Starting phenix.real_space_refine
on Tue Feb  3 16:48:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hix_52205/02_2026/9hix_52205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hix_52205/02_2026/9hix_52205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hix_52205/02_2026/9hix_52205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hix_52205/02_2026/9hix_52205.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hix_52205/02_2026/9hix_52205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hix_52205/02_2026/9hix_52205.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      33      5.16       5
     Cl      2      4.86       5
     C    3310      2.51       5
     N     870      2.21       5
     O     965      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5180
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 2260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2260
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 276, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 261}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 2267
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 284, 2261
          Classifications: {'peptide': 284}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 265}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 284, 2261
          Classifications: {'peptide': 284}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 265}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 2309
    Chain: "J"
      Number of atoms: 82
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 41
          Unusual residues: {'V0G': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 41
          Unusual residues: {'V0G': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "I"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 25
          Classifications: {'water': 25}
          Link IDs: {None: 24}
    Chain: "J"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 26
          Classifications: {'water': 26}
          Link IDs: {None: 25}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ACYS J 312 " occ=0.59
      ... (10 atoms not shown)
      pdb=" SG BCYS J 312 " occ=0.41
    residue:
      pdb=" C02AV0G J 401 " occ=0.81
      ... (80 atoms not shown)
      pdb="CL01BV0G J 401 " occ=0.19
  Time building chain proxies: 1.49, per 1000 atoms: 0.29
  Number of scatterers: 5180
  At special positions: 0
  Unit cell: (85.248, 95.616, 66.816, 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)
     Cl      2     17.00
     S      33     16.00
     O     965      8.00
     N     870      7.00
     C    3310      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 500.3 milliseconds
  

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1190

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      61.6% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'H' and resid 262 through 266
    Processing helix  chain 'H' and resid 270 through 275
      removed outlier: 3.587A  pdb=" N   VAL H 275 " --> pdb=" O   LEU H 272 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 279 through 286
    Processing helix  chain 'H' and resid 288 through 302
      removed outlier: 3.852A  pdb=" N   ALA H 292 " --> pdb=" O   THR H 288 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1 through 4
      removed outlier: 3.605A  pdb=" N   ASN I   4 " --> pdb=" O   MET I   1 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 1 through 4'
    Processing helix  chain 'I' and resid 5 through 11
    Processing helix  chain 'I' and resid 15 through 36
      removed outlier: 3.666A  pdb=" N   LEU I  19 " --> pdb=" O   SER I  15 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 49 through 70
      removed outlier: 3.653A  pdb=" N   VAL I  70 " --> pdb=" O   GLU I  66 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 76 through 91
    Processing helix  chain 'I' and resid 100 through 116
      removed outlier: 3.835A  pdb=" N   LEU I 106 " --> pdb=" O   ARG I 102 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 121 through 127
    Processing helix  chain 'I' and resid 132 through 154
      removed outlier: 4.738A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   LEU I 149 " --> pdb=" O   GLU I 145 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 163 through 178
    Processing helix  chain 'I' and resid 183 through 186
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.597A  pdb=" N   LEU I 200 " --> pdb=" O   ASN I 196 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   THR I 201 " --> pdb=" O   ARG I 197 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 224
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.613A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 241 through 261
    Processing helix  chain 'I' and resid 266 through 283
    Processing helix  chain 'J' and resid 56 through 67
    Processing helix  chain 'J' and resid 98 through 104
    Processing helix  chain 'J' and resid 110 through 131
      removed outlier: 3.575A  pdb=" N   HIS J 131 " --> pdb=" O   TYR J 127 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 155 through 159
      removed outlier: 4.442A  pdb=" N   LEU J 158 " --> pdb=" O   ASP J 155 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 175 through 179
    Processing helix  chain 'J' and resid 180 through 185
    Processing helix  chain 'J' and resid 192 through 209
      removed outlier: 3.600A  pdb=" N   ALA J 198 " --> pdb=" O   VAL J 194 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 217 through 230
    Processing helix  chain 'J' and resid 239 through 243
      removed outlier: 3.728A  pdb=" N   LEU J 243 " --> pdb=" O   MET J 240 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 256 through 261
    Processing helix  chain 'J' and resid 265 through 276
    Processing helix  chain 'J' and resid 285 through 291
    Processing helix  chain 'J' and resid 292 through 297
      removed outlier: 3.914A  pdb=" N   SER J 296 " --> pdb=" O   MET J 292 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 303 through 307
    Processing sheet with id=AA1, first strand: chain 'J' and resid 19 through 20
      removed outlier: 5.200A  pdb=" N   ILE J  87 " --> pdb=" O   ILE J  43 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   LEU J  77 " --> pdb=" O   ASP J  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97
    Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134

    267 hydrogen bonds defined for protein.
