Starting phenix.real_space_refine
on Thu Jul 24 05:23:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p78_17521/07_2025/8p78_17521.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p78_17521/07_2025/8p78_17521.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p78_17521/07_2025/8p78_17521.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p78_17521/07_2025/8p78_17521.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p78_17521/07_2025/8p78_17521.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p78_17521/07_2025/8p78_17521.cif"
  }
  resolution = 1.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    3311      2.51       5
     N     876      2.21       5
     O    1086      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5304
  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: 2281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2281
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 279, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 2283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2283
          Classifications: {'peptide': 286}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 58
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 29
          Unusual residues: {'1QK': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 29
          Unusual residues: {'1QK': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
    Chain: "I"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 64
          Classifications: {'water': 64}
          Link IDs: {None: 63}
    Chain: "J"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 84
          Classifications: {'water': 84}
          Link IDs: {None: 83}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C01A1QK J 401 " occ=0.54
      ... (56 atoms not shown)
      pdb=" O29B1QK J 401 " occ=0.46
  Time building chain proxies: 4.58, per 1000 atoms: 0.86
  Number of scatterers: 5304
  At special positions: 0
  Unit cell: (84.7875, 94.05, 68.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1086      8.00
     N     876      7.00
     C    3311      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: 1.50
  Conformation dependent library (CDL) restraints added in 558.0 milliseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1196

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 3 sheets defined
      63.5% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'H' and resid 262 through 264
      No H-bonds generated for 'chain 'H' and resid 262 through 264'
    Processing helix  chain 'H' and resid 265 through 270
    Processing helix  chain 'H' and resid 271 through 275
      removed outlier: 3.523A  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: 3.837A  pdb=" N   ALA H 292 " --> pdb=" O   THR H 288 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1 through 4
    Processing helix  chain 'I' and resid 5 through 11
    Processing helix  chain 'I' and resid 15 through 38
    Processing helix  chain 'I' and resid 49 through 70
    Processing helix  chain 'I' and resid 76 through 93
      removed outlier: 3.947A  pdb=" N   ASN I  93 " --> pdb=" O   ARG I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 116
      removed outlier: 3.711A  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: 4.617A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.529A  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: 3.654A  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 225
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.690A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 237 through 240
    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
    Processing helix  chain 'J' and resid 139 through 141
      No H-bonds generated for 'chain 'J' and resid 139 through 141'
    Processing helix  chain 'J' and resid 155 through 159
      removed outlier: 4.380A  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
    Processing helix  chain 'J' and resid 217 through 230
    Processing helix  chain 'J' and resid 239 through 243
    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: 3.779A  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 13 through 20
      removed outlier: 3.630A  pdb=" N   GLU J  13 " --> pdb=" O   ARG J  30 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LYS J  28 " --> pdb=" O   LEU J  15 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   PHE J  17 " --> pdb=" O   VAL J  26 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   VAL J  26 " --> pdb=" O   PHE J  17 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU J  89 " --> pdb=" O   LYS J  41 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASP J  79 " --> pdb=" O   VAL J  90 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 7.825A  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

    273 hydrogen bonds defined for protein.
    768 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: 1.35

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1648
        1.34 -     1.46: 1040
        1.46 -     1.58: 2524
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 5261
  Sorted by residual:
  bond pdb=" C11B1QK J 401 "
       pdb=" N12B1QK J 401 "
    ideal  model  delta    sigma   weight residual
    1.347  1.454 -0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" C11A1QK J 401 "
       pdb=" N12A1QK J 401 "
    ideal  model  delta    sigma   weight residual
    1.347  1.451 -0.104 2.00e-02 2.50e+03 2.70e+01
  bond pdb=" C09A1QK J 401 "
       pdb=" N21A1QK J 401 "
    ideal  model  delta    sigma   weight residual
    1.372  1.458 -0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" C23B1QK J 401 "
       pdb=" C24B1QK J 401 "
    ideal  model  delta    sigma   weight residual
    1.527  1.443  0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" C24B1QK J 401 "
       pdb=" C25B1QK J 401 "
    ideal  model  delta    sigma   weight residual
    1.528  1.447  0.081 2.00e-02 2.50e+03 1.64e+01
  ... (remaining 5256 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 6894
        1.55 -     3.10: 172
