Starting phenix.real_space_refine
on Fri Oct 10 12:44:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p78_17521/10_2025/8p78_17521.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p78_17521/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p78_17521/10_2025/8p78_17521.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p78_17521/10_2025/8p78_17521.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p78_17521/10_2025/8p78_17521.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p78_17521/10_2025/8p78_17521.map"
  }
  resolution = 1.9
  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=   0.002
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.33, per 1000 atoms: 0.25
  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: 0.38
  Conformation dependent library (CDL) restraints added in 195.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.18
  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: 0.87

  Time building geometry restraints manager: 0.47 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:             3.410
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.680
  Find NCS groups from input model:        0.030
  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:6.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.290
-------------------------------------------------------------------------------
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 : 5.06
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG I  31 
 TYR   0.023   0.002   TYR H 287 
 PHE   0.015   0.002   PHE J 295 
 TRP   0.010   0.002   TRP J 132 
 HIS   0.007   0.001   HIS J 131 

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

*********************** 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  : 0.218 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 95
  average time/residue: 0.6735
  time to fit residues: 66.4613
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  : 0.218 
-------------------------------------------------------------------------------
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 54 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0030
   chunk 56 optimal weight:    0.0770
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7550

-------------------------------------------------------------------------------
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 = 0.4070 r_free = 0.4070 target = 0.177365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.147892 restraints weight = 10483.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 1.32
r_work: 0.3569 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3469 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    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 = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.0770

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= 0.118
  Angle     :  0.532   6.164   7121  Z= 0.270
  Chirality :  0.040   0.138    777
  Planarity :  0.004   0.036    905
  Dihedral  : 14.133 111.117    739
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.78 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.34 (0.34), residues: 618
  helix:  2.36 (0.28), residues: 340
  sheet:  0.15 (1.85), residues: 8
  loop :  0.66 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 188 
 TYR   0.019   0.002   TYR I  91 
 PHE   0.013   0.001   PHE I  30 
 TRP   0.008   0.001   TRP H 306 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5261)
  covalent geometry    : angle       0.53157 ( 7121)
  hydrogen bonds       : bond        0.04599 (  273)
  hydrogen bonds       : angle       4.55364 (  768)

*********************** 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
  105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.178 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6872 (ttmt)
  outliers start: 8
  outliers final: 1
  residues processed: 102
  average time/residue: 0.7038
  time to fit residues: 74.3918
Evaluate side-chains
  94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 43 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 34 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6960

-------------------------------------------------------------------------------
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 = 0.4075 r_free = 0.4075 target = 0.177878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.150493 restraints weight = 9063.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 1.30
r_work: 0.3581 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    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 = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.0903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5261  Z= 0.112
  Angle     :  0.508   4.836   7121  Z= 0.259
  Chirality :  0.039   0.137    777
  Planarity :  0.004   0.037    905
  Dihedral  : 14.165 123.362    737
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.09 %
    Favored  : 86.28 %
  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 aren not related in a simple way.
  whole:  2.39 (0.34), residues: 618
  helix:  2.47 (0.28), residues: 338
  sheet:  0.14 (1.79), residues: 8
  loop :  0.59 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  28 
 TYR   0.018   0.002   TYR I  91 
 PHE   0.013   0.001   PHE I  30 
 TRP   0.007   0.001   TRP H 306 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 5261)
  covalent geometry    : angle       0.50835 ( 7121)
  hydrogen bonds       : bond        0.04410 (  273)
  hydrogen bonds       : angle       4.40939 (  768)

*********************** 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: 9
    poor density    : 96
  time to evaluate  : 0.140 
Fit side-chains
REVERT: I   29 LYS cc_start: 0.7696 (mttt) cc_final: 0.7447 (mttt)
REVERT: I  260 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6876 (ttmt)
  outliers start: 9
  outliers final: 4
  residues processed: 102
  average time/residue: 0.6615
  time to fit residues: 69.8415
Evaluate side-chains
  101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 I residue  270 VAL
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 14 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4050 r_free = 0.4050 target = 0.175561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.149800 restraints weight = 7936.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 1.20
r_work: 0.3571 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3453
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3453
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.0773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5261  Z= 0.147
  Angle     :  0.572   5.733   7121  Z= 0.290
  Chirality :  0.042   0.141    777
  Planarity :  0.005   0.038    905
  Dihedral  : 14.247 120.716    737
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.34), residues: 618
  helix:  2.26 (0.28), residues: 340
  sheet:  0.18 (1.77), residues: 8
  loop :  0.56 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J  61 
 TYR   0.020   0.002   TYR I  91 
 PHE   0.015   0.002   PHE J 295 
 TRP   0.008   0.002   TRP H 306 
 HIS   0.008   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5261)
  covalent geometry    : angle       0.57202 ( 7121)
  hydrogen bonds       : bond        0.04999 (  273)
  hydrogen bonds       : angle       4.56762 (  768)

