Starting phenix.real_space_refine
on Wed Feb  4 11:25:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s0t_19628/02_2026/8s0t_19628_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s0t_19628/02_2026/8s0t_19628.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s0t_19628/02_2026/8s0t_19628_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s0t_19628/02_2026/8s0t_19628_neut_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s0t_19628/02_2026/8s0t_19628.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s0t_19628/02_2026/8s0t_19628.map"
  }
  resolution = 2.3
  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=   0.004
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: 7
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      31      5.16       5
     C    3297      2.51       5
     N     870      2.21       5
     O    1059      1.98       5
     F       3      1.80       5
     H    5404      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10665
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 998
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 4515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 4515
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 13, 'TRANS': 260}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 4683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 4683
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 17, 'TRANS': 273}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'YNK': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 63
          Classifications: {'water': 21}
          Link IDs: {None: 20}
    Chain: "I"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 162
          Classifications: {'water': 54}
          Link IDs: {None: 53}
    Chain: "J"
      Number of atoms: 210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 210
          Classifications: {'water': 70}
          Link IDs: {None: 69}
  Time building chain proxies: 2.11, per 1000 atoms: 0.20
  Number of scatterers: 10665
  At special positions: 0
  Unit cell: (85.635, 93.42, 72.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      31     16.00
     P       1     15.00
     F       3      9.00
     O    1059      8.00
     N     870      7.00
     C    3297      6.00
     H    5404      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 357.7 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:  1198

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      61.3% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'H' and resid 264 through 269
      removed outlier: 4.553A  pdb=" N   ARG H 268 " --> pdb=" O   GLU H 264 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 270 through 275
      removed outlier: 3.601A  pdb=" N   ASN H 273 " --> pdb=" O   GLY H 270 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL H 275 " --> pdb=" O   LEU H 272 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 279 through 285
    Processing helix  chain 'H' and resid 288 through 302
      removed outlier: 3.942A  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 12
      removed outlier: 4.076A  pdb=" N   THR I  12 " --> pdb=" O   LYS I   8 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 15 through 36
    Processing helix  chain 'I' and resid 49 through 71
    Processing helix  chain 'I' and resid 76 through 91
      removed outlier: 3.542A  pdb=" N   TYR I  91 " --> pdb=" O   PHE I  87 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 116
      removed outlier: 3.841A  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: 4.913A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.932A  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: 3.575A  pdb=" N   LEU I 200 " --> pdb=" O   ASN I 196 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR I 201 " --> pdb=" O   ARG I 197 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 224
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.601A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 241 through 262
    Processing helix  chain 'I' and resid 266 through 283
      removed outlier: 3.769A  pdb=" N   VAL I 272 " --> pdb=" O   GLU I 268 " (cutoff:3.500A)
    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 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: 3.871A  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 12 through 20
      removed outlier: 6.664A  pdb=" N   LYS J  28 " --> pdb=" O   LEU J  15 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   PHE J  17 " --> pdb=" O   VAL J  26 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   VAL J  26 " --> pdb=" O   PHE J  17 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   GLY J  19 " --> pdb=" O   ALA J  24 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   ALA J  24 " --> pdb=" O   GLY J  19 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   ILE J  87 " --> pdb=" O   ILE J  43 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 7.878A  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