        3.10 -     4.65: 37
        4.65 -     6.20: 15
        6.20 -     7.75: 3
  Bond angle restraints: 7121
  Sorted by residual:
  angle pdb=" CB  LYS J 293 "
        pdb=" CG  LYS J 293 "
        pdb=" CD  LYS J 293 "
      ideal   model   delta    sigma   weight residual
     111.30  118.25   -6.95 2.30e+00 1.89e-01 9.12e+00
  angle pdb=" CA  TYR I  91 "
        pdb=" CB  TYR I  91 "
        pdb=" CG  TYR I  91 "
      ideal   model   delta    sigma   weight residual
     113.90  109.25    4.65 1.80e+00 3.09e-01 6.68e+00
  angle pdb=" CA  LYS J 293 "
        pdb=" CB  LYS J 293 "
        pdb=" CG  LYS J 293 "
      ideal   model   delta    sigma   weight residual
     114.10  119.22   -5.12 2.00e+00 2.50e-01 6.55e+00
  angle pdb=" CA  LEU H 263 "
        pdb=" CB  LEU H 263 "
        pdb=" CG  LEU H 263 "
      ideal   model   delta    sigma   weight residual
     116.30  124.05   -7.75 3.50e+00 8.16e-02 4.91e+00
  angle pdb=" C10B1QK J 401 "
        pdb=" C11B1QK J 401 "
        pdb=" N12B1QK J 401 "
      ideal   model   delta    sigma   weight residual
     127.66  121.26    6.40 3.00e+00 1.11e-01 4.55e+00
  ... (remaining 7116 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.40: 2915
       23.40 -    46.81: 221
       46.81 -    70.21: 32
       70.21 -    93.61: 19
       93.61 -   117.02: 6
  Dihedral angle restraints: 3193
    sinusoidal: 1346
      harmonic: 1847
  Sorted by residual:
  dihedral pdb=" C09B1QK J 401 "
           pdb=" C26B1QK J 401 "
           pdb=" N21B1QK J 401 "
           pdb=" C27B1QK J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -52.34   64.68 -117.02     1      3.00e+01 1.11e-03 1.55e+01
  dihedral pdb=" C22B1QK J 401 "
           pdb=" C26B1QK J 401 "
           pdb=" N21B1QK J 401 "
           pdb=" C27B1QK J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     163.80  -80.82 -115.38     1      3.00e+01 1.11e-03 1.52e+01
  dihedral pdb=" C09B1QK J 401 "
           pdb=" C22B1QK J 401 "
           pdb=" N21B1QK J 401 "
           pdb=" C23B1QK J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     277.63  164.86  112.77     1      3.00e+01 1.11e-03 1.48e+01
  ... (remaining 3190 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 715
       0.081 -    0.162: 60
       0.162 -    0.243: 0
       0.243 -    0.323: 0
       0.323 -    0.404: 2
  Chirality restraints: 777
  Sorted by residual:
  chirality pdb=" C26A1QK J 401 "
            pdb=" C25A1QK J 401 "
            pdb=" C27A1QK J 401 "
            pdb=" N21A1QK J 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.17   -2.58    0.40 2.00e-01 2.50e+01 4.09e+00
  chirality pdb=" C26B1QK J 401 "
            pdb=" C25B1QK J 401 "
            pdb=" C27B1QK J 401 "
            pdb=" N21B1QK J 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.17   -2.51    0.34 2.00e-01 2.50e+01 2.92e+00
  chirality pdb=" CA  TYR I  91 "
            pdb=" N   TYR I  91 "
            pdb=" C   TYR I  91 "
            pdb=" CB  TYR I  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.60e-01
  ... (remaining 774 not shown)

  Planarity restraints: 905
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS J 139 "    0.025 5.00e-02 4.00e+02   3.84e-02 2.35e+00
        pdb=" N   PRO J 140 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO J 140 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO J 140 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 287 "    0.016 2.00e-02 2.50e+03   1.01e-02 2.04e+00
        pdb=" CG  TYR H 287 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 287 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 287 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 287 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 287 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 287 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR H 287 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU I 195 "   -0.007 2.00e-02 2.50e+03   1.42e-02 2.00e+00
        pdb=" C   LEU I 195 "    0.024 2.00e-02 2.50e+03
        pdb=" O   LEU I 195 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASN I 196 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 902 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 663
        2.75 -     3.28: 5531
        3.28 -     3.82: 9973
        3.82 -     4.36: 12081
        4.36 -     4.90: 19693
  Nonbonded interactions: 47941
  Sorted by model distance:
  nonbonded pdb=" OG1 THR J 233 "
            pdb=" OE1 GLU J 235 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   GLY H 286 "
            pdb=" O   HOH H 401 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   HOH H 413 "
            pdb=" O   HOH H 422 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD1 ASN J 141 "
            pdb=" O   HOH J 501 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   ASN I 128 "
            pdb=" O   HOH I 401 "
     model   vdw
     2.243 3.040
  ... (remaining 47936 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=0.46 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:             3.730
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.840
  Find NCS groups from input model:        0.070
  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:15.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
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   0.107   5261  Z= 0.279
  Angle     :  0.657   7.754   7121  Z= 0.315
  Chirality :  0.046   0.404    777
  Planarity :  0.005   0.038    905
  Dihedral  : 18.185 117.016   1997
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 12.82 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.33), residues: 618
  helix:  1.85 (0.28), residues: 338
  sheet: -0.28 (1.01), residues: 18
  loop :  0.56 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP J 132 
 HIS   0.007   0.001   HIS J 131 
 PHE   0.015   0.002   PHE J 295 
 TYR   0.023   0.002   TYR H 287 
 ARG   0.003   0.000   ARG I  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11952 (  273)
  hydrogen bonds       : angle       5.71942 (  768)
