Starting phenix.real_space_refine
on Mon Nov 17 19:27:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uke_26578/11_2025/7uke_26578.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uke_26578/11_2025/7uke_26578.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uke_26578/11_2025/7uke_26578.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uke_26578/11_2025/7uke_26578.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uke_26578/11_2025/7uke_26578.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uke_26578/11_2025/7uke_26578.map"
  }
  resolution = 3.01
  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=   0.005 sd=   0.060
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
     K       4      8.98       5
     S      56      5.16       5
     C    5252      2.51       5
     N    1332      2.21       5
     O    1356      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8000
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1999
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 1999
          Classifications: {'peptide': 259}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 10, 'TRANS': 248}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {'  K': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.60, per 1000 atoms: 0.20
  Number of scatterers: 8000
  At special positions: 0
  Unit cell: (116.466, 116.466, 83.426, 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)
     K       4     19.00
     S      56     16.00
     O    1356      8.00
     N    1332      7.00
     C    5252      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: 0.66
  Conformation dependent library (CDL) restraints added in 393.7 milliseconds
  

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1952

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      84.3% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 177
    Processing helix  chain 'A' and resid 178 through 181
    Processing helix  chain 'A' and resid 182 through 205
    Processing helix  chain 'A' and resid 221 through 225
    Processing helix  chain 'A' and resid 225 through 250
    Processing helix  chain 'A' and resid 253 through 260
    Processing helix  chain 'A' and resid 260 through 279
      Proline residue:  A 272  - end of helix
    Processing helix  chain 'A' and resid 287 through 296
    Processing helix  chain 'A' and resid 297 through 307
      removed outlier: 3.578A  pdb=" N   ARG A 305 " --> pdb=" O   LYS A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 320
    Processing helix  chain 'A' and resid 320 through 347
    Processing helix  chain 'A' and resid 356 through 369
      removed outlier: 3.939A  pdb=" N   TRP A 362 " --> pdb=" O   PRO A 358 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   TYR A 363 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR A 369 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 398
    Processing helix  chain 'A' and resid 400 through 424
      removed outlier: 4.749A  pdb=" N   VAL A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 177
    Processing helix  chain 'B' and resid 178 through 181
    Processing helix  chain 'B' and resid 182 through 205
    Processing helix  chain 'B' and resid 221 through 225
    Processing helix  chain 'B' and resid 225 through 250
    Processing helix  chain 'B' and resid 253 through 260
    Processing helix  chain 'B' and resid 260 through 279
      Proline residue:  B 272  - end of helix
    Processing helix  chain 'B' and resid 287 through 296
    Processing helix  chain 'B' and resid 297 through 307
      removed outlier: 3.578A  pdb=" N   ARG B 305 " --> pdb=" O   LYS B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 320
    Processing helix  chain 'B' and resid 320 through 347
    Processing helix  chain 'B' and resid 356 through 369
      removed outlier: 3.939A  pdb=" N   TRP B 362 " --> pdb=" O   PRO B 358 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   TYR B 363 " --> pdb=" O   ALA B 359 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR B 369 " --> pdb=" O   ILE B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 398
    Processing helix  chain 'B' and resid 400 through 424
      removed outlier: 4.749A  pdb=" N   VAL B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 177
    Processing helix  chain 'C' and resid 178 through 181
    Processing helix  chain 'C' and resid 182 through 205
    Processing helix  chain 'C' and resid 221 through 225
    Processing helix  chain 'C' and resid 225 through 250
    Processing helix  chain 'C' and resid 253 through 260