    270 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: 2.35

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 5391
        1.13 -     1.30: 822
        1.30 -     1.48: 2133
        1.48 -     1.65: 2244
        1.65 -     1.82: 52
  Bond restraints: 10642
  Sorted by residual:
  bond pdb=" O   HOH J 525 "
       pdb=" H1  HOH J 525 "
    ideal  model  delta    sigma   weight residual
    0.850  1.027 -0.177 2.00e-02 2.50e+03 7.83e+01
  bond pdb=" O   HOH J 559 "
       pdb=" H2  HOH J 559 "
    ideal  model  delta    sigma   weight residual
    0.850  1.027 -0.177 2.00e-02 2.50e+03 7.82e+01
  bond pdb=" O   HOH J 556 "
       pdb=" H1  HOH J 556 "
    ideal  model  delta    sigma   weight residual
    0.850  1.026 -0.176 2.00e-02 2.50e+03 7.75e+01
  bond pdb=" O   HOH I 412 "
       pdb=" H2  HOH I 412 "
    ideal  model  delta    sigma   weight residual
    0.850  1.026 -0.176 2.00e-02 2.50e+03 7.71e+01
  bond pdb=" O   HOH H 419 "
       pdb=" H2  HOH H 419 "
    ideal  model  delta    sigma   weight residual
    0.850  1.025 -0.175 2.00e-02 2.50e+03 7.67e+01
  ... (remaining 10637 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 14097
        2.75 -     5.50: 4247
        5.50 -     8.26: 498
        8.26 -    11.01: 19
       11.01 -    13.76: 13
  Bond angle restraints: 18874
  Sorted by residual:
  angle pdb=" CA  ASP J 146 "
        pdb=" CB  ASP J 146 "
        pdb=" CG  ASP J 146 "
      ideal   model   delta    sigma   weight residual
     112.60  122.82  -10.22 1.00e+00 1.00e+00 1.04e+02
  angle pdb=" CA  ASP I 192 "
        pdb=" CB  ASP I 192 "
        pdb=" CG  ASP I 192 "
      ideal   model   delta    sigma   weight residual
     112.60  121.31   -8.71 1.00e+00 1.00e+00 7.59e+01
  angle pdb=" CA  ASP I  25 "
        pdb=" CB  ASP I  25 "
        pdb=" CG  ASP I  25 "
      ideal   model   delta    sigma   weight residual
     112.60  120.87   -8.27 1.00e+00 1.00e+00 6.85e+01
  angle pdb=" CA  ASP J  97 "
        pdb=" CB  ASP J  97 "
        pdb=" CG  ASP J  97 "
      ideal   model   delta    sigma   weight residual
     112.60  119.97   -7.37 1.00e+00 1.00e+00 5.44e+01
  angle pdb=" N   LYS J 139 "
        pdb=" CA  LYS J 139 "
        pdb=" C   LYS J 139 "
      ideal   model   delta    sigma   weight residual
     108.13  101.81    6.32 9.00e-01 1.23e+00 4.93e+01
  ... (remaining 18869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.89: 4345
       20.89 -    41.77: 363
       41.77 -    62.66: 161
       62.66 -    83.54: 13
       83.54 -   104.43: 7
  Dihedral angle restraints: 4889
    sinusoidal: 2679
      harmonic: 2210
  Sorted by residual:
  dihedral pdb=" CA  THR J 175 "
           pdb=" C   THR J 175 "
           pdb=" N   ARG J 176 "
           pdb=" CA  ARG J 176 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.77  -28.23     0      5.00e+00 4.00e-02 3.19e+01
  dihedral pdb=" CA  LYS I  72 "
           pdb=" C   LYS I  72 "
           pdb=" N   PRO I  73 "
           pdb=" CA  PRO I  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.36   26.64     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" CA  ASN J 297 "
           pdb=" C   ASN J 297 "
           pdb=" N   ARG J 298 "
           pdb=" CA  ARG J 298 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.73  -25.27     0      5.00e+00 4.00e-02 2.55e+01
  ... (remaining 4886 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 383
       0.093 -    0.186: 245
       0.186 -    0.279: 111
       0.279 -    0.372: 32
       0.372 -    0.466: 8
  Chirality restraints: 779
  Sorted by residual:
  chirality pdb=" CG  LEU J 125 "
            pdb=" CB  LEU J 125 "
            pdb=" CD1 LEU J 125 "
            pdb=" CD2 LEU J 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.12   -0.47 2.00e-01 2.50e+01 5.42e+00
  chirality pdb=" CG  LEU I  65 "
            pdb=" CB  LEU I  65 "
            pdb=" CD1 LEU I  65 "
            pdb=" CD2 LEU I  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.15   -0.44 2.00e-01 2.50e+01 4.89e+00
  chirality pdb=" CA  PRO J 238 "
            pdb=" N   PRO J 238 "
            pdb=" C   PRO J 238 "
            pdb=" CB  PRO J 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.28    0.44 2.00e-01 2.50e+01 4.80e+00
  ... (remaining 776 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C14 YNK J 401 "    0.070 2.00e-02 2.50e+03   1.46e-01 6.92e+02
        pdb=" C16 YNK J 401 "    0.028 2.00e-02 2.50e+03
        pdb=" C17 YNK J 401 "    0.198 2.00e-02 2.50e+03
