET cc_start: 0.7685 (mmm) cc_final: 0.7382 (mmm)
REVERT: B  131 MET cc_start: 0.7566 (mpp) cc_final: 0.7264 (mpp)
REVERT: B  427 VAL cc_start: 0.6621 (OUTLIER) cc_final: 0.6297 (p)
  outliers start: 7
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1345
  time to fit residues: 22.5688
Evaluate side-chains
  115 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  427 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.129093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.095996 restraints weight = 39845.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.73
r_work: 0.3226 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6840  Z= 0.150
  Angle     :  0.572  10.972   9326  Z= 0.291
  Chirality :  0.081   1.718   1158
  Planarity :  0.004   0.037   1128
  Dihedral  :  4.247  24.849    908
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.80 %
    Favored  : 88.07 %
  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:  1.10 (0.29), residues: 886
  helix:  1.59 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -3.47 (0.38), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 252 
 TYR   0.008   0.001   TYR A 187 
 PHE   0.010   0.001   PHE B  98 
 TRP   0.012   0.001   TRP B 311 
 HIS   0.002   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6840)
  covalent geometry    : angle       0.57177 ( 9326)
  hydrogen bonds       : bond        0.03690 (  512)
  hydrogen bonds       : angle       3.91253 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  116 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.7494 (mpp) cc_final: 0.7207 (mpp)
REVERT: A  247 MET cc_start: 0.7735 (mmm) cc_final: 0.7428 (mmm)
REVERT: B  131 MET cc_start: 0.7545 (mpp) cc_final: 0.7231 (mpp)
REVERT: B  427 VAL cc_start: 0.6640 (OUTLIER) cc_final: 0.6324 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1296
  time to fit residues: 21.7253
Evaluate side-chains
  114 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  427 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.129880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.097543 restraints weight = 39500.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.63
r_work: 0.3244 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6840  Z= 0.125
  Angle     :  0.564  10.932   9326  Z= 0.286
  Chirality :  0.080   1.712   1158
  Planarity :  0.004   0.037   1128
  Dihedral  :  4.237  25.117    908
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.22 %
    Favored  : 87.64 %
  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:  1.18 (0.29), residues: 886
  helix:  1.63 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -3.50 (0.38), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 252 
 TYR   0.015   0.001   TYR A 187 
 PHE   0.007   0.001   PHE B  98 
 TRP   0.013   0.001   TRP B 311 
 HIS   0.002   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6840)
  covalent geometry    : angle       0.56445 ( 9326)
  hydrogen bonds       : bond        0.03624 (  512)
  hydrogen bonds       : angle       3.85266 ( 1536)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  181 is missing expected H atoms. Skipping.
Residue VAL  181 is missing expected H atoms. Skipping.
Evaluate side-chains
  116 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 MET cc_start: 0.7466 (mpp) cc_final: 0.7173 (mpp)
REVERT: A  247 MET cc_start: 0.7712 (mmm) cc_final: 0.7465 (mmm)
REVERT: A  427 VAL cc_start: 0.6414 (OUTLIER) cc_final: 0.6108 (p)
REVERT: B  131 MET cc_start: 0.7542 (mpp) cc_final: 0.7205 (mpp)
REVERT: B  427 VAL cc_start: 0.6633 (OUTLIER) cc_final: 0.6317 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1261
  time to fit residues: 21.5828
Evaluate side-chains
  115 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  427 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.129705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.096653 restraints weight = 40111.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.75
r_work: 0.3241 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6840  Z= 0.127
  Angle     :  0.566  10.926   9326  Z= 0.286
  Chirality :  0.081   1.714   1158
  Planarity :  0.004   0.037   1128
  Dihedral  :  4.213  24.831    908
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.65 %
    Favored  : 87.22 %
  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:  1.25 (0.29), residues: 886
  helix:  1.67 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -3.47 (0.39), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 252 
 TYR   0.013   0.001   TYR A 187 
 PHE   0.008   0.001   PHE B  98 
 TRP   0.013   0.001   TRP B 311 
 HIS   0.003   0.001   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6840)
  covalent geometry    : angle       0.56632 ( 9326)
  hydrogen bonds       : bond        0.03558 (  512)
  hydrogen bonds       : angle       3.82138 ( 1536)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3532.29 seconds
wall clock time: 60 minutes 21.72 seconds (3621.72 seconds total)