    Processing helix  chain 'C' and resid 260 through 279
      Proline residue:  C 272  - end of helix
    Processing helix  chain 'C' and resid 287 through 296
    Processing helix  chain 'C' and resid 297 through 307
      removed outlier: 3.578A  pdb=" N   ARG C 305 " --> pdb=" O   LYS C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 320
    Processing helix  chain 'C' and resid 320 through 347
    Processing helix  chain 'C' and resid 356 through 369
      removed outlier: 3.939A  pdb=" N   TRP C 362 " --> pdb=" O   PRO C 358 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   TYR C 363 " --> pdb=" O   ALA C 359 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR C 369 " --> pdb=" O   ILE C 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 398
    Processing helix  chain 'C' and resid 400 through 424
      removed outlier: 4.749A  pdb=" N   VAL C 404 " --> pdb=" O   LEU C 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 177
    Processing helix  chain 'D' and resid 178 through 181
    Processing helix  chain 'D' and resid 182 through 205
    Processing helix  chain 'D' and resid 221 through 225
    Processing helix  chain 'D' and resid 225 through 250
    Processing helix  chain 'D' and resid 253 through 260
    Processing helix  chain 'D' and resid 260 through 279
      Proline residue:  D 272  - end of helix
    Processing helix  chain 'D' and resid 287 through 296
    Processing helix  chain 'D' and resid 297 through 307
      removed outlier: 3.578A  pdb=" N   ARG D 305 " --> pdb=" O   LYS D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 320
    Processing helix  chain 'D' and resid 320 through 347
    Processing helix  chain 'D' and resid 356 through 369
      removed outlier: 3.938A  pdb=" N   TRP D 362 " --> pdb=" O   PRO D 358 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   TYR D 363 " --> pdb=" O   ALA D 359 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR D 369 " --> pdb=" O   ILE D 365 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 380 through 398
    Processing helix  chain 'D' and resid 400 through 424
      removed outlier: 4.750A  pdb=" N   VAL D 404 " --> pdb=" O   LEU D 400 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210
      removed outlier: 7.413A  pdb=" N   LEU A 219 " --> pdb=" O   CYS A 209 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 210
      removed outlier: 7.413A  pdb=" N   LEU B 219 " --> pdb=" O   CYS B 209 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 208 through 210
      removed outlier: 7.414A  pdb=" N   LEU C 219 " --> pdb=" O   CYS C 209 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 208 through 210
      removed outlier: 7.413A  pdb=" N   LEU D 219 " --> pdb=" O   CYS D 209 " (cutoff:3.500A)

    629 hydrogen bonds defined for protein.
    1791 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: 1.23

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2436
        1.34 -     1.46: 1837
        1.46 -     1.58: 3827
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 8188
  Sorted by residual:
  bond pdb=" CA  ILE C 398 "
       pdb=" C   ILE C 398 "
    ideal  model  delta    sigma   weight residual
    1.518  1.530 -0.012 1.13e-02 7.83e+03 1.12e+00
  bond pdb=" CA  ILE A 398 "
       pdb=" C   ILE A 398 "
    ideal  model  delta    sigma   weight residual
    1.518  1.530 -0.012 1.13e-02 7.83e+03 1.10e+00
  bond pdb=" CA  ILE B 398 "
       pdb=" C   ILE B 398 "
    ideal  model  delta    sigma   weight residual
    1.518  1.530 -0.011 1.13e-02 7.83e+03 1.00e+00
  bond pdb=" CA  ILE D 398 "
       pdb=" C   ILE D 398 "
    ideal  model  delta    sigma   weight residual
    1.518  1.529 -0.011 1.13e-02 7.83e+03 9.57e-01
  bond pdb=" CA  VAL A 402 "
       pdb=" CB  VAL A 402 "
    ideal  model  delta    sigma   weight residual
    1.534  1.541 -0.006 6.80e-03 2.16e+04 8.62e-01
  ... (remaining 8183 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 10863
        1.60 -     3.20: 189
        3.20 -     4.80: 59
        4.80 -     6.41: 9
        6.41 -     8.01: 4
  Bond angle restraints: 11124
  Sorted by residual:
  angle pdb=" N   ILE C 398 "
        pdb=" CA  ILE C 398 "
        pdb=" C   ILE C 398 "
      ideal   model   delta    sigma   weight residual
     112.98  109.12    3.86 1.25e+00 6.40e-01 9.52e+00
  angle pdb=" N   ILE A 398 "
        pdb=" CA  ILE A 398 "
        pdb=" C   ILE A 398 "
      ideal   model   delta    sigma   weight residual
     112.98  109.19    3.79 1.25e+00 6.40e-01 9.19e+00
  angle pdb=" N   ILE B 398 "
        pdb=" CA  ILE B 398 "
        pdb=" C   ILE B 398 "