    747 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.87

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 816
        1.31 -     1.44: 1418
        1.44 -     1.56: 2960
        1.56 -     1.69: 0
        1.69 -     1.81: 53
  Bond restraints: 5247
  Sorted by residual:
  bond pdb=" C11AV0G J 401 "
       pdb=" N10AV0G J 401 "
    ideal  model  delta    sigma   weight residual
    1.358  1.468 -0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" C05BV0G J 401 "
       pdb=" N06BV0G J 401 "
    ideal  model  delta    sigma   weight residual
    1.362  1.469 -0.107 2.00e-02 2.50e+03 2.88e+01
  bond pdb=" C11BV0G J 401 "
       pdb=" N10BV0G J 401 "
    ideal  model  delta    sigma   weight residual
    1.358  1.464 -0.106 2.00e-02 2.50e+03 2.83e+01
  bond pdb=" C05AV0G J 401 "
       pdb=" N06AV0G J 401 "
    ideal  model  delta    sigma   weight residual
    1.362  1.468 -0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" C17AV0G J 401 "
       pdb=" N16AV0G J 401 "
    ideal  model  delta    sigma   weight residual
    1.363  1.463 -0.100 2.00e-02 2.50e+03 2.49e+01
  ... (remaining 5242 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 6997
        2.30 -     4.61: 82
        4.61 -     6.91: 17
        6.91 -     9.21: 1
        9.21 -    11.52: 3
  Bond angle restraints: 7100
  Sorted by residual:
  angle pdb=" C15AV0G J 401 "
        pdb=" N16AV0G J 401 "
        pdb=" C17AV0G J 401 "
      ideal   model   delta    sigma   weight residual
     129.65  118.13   11.52 3.00e+00 1.11e-01 1.47e+01
  angle pdb=" C09BV0G J 401 "
        pdb=" N10BV0G J 401 "
        pdb=" C11BV0G J 401 "
      ideal   model   delta    sigma   weight residual
     129.31  119.57    9.74 3.00e+00 1.11e-01 1.06e+01
  angle pdb=" C15BV0G J 401 "
        pdb=" N16BV0G J 401 "
        pdb=" C17BV0G J 401 "
      ideal   model   delta    sigma   weight residual
     129.65  120.39    9.26 3.00e+00 1.11e-01 9.53e+00
  angle pdb=" C18AV0G J 401 "
        pdb=" C17AV0G J 401 "
        pdb=" N16AV0G J 401 "
      ideal   model   delta    sigma   weight residual
     114.00  121.20   -7.20 3.00e+00 1.11e-01 5.76e+00
  angle pdb=" CB  MET J 196 "
        pdb=" CG  MET J 196 "
        pdb=" SD  MET J 196 "
      ideal   model   delta    sigma   weight residual
     112.70  119.59   -6.89 3.00e+00 1.11e-01 5.27e+00
  ... (remaining 7095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 2720
       17.07 -    34.14: 315
       34.14 -    51.21: 88
       51.21 -    68.28: 20
       68.28 -    85.35: 7
  Dihedral angle restraints: 3150
    sinusoidal: 1315
      harmonic: 1835
  Sorted by residual:
  dihedral pdb=" CA  ASP J 216 "
           pdb=" CB  ASP J 216 "
           pdb=" CG  ASP J 216 "
           pdb=" OD1 ASP J 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.36   59.36     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CB  GLU I 185 "
           pdb=" CG  GLU I 185 "
           pdb=" CD  GLU I 185 "
           pdb=" OE1 GLU I 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.35   85.35     1      3.00e+01 1.11e-03 9.80e+00
  dihedral pdb=" CB  GLU I 147 "
           pdb=" CG  GLU I 147 "
           pdb=" CD  GLU I 147 "
           pdb=" OE1 GLU I 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.77   84.77     1      3.00e+01 1.11e-03 9.69e+00
  ... (remaining 3147 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 450
       0.025 -    0.050: 188
       0.050 -    0.075: 79
       0.075 -    0.100: 36
       0.100 -    0.125: 19
  Chirality restraints: 772
  Sorted by residual:
  chirality pdb=" CA  ILE J 255 "
            pdb=" N   ILE J 255 "
            pdb=" C   ILE J 255 "
            pdb=" CB  ILE J 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  VAL J 210 "
            pdb=" N   VAL J 210 "
            pdb=" C   VAL J 210 "
            pdb=" CB  VAL J 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.88e-01
  chirality pdb=" CA  VAL I 120 "
            pdb=" N   VAL I 120 "
            pdb=" C   VAL I 120 "
            pdb=" CB  VAL I 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.67e-01
  ... (remaining 769 not shown)

  Planarity restraints: 903
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS J 139 "    0.023 5.00e-02 4.00e+02   3.54e-02 2.00e+00
