Starting phenix.real_space_refine
on Wed Mar 12 11:01:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l0q_23100/03_2025/7l0q_23100_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l0q_23100/03_2025/7l0q_23100.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l0q_23100/03_2025/7l0q_23100.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l0q_23100/03_2025/7l0q_23100.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l0q_23100/03_2025/7l0q_23100_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l0q_23100/03_2025/7l0q_23100_neut.cif"
  }
  resolution = 4.3
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5026      2.51       5
     N    1340      2.21       5
     O    1469      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7891
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 2409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2409
          Classifications: {'peptide': 309}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 298}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "D"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "A"
      Number of atoms: 2729
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 337, 2694
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 4, 'TRANS': 332}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 337, 2694
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 4, 'TRANS': 332}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 2697
    Chain: "B"
      Number of atoms: 2385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2385
          Classifications: {'peptide': 311}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 305}
    Chain: "G"
      Number of atoms: 310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 310
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 3, 'TRANS': 35}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AASP A  97 " occ=0.56
      ... (14 atoms not shown)
      pdb=" OD2BASP A  97 " occ=0.44
    residue:
      pdb=" N  AARG A 105 " occ=0.68
      ... (20 atoms not shown)
      pdb=" NH2BARG A 105 " occ=0.32
    residue:
      pdb=" N  AASP A 158 " occ=0.51
      ... (14 atoms not shown)
      pdb=" OD2BASP A 158 " occ=0.49
    residue:
      pdb=" N  AASP A 160 " occ=0.44
      ... (14 atoms not shown)
      pdb=" OD2BASP A 160 " occ=0.56
  Time building chain proxies: 6.19, per 1000 atoms: 0.78
  Number of scatterers: 7891
  At special positions: 0
  Unit cell: (91.575, 113.025, 124.575, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1469      8.00
     N    1340      7.00
     C    5026      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 142 " - pdb=" SG  CYS C 225 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1892

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      47.2% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'C' and resid 60 through 90
    Processing helix  chain 'C' and resid 102 through 128
      Proline residue:  C 122  - end of helix
    Processing helix  chain 'C' and resid 138 through 172
    Processing helix  chain 'C' and resid 173 through 180
    Processing helix  chain 'C' and resid 182 through 206
      Proline residue:  C 203  - end of helix
    Processing helix  chain 'C' and resid 230 through 269
      Proline residue:  C 249  - end of helix
    Processing helix  chain 'C' and resid 298 through 334
      removed outlier: 3.791A  pdb=" N   VAL C 313 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
      Proline residue:  C 323  - end of helix
      removed outlier: 3.602A  pdb=" N   ILE C 334 " --> pdb=" O   MET C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 371
      Proline residue:  C 366  - end of helix
    Processing helix  chain 'C' and resid 373 through 385
    Processing helix  chain 'A' and resid 4 through 7
    Processing helix  chain 'A' and resid 8 through 33
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.572A  pdb=" N   ILE A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 68
    Processing helix  chain 'A' and resid 69 through 92
      removed outlier: 3.598A  pdb=" N   GLY A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 114
      removed outlier: 3.851A  pdb=" N   ASP A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 133
    Processing helix  chain 'A' and resid 133 through 141
    Processing helix  chain 'A' and resid 142 through 146
    Processing helix  chain 'A' and resid 151 through 158