        pdb=" C19 YNK J 401 "   -0.007 2.00e-02 2.50e+03
        pdb=" C20 YNK J 401 "   -0.092 2.00e-02 2.50e+03
        pdb=" C21 YNK J 401 "   -0.066 2.00e-02 2.50e+03
        pdb=" C22 YNK J 401 "    0.125 2.00e-02 2.50e+03
        pdb=" C24 YNK J 401 "   -0.148 2.00e-02 2.50e+03
        pdb=" C25 YNK J 401 "   -0.166 2.00e-02 2.50e+03
        pdb=" C26 YNK J 401 "   -0.063 2.00e-02 2.50e+03
        pdb=" N18 YNK J 401 "    0.092 2.00e-02 2.50e+03
        pdb=" N23 YNK J 401 "    0.281 2.00e-02 2.50e+03
        pdb=" P27 YNK J 401 "   -0.251 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS I 157 "   -0.137 2.00e-02 2.50e+03   9.99e-02 2.24e+02
        pdb=" CG  HIS I 157 "   -0.039 2.00e-02 2.50e+03
        pdb=" ND1 HIS I 157 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 HIS I 157 "    0.039 2.00e-02 2.50e+03
        pdb=" CE1 HIS I 157 "   -0.081 2.00e-02 2.50e+03
        pdb=" NE2 HIS I 157 "   -0.005 2.00e-02 2.50e+03
        pdb=" HD1 HIS I 157 "    0.210 2.00e-02 2.50e+03
        pdb=" HD2 HIS I 157 "    0.104 2.00e-02 2.50e+03
        pdb=" HE1 HIS I 157 "   -0.078 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP J 177 "    0.171 2.00e-02 2.50e+03   7.12e-02 2.03e+02
        pdb=" CG  TRP J 177 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP J 177 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD2 TRP J 177 "    0.010 2.00e-02 2.50e+03
        pdb=" NE1 TRP J 177 "   -0.055 2.00e-02 2.50e+03
        pdb=" CE2 TRP J 177 "    0.016 2.00e-02 2.50e+03
        pdb=" CE3 TRP J 177 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ2 TRP J 177 "    0.064 2.00e-02 2.50e+03
        pdb=" CZ3 TRP J 177 "   -0.055 2.00e-02 2.50e+03
        pdb=" CH2 TRP J 177 "    0.039 2.00e-02 2.50e+03
        pdb=" HD1 TRP J 177 "   -0.052 2.00e-02 2.50e+03
        pdb=" HE1 TRP J 177 "   -0.095 2.00e-02 2.50e+03
        pdb=" HE3 TRP J 177 "   -0.044 2.00e-02 2.50e+03
        pdb=" HZ2 TRP J 177 "    0.090 2.00e-02 2.50e+03
        pdb=" HZ3 TRP J 177 "   -0.105 2.00e-02 2.50e+03
        pdb=" HH2 TRP J 177 "    0.053 2.00e-02 2.50e+03
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 766
        2.15 -     2.76: 18737
        2.76 -     3.38: 35556
        3.38 -     3.99: 47565
        3.99 -     4.60: 68701
  Nonbonded interactions: 171325
  Sorted by model distance:
  nonbonded pdb=" O   GLY H 285 "
            pdb=" H2  HOH H 401 "
     model   vdw
     1.538 2.450
  nonbonded pdb=" O   PHE J 295 "
            pdb=" H2  HOH J 501 "
     model   vdw
     1.567 2.450
  nonbonded pdb=" HE1 TRP I  11 "
            pdb=" HD1 HIS I 157 "
     model   vdw
     1.594 2.100
  nonbonded pdb=" O   VAL J 194 "
            pdb=" H2  HOH J 503 "
     model   vdw
     1.598 2.450
  nonbonded pdb=" H1  HOH J 525 "
            pdb=" O   HOH J 568 "
     model   vdw
     1.603 2.450
  ... (remaining 171320 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.050
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     11.270
  Find NCS groups from input model:        0.040
  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:7.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
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      :  0.013   0.077   5238  Z= 0.819
  Angle     :  2.144  10.215   7093  Z= 1.481
  Chirality :  0.144   0.466    779
  Planarity :  0.018   0.146    900
  Dihedral  : 16.207 104.429   1983
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  3.56 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  :  7.55 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.67 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.29), residues: 618
  helix: -1.90 (0.22), residues: 346
  sheet: -0.73 (1.03), residues: 27
  loop : -1.45 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG J 309 
 TYR   0.138   0.031   TYR I   2 
 PHE   0.110   0.025   PHE I  47 
 TRP   0.103   0.029   TRP J 177 
 HIS   0.039   0.010   HIS I 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.01310 ( 5238)
  covalent geometry    : angle       2.14425 ( 7093)
  hydrogen bonds       : bond        0.17300 (  270)
  hydrogen bonds       : angle       7.52015 (  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
  113 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: H  276 ARG cc_start: 0.5779 (ttp80) cc_final: 0.4971 (pmt170)
REVERT: I   65 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7444 (mm)
REVERT: I  131 GLU cc_start: 0.4709 (OUTLIER) cc_final: 0.4299 (mt-10)
REVERT: I  144 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7984 (mt)
REVERT: I  279 ARG cc_start: 0.6363 (ttm110) cc_final: 0.5807 (ttt180)
  outliers start: 18
  outliers final: 5
  residues processed: 106
  average time/residue: 1.2054
  time to fit residues: 133.3975
Evaluate side-chains