      ideal   model   delta    sigma   weight residual
     112.98  109.20    3.78 1.25e+00 6.40e-01 9.15e+00
  angle pdb=" N   ILE D 398 "
        pdb=" CA  ILE D 398 "
        pdb=" C   ILE D 398 "
      ideal   model   delta    sigma   weight residual
     112.98  109.20    3.78 1.25e+00 6.40e-01 9.13e+00
  angle pdb=" CA  LEU D 271 "
        pdb=" CB  LEU D 271 "
        pdb=" CG  LEU D 271 "
      ideal   model   delta    sigma   weight residual
     116.30  124.31   -8.01 3.50e+00 8.16e-02 5.23e+00
  ... (remaining 11119 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.04: 4144
       12.04 -    24.09: 408
       24.09 -    36.13: 196
       36.13 -    48.17: 32
       48.17 -    60.22: 12
  Dihedral angle restraints: 4792
    sinusoidal: 1760
      harmonic: 3032
  Sorted by residual:
  dihedral pdb=" CA  ASN A 408 "
           pdb=" CB  ASN A 408 "
           pdb=" CG  ASN A 408 "
           pdb=" OD1 ASN A 408 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -150.22   60.22     2      2.00e+01 2.50e-03 9.04e+00
  dihedral pdb=" CA  ASN D 408 "
           pdb=" CB  ASN D 408 "
           pdb=" CG  ASN D 408 "
           pdb=" OD1 ASN D 408 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -150.20   60.20     2      2.00e+01 2.50e-03 9.04e+00
  dihedral pdb=" CA  ASN B 408 "
           pdb=" CB  ASN B 408 "
           pdb=" CG  ASN B 408 "
           pdb=" OD1 ASN B 408 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -150.19   60.19     2      2.00e+01 2.50e-03 9.03e+00
  ... (remaining 4789 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 617
       0.024 -    0.047: 392
       0.047 -    0.071: 188
       0.071 -    0.095: 79
       0.095 -    0.118: 44
  Chirality restraints: 1320
  Sorted by residual:
  chirality pdb=" CA  VAL C 207 "
            pdb=" N   VAL C 207 "
            pdb=" C   VAL C 207 "
            pdb=" CB  VAL C 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.50e-01
  chirality pdb=" CA  THR B 370 "
            pdb=" N   THR B 370 "
            pdb=" C   THR B 370 "
            pdb=" CB  THR B 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.41    0.12 2.00e-01 2.50e+01 3.49e-01
  chirality pdb=" CA  VAL A 207 "
            pdb=" N   VAL A 207 "
            pdb=" C   VAL A 207 "
            pdb=" CB  VAL A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.44e-01
  ... (remaining 1317 not shown)

  Planarity restraints: 1360
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 271 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.87e+00
        pdb=" N   PRO D 272 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO D 272 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 272 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 271 "    0.043 5.00e-02 4.00e+02   6.54e-02 6.85e+00
        pdb=" N   PRO A 272 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 272 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 272 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 271 "   -0.043 5.00e-02 4.00e+02   6.53e-02 6.82e+00
        pdb=" N   PRO C 272 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C 272 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 272 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1357 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.74: 917
        2.74 -     3.34: 10239
        3.34 -     3.94: 15209
        3.94 -     4.54: 21443
        4.54 -     5.14: 31509
  Nonbonded interactions: 79317
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 319 "
            pdb=" OD1 ASN D 408 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OG  SER C 319 "
            pdb=" OD1 ASN C 408 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OG  SER B 319 "
            pdb=" OD1 ASN B 408 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OG  SER A 319 "
            pdb=" OD1 ASN A 408 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   SER B 410 "
            pdb=" ND1 HIS B 414 "
     model   vdw
     2.207 3.120
  ... (remaining 79312 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 166 through 424)
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             2.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.270
  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:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8188  Z= 0.152
  Angle     :  0.626   8.007  11124  Z= 0.353
  Chirality :  0.041   0.118   1320
  Planarity :  0.006   0.066   1360
  Dihedral  : 12.429  60.217   2840
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.28 (0.27), residues: 1028