      removed outlier: 3.540A  pdb=" N  AASP A 158 " --> pdb=" O   TYR A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 200 through 204
      removed outlier: 4.064A  pdb=" N   GLY A 203 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.605A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 349
      removed outlier: 4.755A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 48
    Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212
    Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191
    Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 222
      removed outlier: 6.222A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 222
      removed outlier: 6.222A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.631A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.597A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 105
      removed outlier: 6.523A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 153
      removed outlier: 6.527A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.760A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 235
      removed outlier: 4.573A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 235 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.427A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1219 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: 2.22

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1712
        1.33 -     1.45: 1960
        1.45 -     1.58: 4293
        1.58 -     1.70: 1
        1.70 -     1.83: 81
  Bond restraints: 8047
  Sorted by residual:
  bond pdb=" N   ILE B 232 "
       pdb=" CA  ILE B 232 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.08e-02 8.57e+03 1.16e+01
  bond pdb=" N   PRO B 236 "
       pdb=" CA  PRO B 236 "
    ideal  model  delta    sigma   weight residual
    1.469  1.508 -0.039 1.28e-02 6.10e+03 9.45e+00
  bond pdb=" N   CYS B 233 "
       pdb=" CA  CYS B 233 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.23e-02 6.61e+03 6.82e+00
  bond pdb=" CA  GLU B 138 "
       pdb=" C   GLU B 138 "
    ideal  model  delta    sigma   weight residual
    1.527  1.493  0.034 1.32e-02 5.74e+03 6.78e+00
  bond pdb=" N   PHE B 234 "
       pdb=" CA  PHE B 234 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.21e-02 6.83e+03 6.21e+00
  ... (remaining 8042 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 10232
        1.97 -     3.93: 572
        3.93 -     5.90: 64
        5.90 -     7.87: 19
        7.87 -     9.84: 19
  Bond angle restraints: 10906
  Sorted by residual:
  angle pdb=" N   PRO C 297 "
        pdb=" CA  PRO C 297 "
        pdb=" CB  PRO C 297 "
      ideal   model   delta    sigma   weight residual
     103.25  111.61   -8.36 1.05e+00 9.07e-01 6.34e+01
  angle pdb=" C   PHE B 235 "
        pdb=" N   PRO B 236 "
        pdb=" CA  PRO B 236 "
      ideal   model   delta    sigma   weight residual
     119.84  127.37   -7.53 1.25e+00 6.40e-01 3.63e+01
  angle pdb=" C   ASP B 195 "
        pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
      ideal   model   delta    sigma   weight residual
     122.08  129.12   -7.04 1.47e+00 4.63e-01 2.29e+01
  angle pdb=" C   SER C 335 "
        pdb=" N   ASP C 336 "
        pdb=" CA  ASP C 336 "
      ideal   model   delta    sigma   weight residual
     121.54  130.63   -9.09 1.91e+00 2.74e-01 2.26e+01
  angle pdb=" CA  ASN B 268 "
        pdb=" CB  ASN B 268 "
        pdb=" CG  ASN B 268 "
      ideal   model   delta    sigma   weight residual
     112.60  117.29   -4.69 1.00e+00 1.00e+00 2.20e+01
  ... (remaining 10901 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 4121
       16.04 -    32.07: 496
       32.07 -    48.10: 126
       48.10 -    64.14: 26
       64.14 -    80.17: 6
  Dihedral angle restraints: 4775
    sinusoidal: 1845
      harmonic: 2930
  Sorted by residual:
  dihedral pdb=" CA  SER B 160 "
           pdb=" C   SER B 160 "
           pdb=" N   SER B 161 "
           pdb=" CA  SER B 161 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.17  -23.83     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  LEU B 192 "
           pdb=" C   LEU B 192 "
           pdb=" N   ALA B 193 "
           pdb=" CA  ALA B 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.73   23.27     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  PHE C 248 "
           pdb=" C   PHE C 248 "
           pdb=" N   PRO C 249 "