        pdb=" N   PRO J 140 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO J 140 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO J 140 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU I  49 "    0.023 5.00e-02 4.00e+02   3.47e-02 1.93e+00
        pdb=" N   PRO I  50 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO I  50 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO I  50 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS J  71 "   -0.021 5.00e-02 4.00e+02   3.17e-02 1.60e+00
        pdb=" N   PRO J  72 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO J  72 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO J  72 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 900 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 296
        2.73 -     3.28: 5018
        3.28 -     3.82: 9058
        3.82 -     4.36: 11240
        4.36 -     4.90: 18367
  Nonbonded interactions: 43979
  Sorted by model distance:
  nonbonded pdb=" O   ASP J 137 "
            pdb=" ND2 ASN J 142 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" O   HOH J 507 "
            pdb=" O   HOH J 514 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   TRP I  11 "
            pdb=" O   HOH I 401 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OH  TYR J 294 "
            pdb=" O   HOH J 501 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" NZ  LYS I 114 "
            pdb=" O   ILE J  55 "
     model   vdw
     2.302 3.120
  ... (remaining 43974 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.19 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.730
  Find NCS groups from input model:        0.030
  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:11.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
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      :  0.006   0.110   5249  Z= 0.289
  Angle     :  0.623  11.516   7100  Z= 0.267
  Chirality :  0.038   0.125    772
  Planarity :  0.004   0.035    903
  Dihedral  : 16.092  85.349   1960
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.15 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 19.20 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.82 (0.34), residues: 612
  helix:  2.29 (0.29), residues: 332
  sheet: -0.98 (0.93), residues: 22
  loop :  0.01 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  77 
 TYR   0.013   0.001   TYR I  91 
 PHE   0.009   0.001   PHE I 110 
 TRP   0.006   0.001   TRP I  11 
 HIS   0.002   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 5247)
  covalent geometry    : angle       0.62270 ( 7100)
  hydrogen bonds       : bond        0.13514 (  267)
  hydrogen bonds       : angle       5.34472 (  747)
  Misc. bond           : bond        0.03614 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: H  295 ARG cc_start: 0.7967 (ttt180) cc_final: 0.7757 (ttt-90)
REVERT: I   61 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7269 (tt0)
REVERT: I   62 LYS cc_start: 0.8145 (mppt) cc_final: 0.7888 (ttpp)
REVERT: I   63 ARG cc_start: 0.8041 (mmp80) cc_final: 0.7441 (mtp-110)
REVERT: I  102 ARG cc_start: 0.7961 (tpt90) cc_final: 0.7492 (ttm110)
REVERT: J  160 LYS cc_start: 0.8312 (tptt) cc_final: 0.7941 (tppt)
REVERT: J  188 ARG cc_start: 0.7672 (mpt180) cc_final: 0.7283 (mmm160)
REVERT: J  234 GLU cc_start: 0.7036 (tp30) cc_final: 0.6380 (mm-30)
REVERT: J  240 MET cc_start: 0.6399 (mtp) cc_final: 0.6003 (mmt)
REVERT: J  241 CYS cc_start: 0.6943 (m) cc_final: 0.6668 (p)
REVERT: J  298 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.7051 (mpp-170)
  outliers start: 5
  outliers final: 3
  residues processed: 91
  average time/residue: 0.6933
  time to fit residues: 65.1246
Evaluate side-chains
  91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain J residue   92 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
J 297 ASN
J 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.154066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.130387 restraints weight = 10090.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.69
r_work: 0.3245 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.0599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5249  Z= 0.107
  Angle     :  0.488   5.987   7100  Z= 0.245
  Chirality :  0.039   0.133    772
  Planarity :  0.004   0.036    903
  Dihedral  :  6.437  58.208    712