  82 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue  131 GLU
Chi-restraints excluded: chain I residue  144 LEU
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  164 SER
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I 124 GLN
J  86 ASN
J 171 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.178886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.160833 restraints weight = 17324.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 1.42
r_work: 0.3843 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3740 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3738
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3738 r_free = 0.3738    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3737 r_free = 0.3737    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3737
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   5238  Z= 0.166
  Angle     :  0.689   6.211   7093  Z= 0.363
  Chirality :  0.042   0.166    779
  Planarity :  0.005   0.051    900
  Dihedral  :  9.749  84.238    733
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.25 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.30), residues: 618
  helix: -0.14 (0.25), residues: 349
  sheet: -1.57 (1.14), residues: 19
  loop : -1.45 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG I  28 
 TYR   0.015   0.002   TYR J 169 
 PHE   0.023   0.002   PHE I  30 
 TRP   0.011   0.002   TRP J 132 
 HIS   0.008   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5238)
  covalent geometry    : angle       0.68897 ( 7093)
  hydrogen bonds       : bond        0.05369 (  270)
  hydrogen bonds       : angle       5.53910 (  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
  97 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6115 (mt) cc_final: 0.5795 (mp)
REVERT: H  276 ARG cc_start: 0.5639 (ttp80) cc_final: 0.4743 (pmt170)
REVERT: I  250 ASP cc_start: 0.5582 (OUTLIER) cc_final: 0.5164 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 93
  average time/residue: 1.3579
  time to fit residues: 131.2095
Evaluate side-chains
  80 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue  250 ASP
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  164 SER
Chi-restraints excluded: chain J residue  189 MET
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.180104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.161705 restraints weight = 17405.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 1.47
r_work: 0.3855 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   5238  Z= 0.126
  Angle     :  0.566   4.536   7093  Z= 0.296
  Chirality :  0.039   0.143    779
  Planarity :  0.005   0.069    900
  Dihedral  :  7.960  81.008    724
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.07 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.33 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.32), residues: 618
  helix:  0.77 (0.27), residues: 350
  sheet: -1.67 (1.11), residues: 19
  loop : -1.14 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG I 279 
 TYR   0.014   0.001   TYR J 178 
 PHE   0.016   0.002   PHE I 110 
 TRP   0.009   0.001   TRP J 132 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5238)
  covalent geometry    : angle       0.56583 ( 7093)
  hydrogen bonds       : bond        0.04482 (  270)
  hydrogen bonds       : angle       5.12593 (  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
  90 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.5947 (mt) cc_final: 0.5645 (mp)
REVERT: H  276 ARG cc_start: 0.5720 (ttp80) cc_final: 0.4753 (pmt170)
REVERT: I   65 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7487 (mm)
REVERT: I  202 ASP cc_start: 0.7222 (m-30) cc_final: 0.6777 (m-30)
REVERT: I  260 LYS cc_start: 0.6897 (ttmp) cc_final: 0.6363 (tttp)
REVERT: I  279 ARG cc_start: 0.6773 (mtm110) cc_final: 0.5279 (ptt-90)
REVERT: J   96 THR cc_start: 0.7555 (p) cc_final: 0.7311 (t)
  outliers start: 7
  outliers final: 3
  residues processed: 87
  average time/residue: 1.3932
  time to fit residues: 126.1494
Evaluate side-chains
  79 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
J  36 GLN
** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.175853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.157280 restraints weight = 17668.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 1.48
r_work: 0.3812 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3709 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3709 r_free = 0.3709    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5238  Z= 0.190
  Angle     :  0.598   4.873   7093  Z= 0.311
  Chirality :  0.040   0.144    779
  Planarity :  0.004   0.038    900
  Dihedral  :  7.918  79.550    723
