Starting phenix.real_space_refine
on Fri Feb 14 17:28:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s0t_19628/02_2025/8s0t_19628_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s0t_19628/02_2025/8s0t_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s0t_19628/02_2025/8s0t_19628.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s0t_19628/02_2025/8s0t_19628.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s0t_19628/02_2025/8s0t_19628_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s0t_19628/02_2025/8s0t_19628_neut_trim.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.12, per 1000 atoms: 0.48
  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: 2.89
  Conformation dependent library (CDL) restraints added in 703.0 milliseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  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: 0.80
  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: 3.85

  Time building geometry restraints manager: 3.35 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:             0.550
  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:             0.190
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     25.550
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.140
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.110
-------------------------------------------------------------------------------
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= 0.848
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (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
 TRP   0.103   0.029   TRP J 177 
 HIS   0.039   0.010   HIS I 157 
 PHE   0.110   0.025   PHE I  47 
 TYR   0.138   0.031   TYR I   2 
 ARG   0.009   0.002   ARG J 309 

*********************** 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  : 0.852 
Fit side-chains
   revert: symmetry clash
REVERT: H  276 ARG cc_start: 0.5779 (ttp80) cc_final: 0.4970 (pmt170)
REVERT: I   65 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7443 (mm)
REVERT: I  131 GLU cc_start: 0.4709 (OUTLIER) cc_final: 0.4299 (mt-10)
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: 2.5503
  time to fit residues: 283.0868
Evaluate side-chains
  81 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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 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 52 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.3990

-------------------------------------------------------------------------------
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  22 GLN
J  86 ASN
** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.177144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.158773 restraints weight = 17327.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 1.44
r_work: 0.3829 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   5238  Z= 0.241
  Angle     :  0.704   6.192   7093  Z= 0.374
  Chirality :  0.043   0.171    779
  Planarity :  0.005   0.046    900
  Dihedral  :  9.618  84.198    731
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.10 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.07 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.30), residues: 618
  helix: -0.22 (0.25), residues: 349
  sheet: -1.59 (1.14), residues: 19
  loop : -1.47 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP J 132 
 HIS   0.009   0.002   HIS J 131 
 PHE   0.022   0.002   PHE I  30 
 TYR   0.015   0.002   TYR J 178 
 ARG   0.004   0.001   ARG I  28 

*********************** 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
  94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6202 (mt) cc_final: 0.5832 (mp)
REVERT: H  276 ARG cc_start: 0.5637 (ttp80) cc_final: 0.4741 (pmt170)
REVERT: I  250 ASP cc_start: 0.5589 (OUTLIER) cc_final: 0.5175 (m-30)
REVERT: J  172 GLN cc_start: 0.5468 (tp40) cc_final: 0.5113 (mp-120)
  outliers start: 11
  outliers final: 6
  residues processed: 90
  average time/residue: 2.7079
  time to fit residues: 254.3839
Evaluate side-chains
  84 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue  250 ASP
Chi-restraints excluded: chain I residue  272 VAL
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  277 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.176459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.157582 restraints weight = 17436.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 1.48
r_work: 0.3806 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3703 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3702 r_free = 0.3702    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5238  Z= 0.278
  Angle     :  0.640   5.124   7093  Z= 0.336
  Chirality :  0.041   0.152    779
  Planarity :  0.005   0.048    900
  Dihedral  :  8.346  81.374    724
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.43 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.51 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.31), residues: 618
  helix:  0.28 (0.26), residues: 350
  sheet: -1.66 (1.16), residues: 19
  loop : -1.34 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP J 132 
 HIS   0.009   0.002   HIS J 131 
 PHE   0.016   0.002   PHE I  71 
 TYR   0.017   0.002   TYR J 178 
 ARG   0.007   0.001   ARG I 279 