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.15 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.49 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.34), residues: 612
  helix:  2.27 (0.29), residues: 336
  sheet:  0.59 (1.23), residues: 12
  loop :  0.03 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  77 
 TYR   0.016   0.001   TYR I  91 
 PHE   0.010   0.001   PHE I 194 
 TRP   0.005   0.001   TRP J 237 
 HIS   0.003   0.001   HIS I  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 5247)
  covalent geometry    : angle       0.48806 ( 7100)
  hydrogen bonds       : bond        0.04105 (  267)
  hydrogen bonds       : angle       4.52555 (  747)
  Misc. bond           : bond        0.00043 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: H  295 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7803 (ttt-90)
REVERT: I   63 ARG cc_start: 0.8123 (mmp80) cc_final: 0.7376 (mtp-110)
REVERT: I   75 MET cc_start: 0.8432 (ttt) cc_final: 0.8050 (mtp)
REVERT: I  102 ARG cc_start: 0.8117 (tpt90) cc_final: 0.7591 (ttm110)
REVERT: I  244 CYS cc_start: 0.7340 (OUTLIER) cc_final: 0.5909 (t)
REVERT: J   78 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7706 (mp)
REVERT: J  160 LYS cc_start: 0.8431 (tptt) cc_final: 0.7998 (tppt)
REVERT: J  188 ARG cc_start: 0.7789 (mpt180) cc_final: 0.7220 (mmm160)
REVERT: J  241 CYS cc_start: 0.7053 (m) cc_final: 0.6818 (p)
REVERT: J  298 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.7215 (mpp-170)
  outliers start: 10
  outliers final: 4
  residues processed: 91
  average time/residue: 0.6911
  time to fit residues: 64.9712
Evaluate side-chains
  92 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  244 CYS
Chi-restraints excluded: chain I residue  278 GLU
Chi-restraints excluded: chain J residue   78 LEU
Chi-restraints excluded: chain J residue  219 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 59 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
J 236 GLN
J 297 ASN
J 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.149767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.124831 restraints weight = 8645.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.72
r_work: 0.3213 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3063
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3063 r_free = 0.3063    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.0946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   5249  Z= 0.175
  Angle     :  0.575   6.767   7100  Z= 0.292
  Chirality :  0.044   0.148    772
  Planarity :  0.005   0.039    903
  Dihedral  :  6.176  52.611    707
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.47 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 15.40 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.36 (0.33), residues: 612
  helix:  1.83 (0.28), residues: 336
  sheet:  0.54 (1.22), residues: 12
  loop : -0.25 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J 283 
 TYR   0.020   0.002   TYR I  91 
 PHE   0.016   0.002   PHE I 194 
 TRP   0.009   0.002   TRP J 237 
 HIS   0.005   0.002   HIS I  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 5247)
  covalent geometry    : angle       0.57454 ( 7100)
  hydrogen bonds       : bond        0.05039 (  267)
  hydrogen bonds       : angle       4.65406 (  747)
  Misc. bond           : bond        0.00021 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.129 
Fit side-chains
REVERT: H  265 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7311 (mmm)
REVERT: I  138 LYS cc_start: 0.7007 (tptp) cc_final: 0.6804 (tptp)
REVERT: I  244 CYS cc_start: 0.7340 (OUTLIER) cc_final: 0.5908 (t)
REVERT: J  298 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.7143 (mpp-170)
  outliers start: 16
  outliers final: 7
  residues processed: 93
  average time/residue: 0.6450
  time to fit residues: 61.9998
Evaluate side-chains
  94 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  265 MET
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  244 CYS
Chi-restraints excluded: chain I residue  278 GLU
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  219 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0170
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.1222

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

Flipped N/Q/H residues before XYZ refinement:
J 297 ASN