           pdb=" CA  PRO C 249 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.92   23.08     0      5.00e+00 4.00e-02 2.13e+01
  ... (remaining 4772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 885
       0.060 -    0.119: 290
       0.119 -    0.179: 57
       0.179 -    0.239: 16
       0.239 -    0.298: 4
  Chirality restraints: 1252
  Sorted by residual:
  chirality pdb=" CA  PRO C 297 "
            pdb=" N   PRO C 297 "
            pdb=" C   PRO C 297 "
            pdb=" CB  PRO C 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  HIS C 133 "
            pdb=" N   HIS C 133 "
            pdb=" C   HIS C 133 "
            pdb=" CB  HIS C 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  ILE A 168 "
            pdb=" N   ILE A 168 "
            pdb=" C   ILE A 168 "
            pdb=" CB  ILE A 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 1249 not shown)

  Planarity restraints: 1381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 248 "   -0.063 5.00e-02 4.00e+02   9.43e-02 1.42e+01
        pdb=" N   PRO C 249 "    0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO C 249 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO C 249 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A   4 "   -0.016 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   THR A   4 "    0.057 2.00e-02 2.50e+03
        pdb=" O   THR A   4 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A   5 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 340 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   THR A 340 "    0.055 2.00e-02 2.50e+03
        pdb=" O   THR A 340 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP A 341 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1378 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 713
        2.74 -     3.28: 7947
        3.28 -     3.82: 13494
        3.82 -     4.36: 15647
        4.36 -     4.90: 26762
  Nonbonded interactions: 64563
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 128 "
            pdb=" OD1AASP A 160 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR C 146 "
            pdb=" OXT LEU D  13 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG  SER B 277 "
            pdb=" O   LEU B 318 "
     model   vdw
     2.298 3.040
  ... (remaining 64558 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=0.32 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.800
  Find NCS groups from input model:        0.120
  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:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
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      :  0.007   0.093   8047  Z= 0.461
  Angle     :  1.072   9.835  10906  Z= 0.628
  Chirality :  0.063   0.298   1252
  Planarity :  0.007   0.094   1381
  Dihedral  : 14.952  80.175   2880
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.21 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 12.75 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.11 %
  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: -3.51 (0.22), residues: 993
  helix: -1.99 (0.19), residues: 453
  sheet: -2.14 (0.39), residues: 151
  loop : -2.63 (0.27), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP C 135 
 HIS   0.005   0.001   HIS A 195 
 PHE   0.022   0.003   PHE A 189 
 TYR   0.019   0.003   TYR A 167 
 ARG   0.012   0.001   ARG A 176 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 274
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.7480 (tpt) cc_final: 0.6103 (tpt)
REVERT: C  167 ARG cc_start: 0.6957 (mtt180) cc_final: 0.6171 (ttt180)
REVERT: C  216 ASP cc_start: 0.5743 (p0) cc_final: 0.4798 (t0)
REVERT: C  224 VAL cc_start: 0.7884 (m) cc_final: 0.7594 (m)
REVERT: C  329 LEU cc_start: 0.8133 (mm) cc_final: 0.7572 (tt)
REVERT: C  350 PHE cc_start: 0.8391 (t80) cc_final: 0.8136 (t80)
REVERT: C  359 TYR cc_start: 0.7755 (m-10) cc_final: 0.6904 (m-80)
REVERT: A   28 GLU cc_start: 0.7573 (tt0) cc_final: 0.7226 (tt0)
REVERT: A  188 HIS cc_start: 0.8697 (m90) cc_final: 0.8032 (t70)
REVERT: A  195 HIS cc_start: 0.7560 (t70) cc_final: 0.6543 (t70)
REVERT: A  304 GLN cc_start: 0.8656 (tt0) cc_final: 0.8277 (tt0)
REVERT: A  305 CYS cc_start: 0.8437 (m) cc_final: 0.7881 (t)
REVERT: B   47 THR cc_start: 0.8969 (m) cc_final: 0.8346 (p)
REVERT: B  108 SER cc_start: 0.8585 (m) cc_final: 0.8381 (p)
REVERT: B  222 PHE cc_start: 0.8500 (m-80) cc_final: 0.8173 (m-80)
REVERT: B  234 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7802 (m-80)