  covalent geometry    : bond        0.00574 ( 5261)
  covalent geometry    : angle       0.65662 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.615 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 95
  average time/residue: 1.4402
  time to fit residues: 141.9248
Evaluate side-chains
  93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  305 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    7.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0030
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 141 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.178145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148890 restraints weight = 10160.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 1.32
r_work: 0.3578 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.0837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5261  Z= 0.110
  Angle     :  0.520   6.202   7121  Z= 0.263
  Chirality :  0.040   0.140    777
  Planarity :  0.004   0.035    905
  Dihedral  : 14.078 110.326    739
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.78 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.45 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.34), residues: 618
  helix:  2.42 (0.29), residues: 340
  sheet:  0.17 (1.85), residues: 8
  loop :  0.68 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 306 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.013   0.001   PHE I  30 
 TYR   0.017   0.001   TYR I  91 
 ARG   0.002   0.000   ARG I 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04422 (  273)
  hydrogen bonds       : angle       4.51086 (  768)
  covalent geometry    : bond        0.00227 ( 5261)
  covalent geometry    : angle       0.51969 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.707 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6869 (ttmt)
  outliers start: 8
  outliers final: 2
  residues processed: 104
  average time/residue: 1.3610
  time to fit residues: 147.4474
Evaluate side-chains
  94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain J residue  216 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.175228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.145544 restraints weight = 10364.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 1.35
r_work: 0.3535 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.0673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5261  Z= 0.160
  Angle     :  0.588   5.585   7121  Z= 0.299
  Chirality :  0.042   0.143    777
  Planarity :  0.005   0.037    905
  Dihedral  : 14.497 119.317    737
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.09 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.34), residues: 618
  helix:  2.19 (0.28), residues: 340
  sheet:  0.06 (1.78), residues: 8
  loop :  0.55 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP J 132 
 HIS   0.009   0.002   HIS J 131 
 PHE   0.016   0.002   PHE J 295 
 TYR   0.021   0.002   TYR I  91 
 ARG   0.003   0.000   ARG J  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05230 (  273)
  hydrogen bonds       : angle       4.65918 (  768)
  covalent geometry    : bond        0.00348 ( 5261)
  covalent geometry    : angle       0.58764 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.612 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6938 (ttmt)
  outliers start: 11
  outliers final: 5
  residues processed: 102
  average time/residue: 1.4630
  time to fit residues: 154.5154
Evaluate side-chains
  92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  232 LEU
Chi-restraints excluded: chain I residue  237 MET
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain J residue  216 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 46 optimal weight:    0.2980
   chunk 5 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.176369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.148502 restraints weight = 8569.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 1.26
r_work: 0.3573 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3458
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3458
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.0874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5261  Z= 0.125
  Angle     :  0.540   5.747   7121  Z= 0.274
  Chirality :  0.041   0.142    777
  Planarity :  0.004   0.038    905
  Dihedral  : 14.197 121.520    737
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.82 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.34), residues: 618
  helix:  2.33 (0.28), residues: 340
  sheet:  0.09 (1.73), residues: 8
  loop :  0.56 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 306 
 HIS   0.006   0.001   HIS J 131 
 PHE   0.013   0.002   PHE I 110 
 TYR   0.019   0.002   TYR I  91 
 ARG   0.002   0.000   ARG J  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04651 (  273)
  hydrogen bonds       : angle       4.48262 (  768)
  covalent geometry    : bond        0.00266 ( 5261)
  covalent geometry    : angle       0.54028 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.629 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6881 (ttmt)
REVERT: J   87 ILE cc_start: 0.4727 (OUTLIER) cc_final: 0.4505 (mm)
  outliers start: 9
  outliers final: 4
  residues processed: 99
  average time/residue: 1.3853
  time to fit residues: 142.5108
Evaluate side-chains
  96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  232 LEU
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain J residue   87 ILE
Chi-restraints excluded: chain J residue  216 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0870
   chunk 35 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    1.9764

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.174184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.144328 restraints weight = 14809.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 1.71
r_work: 0.3498 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3371
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.0808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5261  Z= 0.185