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.59 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.13 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.32), residues: 618
  helix:  0.71 (0.27), residues: 350
  sheet: -1.75 (1.07), residues: 19
  loop : -1.23 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 283 
 TYR   0.013   0.002   TYR J 178 
 PHE   0.015   0.002   PHE I  71 
 TRP   0.008   0.002   TRP I  11 
 HIS   0.008   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 5238)
  covalent geometry    : angle       0.59767 ( 7093)
  hydrogen bonds       : bond        0.04775 (  270)
  hydrogen bonds       : angle       5.15189 (  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
  91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6067 (mt) cc_final: 0.5818 (mp)
REVERT: H  276 ARG cc_start: 0.5711 (ttp80) cc_final: 0.4755 (pmt170)
REVERT: I   49 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.6085 (mt-10)
REVERT: I  202 ASP cc_start: 0.7323 (m-30) cc_final: 0.6902 (m-30)
REVERT: I  260 LYS cc_start: 0.6924 (ttmp) cc_final: 0.6345 (tttp)
  outliers start: 9
  outliers final: 5
  residues processed: 88
  average time/residue: 1.5138
  time to fit residues: 138.3168
Evaluate side-chains
  85 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  262 SER
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
J  22 GLN
** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.177351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.158703 restraints weight = 17266.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 1.47
r_work: 0.3818 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5238  Z= 0.163
  Angle     :  0.581   4.875   7093  Z= 0.299
  Chirality :  0.040   0.138    779
  Planarity :  0.005   0.048    900
  Dihedral  :  7.725  77.662    721
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.91 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.67 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.33), residues: 618
  helix:  0.89 (0.28), residues: 350
  sheet: -1.71 (1.05), residues: 19
  loop : -1.17 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I 279 
 TYR   0.013   0.002   TYR H 248 
 PHE   0.013   0.002   PHE I  30 
 TRP   0.009   0.002   TRP J 132 
 HIS   0.006   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5238)
  covalent geometry    : angle       0.58068 ( 7093)
  hydrogen bonds       : bond        0.04511 (  270)
  hydrogen bonds       : angle       5.05766 (  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
  87 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6031 (mt) cc_final: 0.5806 (mp)
REVERT: H  276 ARG cc_start: 0.5700 (ttp80) cc_final: 0.4735 (pmt170)
REVERT: I   49 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6172 (mt-10)
REVERT: I  202 ASP cc_start: 0.7269 (m-30) cc_final: 0.7056 (m-30)
REVERT: I  260 LYS cc_start: 0.6930 (ttmp) cc_final: 0.6407 (tttp)
REVERT: I  279 ARG cc_start: 0.6711 (mtm110) cc_final: 0.5286 (ptt-90)
  outliers start: 7
  outliers final: 4
  residues processed: 85
  average time/residue: 1.4406
  time to fit residues: 127.3727
Evaluate side-chains
  82 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  262 SER
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
J  22 GLN
** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.175369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.156719 restraints weight = 17690.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 1.48
r_work: 0.3789 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3688 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5238  Z= 0.201
  Angle     :  0.610   5.283   7093  Z= 0.315
  Chirality :  0.041   0.141    779
  Planarity :  0.005   0.038    900
  Dihedral  :  7.780  77.172    721
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.07 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.13 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.32), residues: 618
  helix:  0.76 (0.27), residues: 350
  sheet: -1.75 (1.02), residues: 19
  loop : -1.16 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 279 
 TYR   0.014   0.002   TYR J 178 
 PHE   0.014   0.002   PHE I  30 
 TRP   0.010   0.002   TRP I  11 
 HIS   0.007   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 5238)
  covalent geometry    : angle       0.61003 ( 7093)
  hydrogen bonds       : bond        0.04775 (  270)
  hydrogen bonds       : angle       5.12181 (  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
  93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6183 (mt) cc_final: 0.5961 (mp)
REVERT: H  276 ARG cc_start: 0.5689 (ttp80) cc_final: 0.4713 (pmt170)
REVERT: I   49 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6177 (mt-10)
REVERT: I  250 ASP cc_start: 0.5630 (OUTLIER) cc_final: 0.5234 (m-30)
  outliers start: 13
  outliers final: 6