  helix:  1.29 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop : -0.40 (0.46), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 296 
 TYR   0.008   0.001   TYR B 274 
 PHE   0.008   0.001   PHE D 329 
 TRP   0.012   0.002   TRP D 172 
 HIS   0.002   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8188)
  covalent geometry    : angle       0.62643 (11124)
  hydrogen bonds       : bond        0.13063 (  629)
  hydrogen bonds       : angle       4.89134 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 ARG cc_start: 0.7060 (mtp85) cc_final: 0.6692 (mtp180)
REVERT: A  326 PHE cc_start: 0.6874 (m-10) cc_final: 0.5859 (t80)
REVERT: A  421 LYS cc_start: 0.8500 (mmpt) cc_final: 0.8278 (tttt)
REVERT: B  420 ASP cc_start: 0.8004 (m-30) cc_final: 0.7738 (m-30)
REVERT: C  247 ARG cc_start: 0.6966 (mtp85) cc_final: 0.6515 (mtp180)
REVERT: D  420 ASP cc_start: 0.8016 (m-30) cc_final: 0.7753 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1081
  time to fit residues: 24.5228
Evaluate side-chains
  128 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 408 ASN
B 408 ASN
C 408 ASN
D 408 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.198181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.128309 restraints weight = 9445.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.44
r_work: 0.3428 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8188  Z= 0.195
  Angle     :  0.633   9.777  11124  Z= 0.322
  Chirality :  0.042   0.145   1320
  Planarity :  0.006   0.072   1360
  Dihedral  :  4.054  13.617   1148
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  8.53 %
    Favored  : 90.88 %
  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:  1.54 (0.26), residues: 1028
  helix:  1.46 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop : -0.24 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 305 
 TYR   0.011   0.001   TYR A 188 
 PHE   0.012   0.001   PHE A 193 
 TRP   0.016   0.002   TRP C 172 
 HIS   0.003   0.001   HIS D 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 8188)
  covalent geometry    : angle       0.63333 (11124)
  hydrogen bonds       : bond        0.04436 (  629)
  hydrogen bonds       : angle       4.22529 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 145
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 ARG cc_start: 0.6436 (mpt180) cc_final: 0.5907 (mmt180)
REVERT: A  326 PHE cc_start: 0.6842 (m-10) cc_final: 0.5417 (t80)
REVERT: B  273 TYR cc_start: 0.7995 (t80) cc_final: 0.7704 (t80)
REVERT: B  420 ASP cc_start: 0.8134 (m-30) cc_final: 0.7834 (m-30)
REVERT: C  183 MET cc_start: 0.5475 (pmm) cc_final: 0.4612 (mpp)
REVERT: C  256 ARG cc_start: 0.6495 (mpt180) cc_final: 0.5954 (mmt180)
REVERT: C  326 PHE cc_start: 0.6869 (m-10) cc_final: 0.5398 (t80)
REVERT: D  273 TYR cc_start: 0.7945 (t80) cc_final: 0.7680 (t80)
REVERT: D  420 ASP cc_start: 0.8123 (m-30) cc_final: 0.7823 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 145
  average time/residue: 0.0977
  time to fit residues: 19.0665
Evaluate side-chains
  133 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  350 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.1980
   chunk 92 optimal weight:    0.5980
   chunk 51 optimal weight:    0.1980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4384 r_free = 0.4384 target = 0.200829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.132058 restraints weight = 9398.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.43
r_work: 0.3476 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8188  Z= 0.130
  Angle     :  0.561   8.018  11124  Z= 0.285
  Chirality :  0.039   0.149   1320
  Planarity :  0.006   0.069   1360
  Dihedral  :  3.783  13.353   1148
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.49 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.26), residues: 1028
  helix:  1.77 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.09 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 311 
 TYR   0.012   0.001   TYR A 188 
 PHE   0.007   0.001   PHE B 257 
 TRP   0.012   0.002   TRP A 172 
 HIS   0.002   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8188)
  covalent geometry    : angle       0.56052 (11124)
  hydrogen bonds       : bond        0.03888 (  629)
  hydrogen bonds       : angle       3.97449 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.7234 (mmp) cc_final: 0.7018 (mmp)
REVERT: A  262 MET cc_start: 0.6734 (mpp) cc_final: 0.6531 (mpp)
REVERT: A  305 ARG cc_start: 0.5864 (mtp-110) cc_final: 0.5652 (mtm-85)
REVERT: B  273 TYR cc_start: 0.7950 (t80) cc_final: 0.7575 (t80)