  Angle     :  0.630   6.424   7121  Z= 0.319
  Chirality :  0.044   0.148    777
  Planarity :  0.005   0.041    905
  Dihedral  : 14.535 118.650    737
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.27 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.64 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.33), residues: 618
  helix:  2.05 (0.28), residues: 339
  sheet:  0.03 (1.74), residues: 8
  loop :  0.41 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP J 237 
 HIS   0.010   0.002   HIS J 131 
 PHE   0.018   0.002   PHE J 295 
 TYR   0.021   0.002   TYR I  91 
 ARG   0.004   0.001   ARG J  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05463 (  273)
  hydrogen bonds       : angle       4.71971 (  768)
  covalent geometry    : bond        0.00405 ( 5261)
  covalent geometry    : angle       0.63023 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.646 
Fit side-chains
REVERT: I   25 ASP cc_start: 0.8087 (t0) cc_final: 0.7827 (t0)
REVERT: I  260 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6950 (ttmt)
REVERT: J   52 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6103 (ptpp)
  outliers start: 11
  outliers final: 5
  residues processed: 99
  average time/residue: 1.4584
  time to fit residues: 149.8285
Evaluate side-chains
  98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  232 LEU
Chi-restraints excluded: chain I residue  237 MET
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue  216 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0970
   chunk 25 optimal weight:    0.0980
   chunk 18 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 141 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.178627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.149793 restraints weight = 9748.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 1.30
r_work: 0.3595 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3496 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5261  Z= 0.103
  Angle     :  0.506   6.371   7121  Z= 0.257
  Chirality :  0.039   0.137    777
  Planarity :  0.004   0.039    905
  Dihedral  : 13.940 123.725    737
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.00 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.34), residues: 618
  helix:  2.54 (0.28), residues: 338
  sheet:  0.08 (1.72), residues: 8
  loop :  0.55 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP I  11 
 HIS   0.003   0.001   HIS J 131 
 PHE   0.013   0.001   PHE I  30 
 TYR   0.016   0.001   TYR I  91 
 ARG   0.002   0.000   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04080 (  273)
  hydrogen bonds       : angle       4.29690 (  768)
  covalent geometry    : bond        0.00214 ( 5261)
  covalent geometry    : angle       0.50560 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.590 
Fit side-chains
REVERT: I   70 VAL cc_start: 0.7547 (m) cc_final: 0.7335 (p)
REVERT: I  260 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6863 (ttmt)
  outliers start: 9
  outliers final: 4
  residues processed: 106
  average time/residue: 1.3939
  time to fit residues: 153.4212
Evaluate side-chains
  96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue   72 LYS
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  232 LEU
Chi-restraints excluded: chain I residue  260 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 3 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0670
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 37 optimal weight:    0.3980
   chunk 6 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 141 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.179015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.150897 restraints weight = 8744.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 1.28
r_work: 0.3595 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3497 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5261  Z= 0.105
  Angle     :  0.517   7.080   7121  Z= 0.260
  Chirality :  0.040   0.135    777
  Planarity :  0.004   0.038    905
  Dihedral  : 13.676 123.975    735
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.78 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.08 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.34), residues: 618
  helix:  2.55 (0.28), residues: 340
  sheet:  0.21 (1.74), residues: 8
  loop :  0.63 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.013   0.001   PHE I 110 
 TYR   0.017   0.001   TYR I  91 
 ARG   0.002   0.000   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  273)
  hydrogen bonds       : angle       4.28564 (  768)
  covalent geometry    : bond        0.00222 ( 5261)
  covalent geometry    : angle       0.51652 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.600 
Fit side-chains
REVERT: I   72 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6463 (mttt)
REVERT: I  260 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6882 (ttmt)
REVERT: J   52 LYS cc_start: 0.6330 (OUTLIER) cc_final: 0.5979 (ptpp)
  outliers start: 10
  outliers final: 3
  residues processed: 103
  average time/residue: 1.4199
  time to fit residues: 151.7368
Evaluate side-chains
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue   72 LYS
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  232 LEU
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain J residue   52 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0060
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.1398

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.176302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.148542 restraints weight = 8690.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.34
r_work: 0.3550 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5261  Z= 0.138
  Angle     :  0.577   6.835   7121  Z= 0.291
  Chirality :  0.042   0.138    777
  Planarity :  0.004   0.038    905
  Dihedral  : 13.955 122.920    735
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.26 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.34), residues: 618
  helix:  2.40 (0.28), residues: 340