*********************** 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
  93 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6135 (mt) cc_final: 0.5839 (mp)
REVERT: H  276 ARG cc_start: 0.5719 (ttp80) cc_final: 0.4760 (pmt170)
REVERT: I   65 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7387 (mm)
REVERT: I  202 ASP cc_start: 0.7293 (m-30) cc_final: 0.6832 (m-30)
REVERT: I  279 ARG cc_start: 0.6830 (mtm110) cc_final: 0.6514 (mtp-110)
REVERT: J  172 GLN cc_start: 0.5176 (tp40) cc_final: 0.4913 (mp-120)
  outliers start: 11
  outliers final: 6
  residues processed: 88
  average time/residue: 2.6140
  time to fit residues: 240.4910
Evaluate side-chains
  84 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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  164 SER
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  262 SER
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 3 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.4083 r_free = 0.4083 target = 0.175003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.156251 restraints weight = 17491.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 1.46
r_work: 0.3779 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3678 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5238  Z= 0.305
  Angle     :  0.636   5.192   7093  Z= 0.333
  Chirality :  0.041   0.152    779
  Planarity :  0.005   0.039    900
  Dihedral  :  8.149  78.283    724
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.91 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 10.97 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.32), residues: 618
  helix:  0.40 (0.26), residues: 350
  sheet: -1.87 (1.10), residues: 19
  loop : -1.37 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP I  11 
 HIS   0.008   0.002   HIS J 131 
 PHE   0.017   0.002   PHE I  71 
 TYR   0.017   0.002   TYR J 178 
 ARG   0.004   0.001   ARG I  28 

*********************** 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
  94 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6124 (mt) cc_final: 0.5879 (mp)
REVERT: H  276 ARG cc_start: 0.5658 (ttp80) cc_final: 0.4704 (pmt170)
REVERT: I   49 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.6065 (mt-10)
REVERT: I  131 GLU cc_start: 0.5253 (OUTLIER) cc_final: 0.4774 (mt-10)
REVERT: I  202 ASP cc_start: 0.7317 (m-30) cc_final: 0.6933 (m-30)
REVERT: I  250 ASP cc_start: 0.5686 (OUTLIER) cc_final: 0.5298 (m-30)
REVERT: I  279 ARG cc_start: 0.6748 (mtm110) cc_final: 0.5213 (ptt-90)
  outliers start: 13
  outliers final: 7
  residues processed: 88
  average time/residue: 2.8024
  time to fit residues: 257.0389
Evaluate side-chains
  89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain I residue  131 GLU
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  189 MET
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  248 THR
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 26 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
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 = 0.4081 r_free = 0.4081 target = 0.174892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.156200 restraints weight = 17404.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 1.46
r_work: 0.3780 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3680 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3679 r_free = 0.3679    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3679 r_free = 0.3679    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5238  Z= 0.302
  Angle     :  0.630   5.193   7093  Z= 0.328
  Chirality :  0.041   0.146    779
  Planarity :  0.005   0.039    900
  Dihedral  :  7.910  77.275    721
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.40 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 11.87 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.32), residues: 618
  helix:  0.54 (0.27), residues: 350
  sheet: -1.68 (0.97), residues: 22
  loop : -1.33 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP J 132 
 HIS   0.008   0.001   HIS J 131 
 PHE   0.015   0.002   PHE I  30 
 TYR   0.016   0.002   TYR J 178 
 ARG   0.003   0.000   ARG I  28 

*********************** 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
  97 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6230 (mt) cc_final: 0.6005 (mp)
REVERT: I   49 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6143 (mt-10)
  outliers start: 16
  outliers final: 5
  residues processed: 88
  average time/residue: 2.7573
  time to fit residues: 253.1440
Evaluate side-chains
  86 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
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  216 ASP
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  262 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4103 r_free = 0.4103 target = 0.177067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.158599 restraints weight = 17587.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 1.46
r_work: 0.3810 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3709 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3707
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3707 r_free = 0.3707    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3707 r_free = 0.3707    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3707
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5238  Z= 0.202
  Angle     :  0.572   5.358   7093  Z= 0.294
  Chirality :  0.039   0.138    779
  Planarity :  0.005   0.061    900
  Dihedral  :  7.373  75.384    719
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.43 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.31 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.33), residues: 618
  helix:  0.82 (0.28), residues: 356
  sheet: -1.90 (1.10), residues: 19
  loop : -1.13 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP J 132 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.017   0.002   PHE I 110 
 TYR   0.013   0.001   TYR J 178 
 ARG   0.011   0.001   ARG I 279 