REVERT: B  413 TYR cc_start: 0.6512 (t80) cc_final: 0.6202 (t80)
REVERT: B  414 HIS cc_start: 0.6473 (m90) cc_final: 0.6267 (m90)
REVERT: B  420 ASP cc_start: 0.8091 (m-30) cc_final: 0.7800 (m-30)
REVERT: C  183 MET cc_start: 0.5482 (pmm) cc_final: 0.4445 (mtt)
REVERT: C  238 MET cc_start: 0.7199 (mmp) cc_final: 0.6658 (mtm)
REVERT: D  413 TYR cc_start: 0.6533 (t80) cc_final: 0.6226 (t80)
REVERT: D  414 HIS cc_start: 0.6489 (m90) cc_final: 0.6274 (m90)
REVERT: D  420 ASP cc_start: 0.8095 (m-30) cc_final: 0.7808 (m-30)
  outliers start: 6
  outliers final: 3
  residues processed: 144
  average time/residue: 0.0881
  time to fit residues: 17.6201
Evaluate side-chains
  130 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 127
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  393 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 81 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0170
   chunk 20 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.4501 r_free = 0.4501 target = 0.208085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.141158 restraints weight = 9626.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 2.65
r_work: 0.3595 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8188  Z= 0.124
  Angle     :  0.537   8.698  11124  Z= 0.275
  Chirality :  0.038   0.133   1320
  Planarity :  0.006   0.068   1360
  Dihedral  :  3.672  13.188   1148
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.15 %
    Favored  : 85.55 %
  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:  2.31 (0.26), residues: 1028
  helix:  1.94 (0.18), residues: 788
  sheet:  None (None), residues: 0
  loop :  0.28 (0.43), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 247 
 TYR   0.013   0.001   TYR A 188 
 PHE   0.010   0.001   PHE B 257 
 TRP   0.012   0.002   TRP A 172 
 HIS   0.001   0.000   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8188)
  covalent geometry    : angle       0.53676 (11124)
  hydrogen bonds       : bond        0.03768 (  629)
  hydrogen bonds       : angle       3.87846 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: B  413 TYR cc_start: 0.6687 (t80) cc_final: 0.6413 (t80)
REVERT: B  420 ASP cc_start: 0.7953 (m-30) cc_final: 0.7600 (m-30)
REVERT: B  421 LYS cc_start: 0.7721 (tptt) cc_final: 0.7160 (ttpt)
REVERT: C  183 MET cc_start: 0.5556 (pmm) cc_final: 0.4648 (mtt)
REVERT: C  238 MET cc_start: 0.7292 (mmp) cc_final: 0.6814 (mtm)
REVERT: D  413 TYR cc_start: 0.6716 (t80) cc_final: 0.6454 (t80)
REVERT: D  420 ASP cc_start: 0.7946 (m-30) cc_final: 0.7583 (m-30)
REVERT: D  421 LYS cc_start: 0.7731 (tptt) cc_final: 0.7179 (ttpt)
  outliers start: 11
  outliers final: 9
  residues processed: 149
  average time/residue: 0.0773
  time to fit residues: 16.5032
Evaluate side-chains
  143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  328 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 37 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4487 r_free = 0.4487 target = 0.206330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.138562 restraints weight = 9511.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 2.49
r_work: 0.3608 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8188  Z= 0.141
  Angle     :  0.553   9.056  11124  Z= 0.283
  Chirality :  0.039   0.131   1320
  Planarity :  0.006   0.067   1360
  Dihedral  :  3.684  13.054   1148
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.00 %
    Favored  : 82.35 %
  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:  2.41 (0.26), residues: 1028
  helix:  1.97 (0.18), residues: 788
  sheet:  None (None), residues: 0
  loop :  0.47 (0.44), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 305 
 TYR   0.013   0.001   TYR C 188 
 PHE   0.013   0.001   PHE B 257 
 TRP   0.013   0.002   TRP A 172 
 HIS   0.002   0.000   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8188)
  covalent geometry    : angle       0.55283 (11124)
  hydrogen bonds       : bond        0.03883 (  629)
  hydrogen bonds       : angle       3.86203 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.7493 (mmp) cc_final: 0.6985 (mtm)
REVERT: A  346 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8181 (mm-30)
REVERT: B  273 TYR cc_start: 0.8079 (t80) cc_final: 0.7627 (t80)
REVERT: B  413 TYR cc_start: 0.6542 (t80) cc_final: 0.6306 (t80)
REVERT: B  420 ASP cc_start: 0.7950 (m-30) cc_final: 0.7674 (m-30)
REVERT: B  421 LYS cc_start: 0.7809 (tptt) cc_final: 0.7243 (ttpt)
REVERT: C  183 MET cc_start: 0.5569 (pmm) cc_final: 0.4639 (mtt)
REVERT: D  273 TYR cc_start: 0.8039 (t80) cc_final: 0.7640 (t80)