*********************** 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
  106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.214 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6861 (ttmt)
  outliers start: 12
  outliers final: 4
  residues processed: 102
  average time/residue: 0.7056
  time to fit residues: 74.5715
Evaluate side-chains
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
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  216 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 58 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.174643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.147371 restraints weight = 8521.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 1.26
r_work: 0.3541 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
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 = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.0769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5261  Z= 0.170
  Angle     :  0.606   6.325   7121  Z= 0.308
  Chirality :  0.043   0.145    777
  Planarity :  0.005   0.039    905
  Dihedral  : 14.445 119.369    737
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.10 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.82 %
    Favored  : 85.74 %
  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 aren not related in a simple way.
  whole:  2.01 (0.33), residues: 618
  helix:  2.12 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop :  0.44 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J  61 
 TYR   0.021   0.002   TYR I  91 
 PHE   0.017   0.002   PHE J 295 
 TRP   0.009   0.002   TRP J 237 
 HIS   0.009   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 5261)
  covalent geometry    : angle       0.60581 ( 7121)
  hydrogen bonds       : bond        0.05317 (  273)
  hydrogen bonds       : angle       4.66456 (  768)

*********************** 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
  100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.214 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6914 (ttmt)
REVERT: J   52 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.6070 (ptpp)
  outliers start: 8
  outliers final: 4
  residues processed: 98
  average time/residue: 0.7252
  time to fit residues: 73.5346
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  : 0.231 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.4056 r_free = 0.4056 target = 0.176060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.148527 restraints weight = 9358.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 1.33
r_work: 0.3551 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3425
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3425
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.0876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5261  Z= 0.130
  Angle     :  0.554   6.600   7121  Z= 0.281
  Chirality :  0.041   0.142    777
  Planarity :  0.004   0.040    905
  Dihedral  : 14.207 121.714    737
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.10 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.36 %
    Favored  : 84.84 %
  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 aren not related in a simple way.
  whole:  2.22 (0.34), residues: 618
  helix:  2.29 (0.28), residues: 340
  sheet:  None (None), residues: 0
  loop :  0.53 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 242 
 TYR   0.019   0.002   TYR I  91 
 PHE   0.014   0.002   PHE J 295 
 TRP   0.008   0.001   TRP H 306 
 HIS   0.006   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5261)
  covalent geometry    : angle       0.55430 ( 7121)
  hydrogen bonds       : bond        0.04723 (  273)
  hydrogen bonds       : angle       4.50492 (  768)

*********************** 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
  104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.270 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6913 (ttmt)
REVERT: J   52 LYS cc_start: 0.6376 (OUTLIER) cc_final: 0.6027 (ptpp)
  outliers start: 10
  outliers final: 4
  residues processed: 100
  average time/residue: 0.7003
  time to fit residues: 72.4552
Evaluate side-chains
  98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 39 optimal weight:    0.1980
   chunk 4 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4071 r_free = 0.4071 target = 0.177392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.147806 restraints weight = 11357.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.43
r_work: 0.3559 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3438
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3438
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5261  Z= 0.115
  Angle     :  0.533   6.622   7121  Z= 0.270
  Chirality :  0.040   0.139    777
  Planarity :  0.004   0.039    905
  Dihedral  : 13.960 123.103    737
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.72 %
    Favored  : 84.48 %
  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 aren not related in a simple way.
  whole:  2.37 (0.34), residues: 618
  helix:  2.43 (0.28), residues: 340
  sheet:  None (None), residues: 0
  loop :  0.58 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 242 
 TYR   0.018   0.002   TYR I  91 
 PHE   0.013   0.001   PHE I 110 
 TRP   0.007   0.001   TRP H 306 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 5261)
  covalent geometry    : angle       0.53273 ( 7121)
  hydrogen bonds       : bond        0.04382 (  273)
  hydrogen bonds       : angle       4.38488 (  768)

*********************** 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
  106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.213 
Fit side-chains
REVERT: I  260 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6914 (ttmt)
  outliers start: 10
  outliers final: 4
  residues processed: 103
  average time/residue: 0.6927
  time to fit residues: 73.8938
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  : 0.239 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0970
   chunk 40 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.9382

-------------------------------------------------------------------------------
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 = 0.4036 r_free = 0.4036 target = 0.174307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.147044 restraints weight = 8462.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 1.28
r_work: 0.3541 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
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 = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.0818