REVERT: B  339 TRP cc_start: 0.8894 (m100) cc_final: 0.8453 (m100)
  outliers start: 5
  outliers final: 1
  residues processed: 279
  average time/residue: 0.2214
  time to fit residues: 80.0382
Evaluate side-chains
  184 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 76 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0670
   chunk 56 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.5724

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

Flipped N/Q/H residues before XYZ refinement:
C 127 ASN
C 132 HIS
C 159 ASN
** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 365 ASN
A  52 GLN
A 188 HIS
A 269 ASN
A 331 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.146096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.122949 restraints weight = 44175.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.125154 restraints weight = 48107.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.127808 restraints weight = 14468.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3683 r_free = 0.3683    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8047  Z= 0.251
  Angle     :  0.687  11.310  10906  Z= 0.362
  Chirality :  0.044   0.183   1252
  Planarity :  0.005   0.082   1381
  Dihedral  :  5.865  80.759   1092
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.28 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.86 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.96 (0.25), residues: 993
  helix: -0.21 (0.23), residues: 460
  sheet: -1.94 (0.37), residues: 165
  loop : -2.29 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.006   0.002   HIS C 325 
 PHE   0.015   0.002   PHE B 278 
 TYR   0.035   0.002   TYR C  71 
 ARG   0.006   0.001   ARG C 185 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.7667 (tpt) cc_final: 0.6102 (tpt)
REVERT: C  216 ASP cc_start: 0.5866 (p0) cc_final: 0.4952 (t0)
REVERT: C  235 LYS cc_start: 0.6277 (mttt) cc_final: 0.6029 (mmtt)
REVERT: C  329 LEU cc_start: 0.8209 (mm) cc_final: 0.7857 (tt)
REVERT: C  359 TYR cc_start: 0.7335 (m-10) cc_final: 0.6740 (m-80)
REVERT: A   15 ARG cc_start: 0.8270 (tpm170) cc_final: 0.7987 (ttm-80)
REVERT: A   36 LEU cc_start: 0.9400 (mt) cc_final: 0.9159 (mp)
REVERT: A  164 GLN cc_start: 0.6496 (tm-30) cc_final: 0.6283 (tm-30)
REVERT: A  304 GLN cc_start: 0.8905 (tt0) cc_final: 0.8517 (tt0)
REVERT: A  305 CYS cc_start: 0.8279 (m) cc_final: 0.7699 (t)
REVERT: A  321 THR cc_start: 0.8830 (t) cc_final: 0.8105 (t)
REVERT: A  325 CYS cc_start: 0.8221 (p) cc_final: 0.7891 (p)
REVERT: A  339 VAL cc_start: 0.8906 (t) cc_final: 0.8648 (t)
REVERT: B   51 LEU cc_start: 0.8922 (mp) cc_final: 0.8695 (mp)
REVERT: B   82 TRP cc_start: 0.9113 (m100) cc_final: 0.8540 (m100)
REVERT: B  108 SER cc_start: 0.8882 (m) cc_final: 0.8502 (p)
REVERT: B  180 PHE cc_start: 0.8068 (m-80) cc_final: 0.7417 (m-10)
REVERT: B  211 TRP cc_start: 0.8139 (m100) cc_final: 0.7851 (m100)
REVERT: B  251 ARG cc_start: 0.7513 (mtt90) cc_final: 0.6944 (ttm-80)
REVERT: B  289 TYR cc_start: 0.8358 (m-10) cc_final: 0.7845 (m-10)
REVERT: B  339 TRP cc_start: 0.8746 (m100) cc_final: 0.8213 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1730
  time to fit residues: 56.6034
Evaluate side-chains
  176 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 36 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 95 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
C 173 HIS
** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 348 HIS
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 GLN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.145966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.122744 restraints weight = 56787.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.124969 restraints weight = 49391.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.128052 restraints weight = 14667.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8047  Z= 0.230
  Angle     :  0.664  10.623  10906  Z= 0.346
  Chirality :  0.043   0.176   1252
  Planarity :  0.005   0.081   1381
  Dihedral  :  5.581  76.608   1092
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.19 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.56 %
    Favored  : 95.32 %
  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: -1.36 (0.26), residues: 993
  helix:  0.26 (0.23), residues: 461
  sheet: -1.84 (0.38), residues: 166
  loop : -1.86 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 339 