REVERT: D  413 TYR cc_start: 0.6601 (t80) cc_final: 0.6358 (t80)
REVERT: D  420 ASP cc_start: 0.7928 (m-30) cc_final: 0.7653 (m-30)
REVERT: D  421 LYS cc_start: 0.7826 (tptt) cc_final: 0.7269 (ttpt)
  outliers start: 14
  outliers final: 10
  residues processed: 145
  average time/residue: 0.0836
  time to fit residues: 16.9958
Evaluate side-chains
  146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  393 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 84 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.4466 r_free = 0.4466 target = 0.204249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.134988 restraints weight = 9458.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.46
r_work: 0.3561 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8188  Z= 0.195
  Angle     :  0.588   7.535  11124  Z= 0.303
  Chirality :  0.040   0.127   1320
  Planarity :  0.006   0.064   1360
  Dihedral  :  3.836  13.093   1148
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.30 %
    Favored  : 80.81 %
  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:  2.21 (0.26), residues: 1028
  helix:  1.81 (0.18), residues: 788
  sheet:  None (None), residues: 0
  loop :  0.48 (0.45), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 305 
 TYR   0.016   0.002   TYR C 188 
 PHE   0.013   0.001   PHE B 257 
 TRP   0.013   0.002   TRP A 172 
 HIS   0.002   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 8188)
  covalent geometry    : angle       0.58832 (11124)
  hydrogen bonds       : bond        0.04220 (  629)
  hydrogen bonds       : angle       3.97475 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.7509 (mmp) cc_final: 0.6943 (mtm)
REVERT: B  262 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5715 (mmp)
REVERT: B  413 TYR cc_start: 0.6623 (t80) cc_final: 0.6409 (t80)
REVERT: B  420 ASP cc_start: 0.7928 (m-30) cc_final: 0.7672 (m-30)
REVERT: C  183 MET cc_start: 0.5572 (pmm) cc_final: 0.4639 (mtm)
REVERT: C  238 MET cc_start: 0.7661 (mmp) cc_final: 0.7144 (mtm)
REVERT: D  273 TYR cc_start: 0.8204 (t80) cc_final: 0.7871 (t80)
REVERT: D  413 TYR cc_start: 0.6595 (t80) cc_final: 0.6384 (t80)
REVERT: D  414 HIS cc_start: 0.6665 (m90) cc_final: 0.6461 (m90)
REVERT: D  420 ASP cc_start: 0.7917 (m-30) cc_final: 0.7667 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 142
  average time/residue: 0.0744
  time to fit residues: 15.1041
Evaluate side-chains
  146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 ARG
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain C residue  256 ARG
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  393 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0770
   chunk 54 optimal weight:    0.0370
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.5616

-------------------------------------------------------------------------------
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 = 0.4201 r_free = 0.4201 target = 0.194462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.148652 restraints weight = 9672.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 1.66
r_work: 0.3384 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8188  Z= 0.128
  Angle     :  0.542   8.327  11124  Z= 0.278
  Chirality :  0.038   0.132   1320
  Planarity :  0.006   0.066   1360
  Dihedral  :  3.665  12.686   1148
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 18.13 %
    Favored  : 80.21 %
  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:  2.57 (0.26), residues: 1028
  helix:  2.08 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.59 (0.44), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 305 
 TYR   0.012   0.001   TYR D 188 
 PHE   0.014   0.001   PHE D 257 
 TRP   0.013   0.002   TRP A 172 
 HIS   0.002   0.000   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8188)
  covalent geometry    : angle       0.54195 (11124)
  hydrogen bonds       : bond        0.03768 (  629)
  hydrogen bonds       : angle       3.84243 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.7464 (mmp) cc_final: 0.7033 (mtm)
REVERT: A  346 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8242 (mm-30)
REVERT: B  262 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5486 (mmp)
REVERT: B  420 ASP cc_start: 0.7684 (m-30) cc_final: 0.7464 (m-30)
REVERT: B  421 LYS cc_start: 0.7832 (tptt) cc_final: 0.7267 (ttpt)
REVERT: C  183 MET cc_start: 0.5628 (pmm) cc_final: 0.4827 (mtt)
REVERT: C  238 MET cc_start: 0.7507 (mmp) cc_final: 0.7104 (mtm)
REVERT: D  273 TYR cc_start: 0.8019 (t80) cc_final: 0.7636 (t80)
REVERT: D  420 ASP cc_start: 0.7667 (m-30) cc_final: 0.7453 (m-30)