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= 0.184
  Angle     :  0.637   7.436   7121  Z= 0.323
  Chirality :  0.043   0.146    777
  Planarity :  0.005   0.039    905
  Dihedral  : 14.407 120.411    735
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.10 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.36 %
    Favored  : 84.84 %
  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 aren not related in a simple way.
  whole:  1.97 (0.33), residues: 618
  helix:  2.09 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop :  0.42 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG J 167 
 TYR   0.021   0.002   TYR I  91 
 PHE   0.017   0.002   PHE J 295 
 TRP   0.012   0.002   TRP J 237 
 HIS   0.010   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 5261)
  covalent geometry    : angle       0.63724 ( 7121)
  hydrogen bonds       : bond        0.05424 (  273)
  hydrogen bonds       : angle       4.69460 (  768)

*********************** 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
  102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.204 
Fit side-chains
REVERT: I   29 LYS cc_start: 0.7732 (mttt) cc_final: 0.7531 (mttt)
REVERT: I  260 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6901 (ttmt)
REVERT: J   42 LYS cc_start: 0.6010 (ttmt) cc_final: 0.5333 (mttp)
REVERT: J   52 LYS cc_start: 0.6437 (OUTLIER) cc_final: 0.6075 (ptpp)
  outliers start: 10
  outliers final: 4
  residues processed: 98
  average time/residue: 0.7362
  time to fit residues: 74.7426
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  : 0.217 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 32 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   overall best weight:    2.6988

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.173428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.143434 restraints weight = 11911.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.58
r_work: 0.3490 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    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 = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.0853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5261  Z= 0.231
  Angle     :  0.705   8.334   7121  Z= 0.355
  Chirality :  0.046   0.169    777
  Planarity :  0.006   0.046    905
  Dihedral  : 14.623 118.104    735
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.10 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.18 %
    Favored  : 84.84 %
  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 aren not related in a simple way.
  whole:  1.64 (0.33), residues: 618
  helix:  1.81 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop :  0.28 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J 167 
 TYR   0.024   0.003   TYR H 287 
 PHE   0.019   0.003   PHE J 295 
 TRP   0.015   0.003   TRP J 237 
 HIS   0.012   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 5261)
  covalent geometry    : angle       0.70456 ( 7121)
  hydrogen bonds       : bond        0.05901 (  273)
  hydrogen bonds       : angle       4.87939 (  768)

*********************** 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
  99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.244 
Fit side-chains
REVERT: J   13 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5820 (pt0)
REVERT: J   52 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6140 (ptpp)
  outliers start: 11
  outliers final: 6
  residues processed: 97
  average time/residue: 0.7565
  time to fit residues: 75.9464
Evaluate side-chains
  94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  235 SER
Chi-restraints excluded: chain J residue   13 GLU
Chi-restraints excluded: chain J residue   52 LYS
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  235 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 183 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 = 0.4033 r_free = 0.4033 target = 0.174082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.144521 restraints weight = 14444.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.66
r_work: 0.3499 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.0824

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= 0.193
  Angle     :  0.658   7.961   7121  Z= 0.333
  Chirality :  0.044   0.163    777
  Planarity :  0.005   0.040    905
  Dihedral  : 14.602 119.810    735
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.54
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.33), residues: 618
  helix:  1.85 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop :  0.26 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG J 167 
 TYR   0.024   0.003   TYR H 287 
 PHE   0.017   0.002   PHE J 295 
 TRP   0.010   0.002   TRP J 237 
 HIS   0.009   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 5261)
  covalent geometry    : angle       0.65774 ( 7121)
  hydrogen bonds       : bond        0.05500 (  273)
  hydrogen bonds       : angle       4.79085 (  768)

********************** 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
  103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.226 
Fit side-chains
REVERT: J   13 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5801 (pt0)
REVERT: J   52 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.6126 (ptpp)
  outliers start: 9
  outliers final: 3
  residues processed: 100
  average time/residue: 0.7743
  time to fit residues: 80.0182
Evaluate side-chains
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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 J residue   13 GLU
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 38 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.4048 r_free = 0.4048 target = 0.175285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.146087 restraints weight = 12486.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 1.55
r_work: 0.3521 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3420 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.0895

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= 0.149
  Angle     :  0.607   7.607   7121  Z= 0.306
  Chirality :  0.042   0.151    777
  Planarity :  0.004   0.040    905
  Dihedral  : 14.308 121.284    735
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.10 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.08 %
    Favored  : 84.48 %
  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 aren not related in a simple way.
  whole:  1.94 (0.33), residues: 618
  helix:  2.09 (0.28), residues: 340
  sheet:  None (None), residues: 0
  loop :  0.37 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J  61 
 TYR   0.019   0.002   TYR I  91 
 PHE   0.015   0.002   PHE J 295 
 TRP   0.009   0.002   TRP J 132 
 HIS   0.007   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5261)
  covalent geometry    : angle       0.60669 ( 7121)
  hydrogen bonds       : bond        0.04984 (  273)
  hydrogen bonds       : angle       4.61108 (  768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3556.79 seconds
wall clock time: 61 minutes 13.64 seconds (3673.64 seconds total)