 HIS   0.006   0.001   HIS A 195 
 PHE   0.025   0.002   PHE B 235 
 TYR   0.030   0.002   TYR C  71 
 ARG   0.005   0.001   ARG A  15 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.7683 (tpt) cc_final: 0.6214 (tpt)
REVERT: C  216 ASP cc_start: 0.5832 (p0) cc_final: 0.4989 (t0)
REVERT: C  235 LYS cc_start: 0.6392 (mttt) cc_final: 0.6097 (mmmm)
REVERT: C  267 MET cc_start: 0.7511 (ttt) cc_final: 0.7234 (ttp)
REVERT: C  329 LEU cc_start: 0.8216 (mm) cc_final: 0.7851 (tt)
REVERT: C  359 TYR cc_start: 0.7553 (m-10) cc_final: 0.6749 (m-80)
REVERT: A   36 LEU cc_start: 0.9420 (mt) cc_final: 0.9196 (mp)
REVERT: A  188 HIS cc_start: 0.8411 (m-70) cc_final: 0.7894 (m-70)
REVERT: A  197 LYS cc_start: 0.8942 (mttt) cc_final: 0.8692 (mttp)
REVERT: A  304 GLN cc_start: 0.8899 (tt0) cc_final: 0.8527 (tt0)
REVERT: A  305 CYS cc_start: 0.8455 (m) cc_final: 0.7837 (t)
REVERT: A  325 CYS cc_start: 0.7882 (p) cc_final: 0.7676 (p)
REVERT: B   57 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8737 (mtmm)
REVERT: B  108 SER cc_start: 0.8904 (m) cc_final: 0.8641 (p)
REVERT: B  180 PHE cc_start: 0.8162 (m-80) cc_final: 0.7616 (m-10)
REVERT: B  222 PHE cc_start: 0.8463 (m-80) cc_final: 0.8244 (m-80)
REVERT: B  251 ARG cc_start: 0.7287 (mtt90) cc_final: 0.6880 (tpp80)
REVERT: B  311 HIS cc_start: 0.8573 (m-70) cc_final: 0.8347 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2527
  time to fit residues: 79.9311
Evaluate side-chains
  163 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C  82 ASN
C 173 HIS
** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 GLN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.147468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.125067 restraints weight = 45024.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.127155 restraints weight = 45869.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.129632 restraints weight = 13757.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8047  Z= 0.192
  Angle     :  0.649  11.662  10906  Z= 0.336
  Chirality :  0.043   0.175   1252
  Planarity :  0.004   0.078   1381
  Dihedral  :  5.635  89.686   1092
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.28 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.69 %
    Favored  : 97.08 %
  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: -1.13 (0.26), residues: 993
  helix:  0.49 (0.23), residues: 461
  sheet: -1.75 (0.35), residues: 192
  loop : -1.73 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.016   0.001   PHE C 246 
 TYR   0.024   0.001   TYR B 264 
 ARG   0.006   0.000   ARG G  41 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   88 THR cc_start: 0.7862 (p) cc_final: 0.7479 (p)
REVERT: C  121 MET cc_start: 0.7494 (tpt) cc_final: 0.6328 (tpt)
REVERT: C  166 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8599 (tm-30)
REVERT: C  167 ARG cc_start: 0.7645 (mtt180) cc_final: 0.6893 (ttt180)
REVERT: C  216 ASP cc_start: 0.5732 (p0) cc_final: 0.4924 (t0)
REVERT: C  267 MET cc_start: 0.7579 (ttt) cc_final: 0.7217 (ttp)
REVERT: C  359 TYR cc_start: 0.7493 (m-10) cc_final: 0.6864 (m-80)
REVERT: A  304 GLN cc_start: 0.8881 (tt0) cc_final: 0.8523 (tt0)
REVERT: A  305 CYS cc_start: 0.8381 (m) cc_final: 0.7737 (t)
REVERT: A  325 CYS cc_start: 0.8079 (p) cc_final: 0.7856 (p)
REVERT: B   57 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8614 (mtmm)
REVERT: B   89 LYS cc_start: 0.8842 (mttp) cc_final: 0.8317 (mtpt)
REVERT: B  172 GLU cc_start: 0.6908 (mp0) cc_final: 0.6443 (mp0)
REVERT: B  222 PHE cc_start: 0.8405 (m-80) cc_final: 0.8110 (m-80)
REVERT: B  303 ASP cc_start: 0.7281 (m-30) cc_final: 0.6997 (m-30)
REVERT: B  311 HIS cc_start: 0.8370 (m-70) cc_final: 0.8168 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2004
  time to fit residues: 59.4478
Evaluate side-chains
  164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    8.9990
   chunk 46 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 93 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 85 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  52 GLN
A 164 GLN
A 188 HIS
A 331 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.136778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.113932 restraints weight = 54425.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.115710 restraints weight = 50735.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.118568 restraints weight = 15048.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.4733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072   8047  Z= 0.470