J 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.151647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.127393 restraints weight = 11965.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.15
r_work: 0.3195 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.0936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5249  Z= 0.119
  Angle     :  0.506   6.424   7100  Z= 0.257
  Chirality :  0.040   0.141    772
  Planarity :  0.004   0.038    903
  Dihedral  :  5.858  52.631    707
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.31 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.85 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.66 (0.34), residues: 612
  helix:  2.06 (0.29), residues: 333
  sheet:  0.45 (1.22), residues: 12
  loop : -0.06 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  77 
 TYR   0.017   0.001   TYR I  91 
 PHE   0.010   0.001   PHE I 194 
 TRP   0.006   0.001   TRP I  11 
 HIS   0.003   0.001   HIS I  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5247)
  covalent geometry    : angle       0.50605 ( 7100)
  hydrogen bonds       : bond        0.04200 (  267)
  hydrogen bonds       : angle       4.43244 (  747)
  Misc. bond           : bond        0.00016 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.125 
Fit side-chains
REVERT: H  254 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7988 (tp30)
REVERT: I   61 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7452 (tt0)
REVERT: I   63 ARG cc_start: 0.8044 (mmp80) cc_final: 0.7336 (mtp-110)
REVERT: J  298 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7080 (mpp-170)
  outliers start: 11
  outliers final: 6
  residues processed: 92
  average time/residue: 0.6634
  time to fit residues: 63.3011
Evaluate side-chains
  94 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  244 CYS
Chi-restraints excluded: chain I residue  278 GLU
Chi-restraints excluded: chain J residue  219 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0980
   chunk 17 optimal weight:    0.5980
   chunk 2 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
J 297 ASN
J 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.153853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.130261 restraints weight = 9592.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.56
r_work: 0.3241 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5249  Z= 0.095
  Angle     :  0.469   6.155   7100  Z= 0.238
  Chirality :  0.039   0.132    772
  Planarity :  0.004   0.038    903
  Dihedral  :  5.493  51.732    707
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.31 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.93 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.92 (0.34), residues: 612
  helix:  2.29 (0.29), residues: 333
  sheet:  0.64 (1.24), residues: 12
  loop :  0.02 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  77 
 TYR   0.014   0.001   TYR I  91 
 PHE   0.010   0.001   PHE I 110 
 TRP   0.005   0.001   TRP I  11 
 HIS   0.002   0.001   HIS J  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 5247)
  covalent geometry    : angle       0.46944 ( 7100)
  hydrogen bonds       : bond        0.03637 (  267)
  hydrogen bonds       : angle       4.25138 (  747)
  Misc. bond           : bond        0.00014 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.207 
Fit side-chains
REVERT: H  254 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8057 (tp30)
REVERT: H  265 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7320 (mmm)
REVERT: I   61 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7250 (tp30)
REVERT: I   62 LYS cc_start: 0.8209 (mppt) cc_final: 0.7800 (ttpp)
REVERT: I   75 MET cc_start: 0.8428 (ttt) cc_final: 0.8128 (mtp)
REVERT: I  102 ARG cc_start: 0.8138 (tpt90) cc_final: 0.7567 (ttm110)
REVERT: J   92 ASP cc_start: 0.7972 (p0) cc_final: 0.7759 (p0)
REVERT: J  241 CYS cc_start: 0.6842 (m) cc_final: 0.6215 (p)
REVERT: J  298 ARG cc_start: 0.7576 (mtm-85) cc_final: 0.7259 (mpp-170)
  outliers start: 10
  outliers final: 5
  residues processed: 93
  average time/residue: 0.5717
  time to fit residues: 55.1488
Evaluate side-chains
  90 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  265 MET
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  278 GLU
Chi-restraints excluded: chain J residue  219 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 53 optimal weight:    0.3980