*********************** 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
  96 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6141 (mt) cc_final: 0.5926 (mp)
REVERT: H  276 ARG cc_start: 0.5633 (tmm160) cc_final: 0.4635 (pmt170)
REVERT: I  279 ARG cc_start: 0.6762 (mtm110) cc_final: 0.5343 (ptt-90)
  outliers start: 11
  outliers final: 4
  residues processed: 90
  average time/residue: 2.8549
  time to fit residues: 267.6817
Evaluate side-chains
  82 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
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  248 THR
Chi-restraints excluded: chain J residue  262 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.4085 r_free = 0.4085 target = 0.175447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.156731 restraints weight = 17724.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.47
r_work: 0.3787 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3687 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5238  Z= 0.271
  Angle     :  0.604   5.291   7093  Z= 0.312
  Chirality :  0.040   0.145    779
  Planarity :  0.005   0.038    900
  Dihedral  :  7.422  75.646    719
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.24 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.85 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.33), residues: 618
  helix:  0.81 (0.27), residues: 350
  sheet: -1.89 (1.09), residues: 19
  loop : -1.14 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP J 237 
 HIS   0.007   0.001   HIS J 131 
 PHE   0.015   0.002   PHE I  30 
 TYR   0.013   0.002   TYR H 248 
 ARG   0.007   0.001   ARG I 279 

*********************** 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
  92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  251 LEU cc_start: 0.6158 (mt) cc_final: 0.5941 (mp)
REVERT: H  276 ARG cc_start: 0.5688 (tmm160) cc_final: 0.4653 (pmt170)
REVERT: I   49 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.6115 (mt-10)
REVERT: I  202 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7040 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 87
  average time/residue: 2.7831
  time to fit residues: 252.7028
Evaluate side-chains
  86 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
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  202 ASP
Chi-restraints excluded: chain J residue   88 SER
Chi-restraints excluded: chain J residue  189 MET
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  262 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.177646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.159146 restraints weight = 17474.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 1.47
r_work: 0.3815 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5238  Z= 0.185
  Angle     :  0.552   4.818   7093  Z= 0.283
  Chirality :  0.038   0.144    779
  Planarity :  0.005   0.066    900
  Dihedral  :  6.908  74.402    716
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.27 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.75 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.33), residues: 618
  helix:  1.01 (0.28), residues: 356
  sheet: -1.89 (1.10), residues: 19
  loop : -0.92 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP J 132 
 HIS   0.005   0.001   HIS J 131 
 PHE   0.017   0.002   PHE I 110 
 TYR   0.012   0.001   TYR H 248 
 ARG   0.011   0.001   ARG I 279 

*********************** 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
  91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  276 ARG cc_start: 0.5659 (tmm160) cc_final: 0.4624 (pmt170)
REVERT: I   49 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.6102 (mt-10)
REVERT: I  202 ASP cc_start: 0.7287 (m-30) cc_final: 0.6997 (m-30)
REVERT: I  260 LYS cc_start: 0.6845 (ttmp) cc_final: 0.6306 (tttp)
REVERT: I  279 ARG cc_start: 0.6691 (mtm110) cc_final: 0.5250 (ptt-90)
  outliers start: 9
  outliers final: 4
  residues processed: 88
  average time/residue: 2.7421
  time to fit residues: 251.8379
Evaluate side-chains
  83 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
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  216 ASP
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  262 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 52 optimal weight:    0.2980
   chunk 15 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0570
   chunk 24 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.3902