  Angle     :  0.821  11.747  10906  Z= 0.433
  Chirality :  0.049   0.171   1252
  Planarity :  0.006   0.085   1381
  Dihedral  :  5.930  67.435   1092
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 19.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.92 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.86 %
    Favored  : 96.02 %
  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: -1.43 (0.26), residues: 993
  helix:  0.22 (0.23), residues: 461
  sheet: -1.92 (0.39), residues: 171
  loop : -1.88 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP B 297 
 HIS   0.009   0.002   HIS A 195 
 PHE   0.028   0.003   PHE A 199 
 TYR   0.030   0.003   TYR C 369 
 ARG   0.007   0.001   ARG B 314 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.7890 (tpt) cc_final: 0.6342 (tpt)
REVERT: C  216 ASP cc_start: 0.6470 (p0) cc_final: 0.5801 (t0)
REVERT: C  228 ILE cc_start: 0.8951 (pt) cc_final: 0.8749 (mm)
REVERT: C  244 MET cc_start: 0.7317 (mmm) cc_final: 0.7014 (tpt)
REVERT: C  267 MET cc_start: 0.7608 (ttt) cc_final: 0.7221 (ttp)
REVERT: C  333 TYR cc_start: 0.5799 (m-10) cc_final: 0.3863 (t80)
REVERT: C  359 TYR cc_start: 0.7942 (m-10) cc_final: 0.6929 (m-80)
REVERT: A  197 LYS cc_start: 0.9156 (ttmm) cc_final: 0.8865 (ttmt)
REVERT: A  304 GLN cc_start: 0.8861 (tt0) cc_final: 0.8616 (tt0)
REVERT: A  305 CYS cc_start: 0.8570 (m) cc_final: 0.7912 (t)
REVERT: B   57 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8824 (mtmm)
REVERT: B  251 ARG cc_start: 0.7295 (mtt90) cc_final: 0.6947 (tpp80)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1785
  time to fit residues: 49.6168
Evaluate side-chains
  150 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 GLN
A 331 ASN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.143343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.112730 restraints weight = 65390.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.116289 restraints weight = 47334.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.117415 restraints weight = 16201.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.4923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   8047  Z= 0.225
  Angle     :  0.675  11.743  10906  Z= 0.346
  Chirality :  0.044   0.172   1252
  Planarity :  0.004   0.079   1381
  Dihedral  :  5.389  57.444   1092
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.97 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.57 %
    Favored  : 97.19 %
  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: -0.97 (0.27), residues: 993
  helix:  0.64 (0.24), residues: 460
  sheet: -1.66 (0.37), residues: 173
  loop : -1.71 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 297 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.019   0.002   PHE A 199 
 TYR   0.023   0.002   TYR C 333 
 ARG   0.004   0.000   ARG C 327 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.7496 (tpt) cc_final: 0.6548 (tpt)
REVERT: C  216 ASP cc_start: 0.6727 (p0) cc_final: 0.5440 (t0)
REVERT: C  267 MET cc_start: 0.7408 (ttt) cc_final: 0.7107 (ttp)
REVERT: C  359 TYR cc_start: 0.7639 (m-10) cc_final: 0.6949 (m-80)
REVERT: A   53 MET cc_start: 0.8667 (mmm) cc_final: 0.8318 (mpp)
REVERT: A  304 GLN cc_start: 0.8780 (tt0) cc_final: 0.8374 (tt0)
REVERT: A  305 CYS cc_start: 0.8337 (m) cc_final: 0.7688 (t)
REVERT: B   57 LYS cc_start: 0.9263 (mtmt) cc_final: 0.9026 (mtmm)
REVERT: B  180 PHE cc_start: 0.8159 (m-80) cc_final: 0.7351 (m-10)
REVERT: B  211 TRP cc_start: 0.8278 (m100) cc_final: 0.7630 (m100)
REVERT: B  289 TYR cc_start: 0.8371 (m-10) cc_final: 0.7903 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1934
  time to fit residues: 56.1345
Evaluate side-chains
  165 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 47 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 94 optimal weight:    0.7980
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** 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 = 0.3966 r_free = 0.3966 target = 0.146486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.123338 restraints weight = 53764.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.125532 restraints weight = 50184.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.128984 restraints weight = 14620.184|
|-----------------------------------------------------------------------------|