REVERT: D  421 LYS cc_start: 0.7812 (tptt) cc_final: 0.7278 (ttpt)
  outliers start: 14
  outliers final: 12
  residues processed: 144
  average time/residue: 0.0789
  time to fit residues: 16.3365
Evaluate side-chains
  149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue  256 ARG
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  393 SER
Chi-restraints excluded: chain D residue  185 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0970
   chunk 99 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0980
   chunk 67 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.4490 r_free = 0.4490 target = 0.206604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.147166 restraints weight = 9435.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 2.29
r_work: 0.3612 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8188  Z= 0.120
  Angle     :  0.520   6.583  11124  Z= 0.269
  Chirality :  0.038   0.134   1320
  Planarity :  0.006   0.065   1360
  Dihedral  :  3.574  12.445   1148
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.65 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.26), residues: 1028
  helix:  2.19 (0.18), residues: 788
  sheet:  None (None), residues: 0
  loop :  0.62 (0.45), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 305 
 TYR   0.024   0.001   TYR B 273 
 PHE   0.014   0.001   PHE B 257 
 TRP   0.012   0.001   TRP A 172 
 HIS   0.001   0.000   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8188)
  covalent geometry    : angle       0.52042 (11124)
  hydrogen bonds       : bond        0.03653 (  629)
  hydrogen bonds       : angle       3.76724 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  238 MET cc_start: 0.7303 (mmp) cc_final: 0.6811 (mtm)
REVERT: A  256 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.5959 (mmt180)
REVERT: A  346 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8170 (mm-30)
REVERT: B  413 TYR cc_start: 0.6606 (t80) cc_final: 0.6339 (t80)
REVERT: B  420 ASP cc_start: 0.7715 (m-30) cc_final: 0.7490 (m-30)
REVERT: B  421 LYS cc_start: 0.7750 (tptt) cc_final: 0.7224 (ttpt)
REVERT: C  183 MET cc_start: 0.5553 (pmm) cc_final: 0.4687 (mtt)
REVERT: C  238 MET cc_start: 0.7407 (mmp) cc_final: 0.6923 (mtm)
REVERT: C  256 ARG cc_start: 0.6430 (mpt180) cc_final: 0.5964 (mmt180)
REVERT: D  420 ASP cc_start: 0.7719 (m-30) cc_final: 0.7493 (m-30)
REVERT: D  421 LYS cc_start: 0.7801 (tptt) cc_final: 0.7297 (ttpt)
  outliers start: 14
  outliers final: 13
  residues processed: 150
  average time/residue: 0.0716
  time to fit residues: 15.5250
Evaluate side-chains
  155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  256 ARG
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  393 SER
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  402 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 20 optimal weight:    0.4980
   chunk 39 optimal weight:    9.9990
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0060
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0470
   chunk 75 optimal weight:   10.0000
   overall best weight:    0.4494

-------------------------------------------------------------------------------
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 = 0.4499 r_free = 0.4499 target = 0.207669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.141586 restraints weight = 9365.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 2.39
r_work: 0.3639 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8188  Z= 0.120
  Angle     :  0.528   8.485  11124  Z= 0.273
  Chirality :  0.038   0.134   1320
  Planarity :  0.005   0.065   1360
  Dihedral  :  3.545  13.123   1148
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 17.18 %
    Favored  : 81.04 %
  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:  2.79 (0.26), residues: 1028
  helix:  2.24 (0.18), residues: 788
  sheet:  None (None), residues: 0
  loop :  0.64 (0.45), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 305 
 TYR   0.021   0.001   TYR B 273 
 PHE   0.016   0.001   PHE D 257 
 TRP   0.011   0.001   TRP A 172 
 HIS   0.001   0.000   HIS D 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8188)
  covalent geometry    : angle       0.52754 (11124)
  hydrogen bonds       : bond        0.03634 (  629)
  hydrogen bonds       : angle       3.74368 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  238 MET cc_start: 0.7483 (mmp) cc_final: 0.6922 (mtm)
REVERT: A  256 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5966 (mmt180)
REVERT: A  346 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8332 (mm-30)