-------------------------------------------------------------------------------
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**
J 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.177074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.158442 restraints weight = 17650.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 1.49
r_work: 0.3808 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5238  Z= 0.211
  Angle     :  0.561   4.748   7093  Z= 0.289
  Chirality :  0.039   0.142    779
  Planarity :  0.005   0.054    900
  Dihedral  :  6.881  74.992    716
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.59 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.47 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.33), residues: 618
  helix:  1.12 (0.28), residues: 350
  sheet: -1.82 (1.10), residues: 19
  loop : -0.94 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP J 132 
 HIS   0.006   0.001   HIS J 131 
 PHE   0.015   0.002   PHE I 110 
 TYR   0.013   0.002   TYR H 248 
 ARG   0.010   0.001   ARG I 279 

*********************** 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
  85 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  276 ARG cc_start: 0.5639 (tmm160) cc_final: 0.4610 (pmt170)
REVERT: I   49 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6126 (mt-10)
REVERT: I  202 ASP cc_start: 0.7308 (m-30) cc_final: 0.7014 (m-30)
REVERT: I  260 LYS cc_start: 0.6896 (ttmp) cc_final: 0.6368 (tttp)
REVERT: I  279 ARG cc_start: 0.6675 (mtm110) cc_final: 0.5261 (ptt-90)
  outliers start: 7
  outliers final: 5
  residues processed: 83
  average time/residue: 2.8662
  time to fit residues: 248.1538
Evaluate side-chains
  83 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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  189 MET
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  248 THR
Chi-restraints excluded: chain J residue  262 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    0.1980
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.6784

-------------------------------------------------------------------------------
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 = 0.4119 r_free = 0.4119 target = 0.178624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.160210 restraints weight = 17598.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 1.48
r_work: 0.3830 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3731 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5238  Z= 0.167
  Angle     :  0.541   4.677   7093  Z= 0.276
  Chirality :  0.038   0.143    779
  Planarity :  0.005   0.053    900
  Dihedral  :  6.766  73.919    716
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.59 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 16.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.34), residues: 618
  helix:  1.33 (0.28), residues: 349
  sheet: -1.80 (1.10), residues: 19
  loop : -0.88 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J 132 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.017   0.001   PHE I 110 
 TYR   0.011   0.001   TYR I  60 
 ARG   0.009   0.001   ARG I 279 

********************** 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
  87 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  276 ARG cc_start: 0.5681 (tmm160) cc_final: 0.4635 (pmt170)
REVERT: I   49 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6073 (mt-10)
REVERT: I  202 ASP cc_start: 0.7249 (m-30) cc_final: 0.6971 (m-30)
REVERT: I  260 LYS cc_start: 0.6959 (ttmp) cc_final: 0.6481 (tttp)
REVERT: I  279 ARG cc_start: 0.6656 (mtm110) cc_final: 0.5274 (ptt-90)
  outliers start: 4
  outliers final: 1
  residues processed: 86
  average time/residue: 2.9392
  time to fit residues: 263.1652
Evaluate side-chains
  79 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   49 GLU
Chi-restraints excluded: chain J residue   88 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    2.2186

-------------------------------------------------------------------------------
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 = 0.175627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.157131 restraints weight = 17690.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.47
r_work: 0.3794 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5238  Z= 0.272
  Angle     :  0.604   5.529   7093  Z= 0.310
  Chirality :  0.040   0.141    779
  Planarity :  0.005   0.044    900
  Dihedral  :  6.909  75.533    716
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.75 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 16.91 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.33), residues: 618
  helix:  1.05 (0.28), residues: 350
  sheet: -1.77 (1.09), residues: 19
  loop : -0.91 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP J 237 
 HIS   0.006   0.001   HIS J 131 
 PHE   0.012   0.002   PHE I  71 
 TYR   0.013   0.002   TYR J 178 
 ARG   0.009   0.001   ARG I 279 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8901.49 seconds
wall clock time: 156 minutes 35.49 seconds (9395.49 seconds total)