  sheet:  None (None), residues: 0
  loop :  0.58 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J 132 
 HIS   0.008   0.001   HIS J 131 
 PHE   0.015   0.002   PHE J 295 
 TYR   0.020   0.002   TYR I  91 
 ARG   0.002   0.000   ARG I  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04744 (  273)
  hydrogen bonds       : angle       4.46527 (  768)
  covalent geometry    : bond        0.00301 ( 5261)
  covalent geometry    : angle       0.57690 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.540 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6931 (ttmt)
REVERT: J   52 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.6052 (ptpp)
  outliers start: 8
  outliers final: 4
  residues processed: 98
  average time/residue: 1.3999
  time to fit residues: 142.2620
Evaluate side-chains
  99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue   72 LYS
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  232 LEU
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain J residue   52 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 54 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0010
   chunk 39 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.8990

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.174762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.145289 restraints weight = 14291.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 1.64
r_work: 0.3508 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.0925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5261  Z= 0.183
  Angle     :  0.645   7.386   7121  Z= 0.327
  Chirality :  0.044   0.152    777
  Planarity :  0.005   0.038    905
  Dihedral  : 14.388 120.276    735
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.10 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.72 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.33), residues: 618
  helix:  2.14 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop :  0.40 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP J 237 
 HIS   0.010   0.002   HIS J 131 
 PHE   0.017   0.002   PHE J 295 
 TYR   0.022   0.002   TYR I  91 
 ARG   0.004   0.001   ARG J 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05344 (  273)
  hydrogen bonds       : angle       4.66213 (  768)
  covalent geometry    : bond        0.00404 ( 5261)
  covalent geometry    : angle       0.64466 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.599 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6952 (ttmt)
REVERT: J   52 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6104 (ptpp)
  outliers start: 9
  outliers final: 4
  residues processed: 98
  average time/residue: 1.4537
  time to fit residues: 147.8816
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  232 LEU
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue  216 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 3 optimal weight:    0.1980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 141 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.176180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.146181 restraints weight = 14733.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 1.76
r_work: 0.3509 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5261  Z= 0.140
  Angle     :  0.586   7.622   7121  Z= 0.297
  Chirality :  0.042   0.171    777
  Planarity :  0.004   0.039    905
  Dihedral  : 14.175 122.320    735
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 14.44 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.34), residues: 618
  helix:  2.26 (0.28), residues: 340
  sheet:  None (None), residues: 0
  loop :  0.49 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 306 
 HIS   0.007   0.001   HIS I  51 
 PHE   0.015   0.002   PHE I  30 
 TYR   0.020   0.002   TYR I  91 
 ARG   0.002   0.000   ARG J  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04785 (  273)
  hydrogen bonds       : angle       4.51074 (  768)
  covalent geometry    : bond        0.00305 ( 5261)
  covalent geometry    : angle       0.58605 ( 7121)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.565 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6967 (ttmt)
REVERT: J   42 LYS cc_start: 0.5952 (ttmt) cc_final: 0.5661 (mmtt)
REVERT: J   52 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.6063 (ptpp)
  outliers start: 7
  outliers final: 3
  residues processed: 99
  average time/residue: 1.4224
  time to fit residues: 146.0958
Evaluate side-chains
  98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  232 LEU
Chi-restraints excluded: chain I residue  260 LYS
Chi-restraints excluded: chain J residue   52 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 12 optimal weight:    0.1980
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
I 183 ASN
J 258 HIS
J 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.174793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146383 restraints weight = 9807.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 1.39
r_work: 0.3514 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.0942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5261  Z= 0.179
  Angle     :  0.644   8.020   7121  Z= 0.328
  Chirality :  0.044   0.209    777
  Planarity :  0.005   0.038    905
  Dihedral  : 14.400 120.423    735
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.26 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.33), residues: 618
  helix:  2.07 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop :  0.34 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP J 237 
 HIS   0.010   0.002   HIS J 131 
 PHE   0.017   0.002   PHE J 252 
 TYR   0.021   0.002   TYR I  91 
 ARG   0.004   0.001   ARG J 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05293 (  273)
  hydrogen bonds       : angle       4.66904 (  768)
  covalent geometry    : bond        0.00394 ( 5261)
  covalent geometry    : angle       0.64412 ( 7121)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7140.19 seconds
wall clock time: 121 minutes 36.90 seconds (7296.90 seconds total)