  residues processed: 86
  average time/residue: 1.2804
  time to fit residues: 114.6128
Evaluate side-chains
  89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  250 ASP
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  262 SER
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 3 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 56 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0970
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
J  22 GLN
** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.179894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.161518 restraints weight = 17291.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 1.48
r_work: 0.3846 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3744 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3744
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3744 r_free = 0.3744    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3744 r_free = 0.3744    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3744
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5238  Z= 0.110
  Angle     :  0.533   4.555   7093  Z= 0.272
  Chirality :  0.038   0.144    779
  Planarity :  0.005   0.061    900
  Dihedral  :  7.534  74.704    721
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.43 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 14.39 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.33), residues: 618
  helix:  1.32 (0.28), residues: 344
  sheet: -1.72 (1.09), residues: 19
  loop : -0.94 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG I 279 
 TYR   0.011   0.001   TYR I  60 
 PHE   0.018   0.001   PHE I 110 
 TRP   0.010   0.001   TRP J 132 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5238)
  covalent geometry    : angle       0.53329 ( 7093)
  hydrogen bonds       : bond        0.03961 (  270)
  hydrogen bonds       : angle       4.81733 (  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
  91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: I  260 LYS cc_start: 0.6987 (ttmp) cc_final: 0.6482 (tttp)
REVERT: I  279 ARG cc_start: 0.6677 (mtm110) cc_final: 0.5304 (ptt-90)
  outliers start: 6
  outliers final: 3
  residues processed: 88
  average time/residue: 1.2173
  time to fit residues: 111.4346
Evaluate side-chains
  80 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
J 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.179789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.161437 restraints weight = 17496.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 1.48
r_work: 0.3843 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5238  Z= 0.115
  Angle     :  0.530   4.510   7093  Z= 0.270
  Chirality :  0.038   0.144    779
  Planarity :  0.004   0.048    900
  Dihedral  :  7.456  75.015    721
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.27 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 16.37 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.33), residues: 618
  helix:  1.35 (0.28), residues: 349
  sheet: -1.57 (1.04), residues: 20
  loop : -0.89 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I 279 
 TYR   0.011   0.001   TYR J 178 
 PHE   0.016   0.001   PHE I 110 
 TRP   0.010   0.001   TRP J 132 
 HIS   0.004   0.001   HIS J 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5238)
  covalent geometry    : angle       0.52950 ( 7093)
  hydrogen bonds       : bond        0.03934 (  270)
  hydrogen bonds       : angle       4.72827 (  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
  87 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: I  202 ASP cc_start: 0.7302 (m-30) cc_final: 0.7007 (m-30)
REVERT: I  260 LYS cc_start: 0.6978 (ttmp) cc_final: 0.6493 (tttp)
REVERT: I  279 ARG cc_start: 0.6680 (mtm110) cc_final: 0.5300 (ptt-90)
REVERT: J  172 GLN cc_start: 0.4396 (mp-120) cc_final: 0.4188 (tp-100)
  outliers start: 4
  outliers final: 3
  residues processed: 85
  average time/residue: 1.1888
  time to fit residues: 105.1336
Evaluate side-chains
  79 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
J  22 GLN
J 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.175875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.157268 restraints weight = 17577.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 1.47
r_work: 0.3795 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3695 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3694 r_free = 0.3694    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3694 r_free = 0.3694    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5238  Z= 0.188
  Angle     :  0.596   4.452   7093  Z= 0.306
  Chirality :  0.040   0.138    779
  Planarity :  0.005   0.039    900
  Dihedral  :  7.646  75.844    721