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
J 297 ASN
J 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.149438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.124870 restraints weight = 10054.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.66
r_work: 0.3186 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   5249  Z= 0.183
  Angle     :  0.584   6.592   7100  Z= 0.297
  Chirality :  0.044   0.148    772
  Planarity :  0.005   0.039    903
  Dihedral  :  5.970  53.148    707
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.47 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.12 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.32 (0.33), residues: 612
  helix:  1.78 (0.28), residues: 336
  sheet:  0.71 (1.26), residues: 12
  loop : -0.27 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J 283 
 TYR   0.020   0.002   TYR I  91 
 PHE   0.015   0.002   PHE I  71 
 TRP   0.009   0.002   TRP I  11 
 HIS   0.005   0.002   HIS I  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 5247)
  covalent geometry    : angle       0.58369 ( 7100)
  hydrogen bonds       : bond        0.05038 (  267)
  hydrogen bonds       : angle       4.56614 (  747)
  Misc. bond           : bond        0.00016 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.120 
Fit side-chains
REVERT: H  265 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7327 (mmm)
REVERT: I   16 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6878 (mm-30)
REVERT: J  298 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7261 (mpp-170)
  outliers start: 18
  outliers final: 10
  residues processed: 94
  average time/residue: 0.5696
  time to fit residues: 55.3423
Evaluate side-chains
  96 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  265 MET
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  244 CYS
Chi-restraints excluded: chain I residue  267 SER
Chi-restraints excluded: chain I residue  278 GLU
Chi-restraints excluded: chain J residue   58 THR
Chi-restraints excluded: chain J residue  219 LEU
Chi-restraints excluded: chain J residue  241 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 59 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
J 297 ASN
J 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.151671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.126383 restraints weight = 13030.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 3.46
r_work: 0.3157 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5249  Z= 0.118
  Angle     :  0.509   6.516   7100  Z= 0.260
  Chirality :  0.040   0.142    772
  Planarity :  0.004   0.039    903
  Dihedral  :  5.707  52.565    707
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.31 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.39 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.69 (0.34), residues: 612
  helix:  2.10 (0.29), residues: 332
  sheet:  0.51 (1.28), residues: 12
  loop : -0.07 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  77 
 TYR   0.016   0.001   TYR I  91 
 PHE   0.009   0.001   PHE I  30 
 TRP   0.007   0.001   TRP I  11 
 HIS   0.003   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5247)
  covalent geometry    : angle       0.50924 ( 7100)
  hydrogen bonds       : bond        0.04158 (  267)
  hydrogen bonds       : angle       4.39545 (  747)
  Misc. bond           : bond        0.00014 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.197 
Fit side-chains
REVERT: H  254 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7984 (tp30)
REVERT: H  265 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7196 (mmm)
REVERT: I   63 ARG cc_start: 0.8110 (mmp80) cc_final: 0.7393 (mtp-110)
REVERT: I   75 MET cc_start: 0.8530 (ttt) cc_final: 0.8216 (mtp)
REVERT: I  102 ARG cc_start: 0.8086 (tpt90) cc_final: 0.7500 (ttm110)
REVERT: I  252 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8089 (mtm)
REVERT: J  298 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.7084 (mpp-170)
  outliers start: 10
  outliers final: 6
  residues processed: 92
  average time/residue: 0.5658
  time to fit residues: 53.8384
Evaluate side-chains
  91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  265 MET
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  252 MET
Chi-restraints excluded: chain I residue  267 SER