REVERT: B  420 ASP cc_start: 0.7808 (m-30) cc_final: 0.7581 (m-30)
REVERT: B  421 LYS cc_start: 0.7823 (tptt) cc_final: 0.7293 (ttpt)
REVERT: C  183 MET cc_start: 0.5562 (pmm) cc_final: 0.4713 (mtt)
REVERT: C  238 MET cc_start: 0.7580 (mmp) cc_final: 0.7027 (mtm)
REVERT: C  256 ARG cc_start: 0.6484 (mpt180) cc_final: 0.5921 (mmt180)
REVERT: D  273 TYR cc_start: 0.7978 (t80) cc_final: 0.7557 (t80)
REVERT: D  420 ASP cc_start: 0.7839 (m-30) cc_final: 0.7605 (m-30)
REVERT: D  421 LYS cc_start: 0.7854 (tptt) cc_final: 0.7407 (ttpt)
  outliers start: 15
  outliers final: 13
  residues processed: 145
  average time/residue: 0.0801
  time to fit residues: 16.7158
Evaluate side-chains
  150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  256 ARG
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  393 SER
Chi-restraints excluded: chain D residue  185 LEU
Chi-restraints excluded: chain D residue  402 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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 = 0.4424 r_free = 0.4424 target = 0.200225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.136044 restraints weight = 9252.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 2.26
r_work: 0.3526 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   8188  Z= 0.289
  Angle     :  0.646   8.675  11124  Z= 0.337
  Chirality :  0.044   0.143   1320
  Planarity :  0.006   0.061   1360
  Dihedral  :  3.972  15.050   1148
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.94 %
    Favored  : 81.16 %
  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:  2.09 (0.26), residues: 1028
  helix:  1.75 (0.18), residues: 780
  sheet:  None (None), residues: 0
  loop :  0.39 (0.44), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 256 
 TYR   0.024   0.002   TYR B 273 
 PHE   0.015   0.002   PHE C 257 
 TRP   0.007   0.002   TRP A 172 
 HIS   0.003   0.001   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00710 ( 8188)
  covalent geometry    : angle       0.64557 (11124)
  hydrogen bonds       : bond        0.04634 (  629)
  hydrogen bonds       : angle       4.12944 ( 1791)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  238 MET cc_start: 0.7588 (mmp) cc_final: 0.6995 (mtm)
REVERT: B  262 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5818 (mmp)
REVERT: B  420 ASP cc_start: 0.7955 (m-30) cc_final: 0.7745 (m-30)
REVERT: C  183 MET cc_start: 0.5589 (pmm) cc_final: 0.4692 (mtm)
REVERT: C  238 MET cc_start: 0.7698 (mmp) cc_final: 0.7142 (mtm)
REVERT: D  420 ASP cc_start: 0.7936 (m-30) cc_final: 0.7726 (m-30)
  outliers start: 16
  outliers final: 14
  residues processed: 146
  average time/residue: 0.0715
  time to fit residues: 15.5065
Evaluate side-chains
  146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  256 ARG
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  393 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain C residue  256 ARG
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  393 SER
Chi-restraints excluded: chain D residue  402 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 34 optimal weight:    0.2980
   chunk 81 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0370
   chunk 21 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.4858

-------------------------------------------------------------------------------
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 = 0.4196 r_free = 0.4196 target = 0.194151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.134865 restraints weight = 9499.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.13
r_work: 0.3256 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8188  Z= 0.126
  Angle     :  0.572  12.332  11124  Z= 0.289
  Chirality :  0.039   0.136   1320
  Planarity :  0.006   0.063   1360
  Dihedral  :  3.689  14.138   1148
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 17.89 %
    Favored  : 81.04 %
  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:  2.50 (0.26), residues: 1028
  helix:  2.06 (0.18), residues: 780
  sheet:  None (None), residues: 0
  loop :  0.46 (0.44), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 305 
 TYR   0.029   0.001   TYR B 273 
 PHE   0.013   0.001   PHE D 257 
 TRP   0.015   0.002   TRP A 172 
 HIS   0.002   0.000   HIS C 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8188)
  covalent geometry    : angle       0.57211 (11124)
  hydrogen bonds       : bond        0.03825 (  629)
  hydrogen bonds       : angle       3.88992 ( 1791)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2807.70 seconds
wall clock time: 48 minutes 41.68 seconds (2921.68 seconds total)