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.75 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 16.01 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.33), residues: 618
  helix:  1.03 (0.27), residues: 350
  sheet: -1.76 (1.03), residues: 19
  loop : -0.92 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG I 279 
 TYR   0.015   0.002   TYR J 178 
 PHE   0.018   0.002   PHE I 125 
 TRP   0.009   0.002   TRP I  11 
 HIS   0.006   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 5238)
  covalent geometry    : angle       0.59582 ( 7093)
  hydrogen bonds       : bond        0.04551 (  270)
  hydrogen bonds       : angle       4.92106 (  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
  81 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: H  276 ARG cc_start: 0.5681 (tmm160) cc_final: 0.4643 (pmt170)
REVERT: I   49 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6182 (mt-10)
REVERT: I  202 ASP cc_start: 0.7452 (m-30) cc_final: 0.7172 (m-30)
REVERT: I  260 LYS cc_start: 0.6914 (ttmp) cc_final: 0.6423 (tttp)
REVERT: I  279 ARG cc_start: 0.6659 (mtm110) cc_final: 0.5258 (ptt-90)
  outliers start: 5
  outliers final: 3
  residues processed: 79
  average time/residue: 1.3781
  time to fit residues: 113.0544
Evaluate side-chains
  79 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 0 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
J  22 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.178137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.159550 restraints weight = 17384.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 1.49
r_work: 0.3823 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3721 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5238  Z= 0.145
  Angle     :  0.564   4.280   7093  Z= 0.288
  Chirality :  0.039   0.142    779
  Planarity :  0.004   0.041    900
  Dihedral  :  7.587  74.853    721
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.59 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 16.37 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.33), residues: 618
  helix:  1.16 (0.28), residues: 350
  sheet: -1.76 (1.04), residues: 19
  loop : -0.85 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I 279 
 TYR   0.012   0.001   TYR J 178 
 PHE   0.018   0.002   PHE I 125 
 TRP   0.009   0.002   TRP J 132 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5238)
  covalent geometry    : angle       0.56417 ( 7093)
  hydrogen bonds       : bond        0.04244 (  270)
  hydrogen bonds       : angle       4.84876 (  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
  80 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: H  276 ARG cc_start: 0.5697 (tmm160) cc_final: 0.4656 (pmt170)
REVERT: I  260 LYS cc_start: 0.6975 (ttmp) cc_final: 0.6477 (tttp)
REVERT: I  279 ARG cc_start: 0.6673 (mtm110) cc_final: 0.5300 (ptt-90)
REVERT: J  172 GLN cc_start: 0.4496 (mp-120) cc_final: 0.4064 (pt0)
  outliers start: 3
  outliers final: 3
  residues processed: 79
  average time/residue: 1.2354
  time to fit residues: 101.4780
Evaluate side-chains
  79 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue   95 GLU
Chi-restraints excluded: chain J residue  277 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.179450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.160963 restraints weight = 17418.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 1.49
r_work: 0.3839 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3739 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3738
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3738 r_free = 0.3738    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3738 r_free = 0.3738    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3738
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   5238  Z= 0.121
  Angle     :  0.537   4.211   7093  Z= 0.274
  Chirality :  0.038   0.143    779
  Planarity :  0.004   0.041    900
  Dihedral  :  7.474  74.480    721
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.75 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 16.55 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.34), residues: 618
  helix:  1.38 (0.28), residues: 349
  sheet: -1.56 (1.02), residues: 20
  loop : -0.73 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I 279 
 TYR   0.010   0.001   TYR J 178 
 PHE   0.018   0.002   PHE I 125 
 TRP   0.010   0.001   TRP J 132 
 HIS   0.003   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 5238)
  covalent geometry    : angle       0.53730 ( 7093)
  hydrogen bonds       : bond        0.03964 (  270)
  hydrogen bonds       : angle       4.71308 (  768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4519.15 seconds
wall clock time: 77 minutes 10.75 seconds (4630.75 seconds total)