Chi-restraints excluded: chain I residue  278 GLU
Chi-restraints excluded: chain J residue  219 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
J 297 ASN
J 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.150070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.125907 restraints weight = 7682.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.55
r_work: 0.3221 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   5249  Z= 0.153
  Angle     :  0.546   6.412   7100  Z= 0.279
  Chirality :  0.042   0.145    772
  Planarity :  0.005   0.040    903
  Dihedral  :  5.832  53.086    707
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.64 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.39 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.43 (0.33), residues: 612
  helix:  1.90 (0.29), residues: 335
  sheet:  0.62 (1.35), residues: 12
  loop : -0.23 (0.36), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 283 
 TYR   0.018   0.002   TYR I  91 
 PHE   0.013   0.002   PHE I  71 
 TRP   0.009   0.002   TRP I  11 
 HIS   0.004   0.001   HIS I  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 5247)
  covalent geometry    : angle       0.54577 ( 7100)
  hydrogen bonds       : bond        0.04656 (  267)
  hydrogen bonds       : angle       4.50128 (  747)
  Misc. bond           : bond        0.00014 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.122 
Fit side-chains
REVERT: H  254 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7955 (tp30)
REVERT: H  265 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7289 (mmm)
REVERT: I  102 ARG cc_start: 0.8125 (tpt90) cc_final: 0.7532 (ttm110)
REVERT: J  142 ASN cc_start: 0.7916 (m-40) cc_final: 0.7651 (m-40)
REVERT: J  298 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7194 (mpp-170)
  outliers start: 12
  outliers final: 7
  residues processed: 94
  average time/residue: 0.5598
  time to fit residues: 54.4208
Evaluate side-chains
  95 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  265 MET
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  244 CYS
Chi-restraints excluded: chain I residue  267 SER
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  219 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
J 297 ASN
J 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.152561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.128737 restraints weight = 14783.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.71
r_work: 0.3141 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5249  Z= 0.107
  Angle     :  0.498   6.386   7100  Z= 0.253
  Chirality :  0.040   0.140    772
  Planarity :  0.004   0.040    903
  Dihedral  :  5.573  52.349    707
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.31 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.93 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.75 (0.34), residues: 612
  helix:  2.17 (0.29), residues: 333
  sheet:  0.51 (1.34), residues: 12
  loop : -0.08 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  77 
 TYR   0.015   0.001   TYR I  91 
 PHE   0.011   0.001   PHE I  30 
 TRP   0.006   0.001   TRP I  11 
 HIS   0.003   0.001   HIS J  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 5247)
  covalent geometry    : angle       0.49827 ( 7100)
  hydrogen bonds       : bond        0.03895 (  267)
  hydrogen bonds       : angle       4.32171 (  747)
  Misc. bond           : bond        0.00015 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.117 
Fit side-chains
REVERT: H  254 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7979 (tp30)
REVERT: H  265 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7277 (mmm)
REVERT: I   63 ARG cc_start: 0.8159 (mmp80) cc_final: 0.7462 (mtp-110)
REVERT: I   75 MET cc_start: 0.8567 (ttt) cc_final: 0.8273 (mtp)
REVERT: I  102 ARG cc_start: 0.8097 (tpt90) cc_final: 0.7528 (ttm110)
REVERT: J   92 ASP cc_start: 0.7946 (p0) cc_final: 0.7704 (p0)
REVERT: J  241 CYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6138 (p)
REVERT: J  298 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7158 (mpp-170)
  outliers start: 10
  outliers final: 6
  residues processed: 92
  average time/residue: 0.5799
  time to fit residues: 55.1122
Evaluate side-chains
  94 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  265 MET
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  244 CYS
Chi-restraints excluded: chain I residue  267 SER
Chi-restraints excluded: chain I residue  278 GLU
Chi-restraints excluded: chain J residue  241 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0670
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.9120

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

Flipped N/Q/H residues before XYZ refinement:
J 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.152708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.128328 restraints weight = 11575.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.20
r_work: 0.3227 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5249  Z= 0.111
  Angle     :  0.509   6.795   7100  Z= 0.257
  Chirality :  0.040   0.136    772
  Planarity :  0.004   0.040    903
  Dihedral  :  5.526  52.244    707
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.47 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 18.48 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.75 (0.34), residues: 612
  helix:  2.17 (0.29), residues: 333
  sheet:  1.14 (1.53), residues: 10
  loop : -0.09 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  77 
 TYR   0.016   0.001   TYR I  91 
 PHE   0.013   0.001   PHE I  30 
 TRP   0.006   0.001   TRP I  11 
 HIS   0.003   0.001   HIS I  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5247)
  covalent geometry    : angle       0.50906 ( 7100)
  hydrogen bonds       : bond        0.03978 (  267)
  hydrogen bonds       : angle       4.31533 (  747)
  Misc. bond           : bond        0.00014 (    2)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.200 
Fit side-chains
REVERT: H  254 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8034 (tp30)
REVERT: H  265 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7293 (mmm)
REVERT: I   63 ARG cc_start: 0.8152 (mmp80) cc_final: 0.7436 (mtp-110)
REVERT: I   75 MET cc_start: 0.8542 (ttt) cc_final: 0.8231 (mtp)
REVERT: I  102 ARG cc_start: 0.8140 (tpt90) cc_final: 0.7544 (ttm110)
REVERT: J   92 ASP cc_start: 0.7884 (p0) cc_final: 0.7636 (p0)
REVERT: J  234 GLU cc_start: 0.7105 (tp30) cc_final: 0.6725 (mm-30)
REVERT: J  241 CYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6191 (p)
REVERT: J  297 ASN cc_start: 0.8413 (m-40) cc_final: 0.8209 (m110)
REVERT: J  298 ARG cc_start: 0.7535 (mtm-85) cc_final: 0.7198 (mpp-170)
  outliers start: 8
  outliers final: 5
  residues processed: 89
  average time/residue: 0.6479
  time to fit residues: 59.6966
Evaluate side-chains
  93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  265 MET
Chi-restraints excluded: chain I residue  198 ILE
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  243 THR
Chi-restraints excluded: chain I residue  267 SER
Chi-restraints excluded: chain I residue  278 GLU
Chi-restraints excluded: chain J residue  241 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    0.2980
   chunk 11 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 18 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
J 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.150834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.126898 restraints weight = 13084.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.37
r_work: 0.3153 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   5249  Z= 0.144
  Angle     :  0.547   6.706   7100  Z= 0.278
  Chirality :  0.042   0.140    772
  Planarity :  0.005   0.040    903
  Dihedral  :  5.689  52.638    707
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.64 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 18.48 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.49 (0.33), residues: 612
  helix:  1.96 (0.29), residues: 336
  sheet:  0.63 (1.40), residues: 12
  loop : -0.24 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 283 
 TYR   0.018   0.002   TYR I  91 
 PHE   0.015   0.002   PHE I  30 
 TRP   0.008   0.001   TRP I  11 
 HIS   0.004   0.001   HIS I  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 5247)
  covalent geometry    : angle       0.54684 ( 7100)
  hydrogen bonds       : bond        0.04497 (  267)
  hydrogen bonds       : angle       4.44894 (  747)
  Misc. bond           : bond        0.00015 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1957.19 seconds
wall clock time: 34 minutes 1.83 seconds (2041.83 seconds total)