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) = 0.126         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.5180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8047  Z= 0.188
  Angle     :  0.673  11.892  10906  Z= 0.344
  Chirality :  0.044   0.177   1252
  Planarity :  0.004   0.076   1381
  Dihedral  :  4.895  22.097   1092
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.68 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.75 %
    Favored  : 98.13 %
  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: -0.76 (0.27), residues: 993
  helix:  0.78 (0.24), residues: 461
  sheet: -1.49 (0.36), residues: 184
  loop : -1.61 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.020   0.001   PHE A 199 
 TYR   0.038   0.002   TYR C  71 
 ARG   0.013   0.001   ARG G  47 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.7768 (tpt) cc_final: 0.6590 (tpt)
REVERT: C  216 ASP cc_start: 0.6582 (p0) cc_final: 0.5414 (t0)
REVERT: C  218 THR cc_start: 0.8373 (m) cc_final: 0.8169 (m)
REVERT: C  244 MET cc_start: 0.7549 (tpt) cc_final: 0.7254 (tpp)
REVERT: C  247 LEU cc_start: 0.9211 (mm) cc_final: 0.8966 (mt)
REVERT: C  267 MET cc_start: 0.7509 (ttt) cc_final: 0.7270 (ttp)
REVERT: C  333 TYR cc_start: 0.5217 (m-10) cc_final: 0.4405 (t80)
REVERT: C  359 TYR cc_start: 0.7498 (m-10) cc_final: 0.7015 (m-80)
REVERT: A  305 CYS cc_start: 0.8531 (m) cc_final: 0.7715 (t)
REVERT: A  321 THR cc_start: 0.8866 (t) cc_final: 0.8411 (t)
REVERT: A  339 VAL cc_start: 0.8851 (t) cc_final: 0.8540 (t)
REVERT: B   45 MET cc_start: 0.8029 (mmm) cc_final: 0.7704 (mmm)
REVERT: B   57 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8503 (mtmm)
REVERT: B  110 ASN cc_start: 0.7228 (t0) cc_final: 0.6844 (t0)
REVERT: B  180 PHE cc_start: 0.8259 (m-80) cc_final: 0.7813 (m-10)
REVERT: B  225 HIS cc_start: 0.7219 (m-70) cc_final: 0.6905 (m-70)
REVERT: B  234 PHE cc_start: 0.8181 (m-80) cc_final: 0.7561 (m-80)
REVERT: B  289 TYR cc_start: 0.8011 (m-10) cc_final: 0.7615 (m-80)
REVERT: B  339 TRP cc_start: 0.8524 (m100) cc_final: 0.8215 (m100)
REVERT: G   47 ARG cc_start: 0.6972 (mtt90) cc_final: 0.6651 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.1654
  time to fit residues: 49.1564
Evaluate side-chains
  159 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 44 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 6 optimal weight:    0.5980
   chunk 16 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
C 211 GLN
** C 325 HIS ** 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 = 0.3947 r_free = 0.3947 target = 0.145121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.122043 restraints weight = 52643.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.124210 restraints weight = 50243.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.126707 restraints weight = 15416.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   8047  Z= 0.250
  Angle     :  0.701  10.747  10906  Z= 0.364
  Chirality :  0.045   0.221   1252
  Planarity :  0.004   0.076   1381
  Dihedral  :  4.920  18.450   1092
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.40 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.40 %
    Favored  : 98.48 %
  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: -0.75 (0.27), residues: 993
  helix:  0.74 (0.23), residues: 461
  sheet: -1.34 (0.37), residues: 184
  loop : -1.61 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 297 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.016   0.002   PHE A 199 
 TYR   0.040   0.002   TYR C  71 
 ARG   0.006   0.001   ARG C 327 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   88 THR cc_start: 0.7905 (p) cc_final: 0.7690 (p)
REVERT: C  173 HIS cc_start: 0.8107 (m-70) cc_final: 0.7201 (m-70)
REVERT: C  216 ASP cc_start: 0.6614 (p0) cc_final: 0.5456 (t0)
REVERT: C  244 MET cc_start: 0.7600 (tpt) cc_final: 0.7362 (tpp)
REVERT: C  247 LEU cc_start: 0.9228 (mm) cc_final: 0.8975 (mt)
REVERT: C  267 MET cc_start: 0.7474 (ttt) cc_final: 0.7219 (ttp)
REVERT: C  359 TYR cc_start: 0.7543 (m-10) cc_final: 0.7214 (m-80)
REVERT: A   53 MET cc_start: 0.8551 (mmm) cc_final: 0.8145 (mpp)
REVERT: A  305 CYS cc_start: 0.8525 (m) cc_final: 0.7903 (t)
REVERT: A  339 VAL cc_start: 0.8799 (t) cc_final: 0.8527 (t)
REVERT: B   45 MET cc_start: 0.8083 (mmm) cc_final: 0.7741 (mmt)
REVERT: B   57 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8615 (mtmm)
REVERT: B  180 PHE cc_start: 0.8342 (m-80) cc_final: 0.7760 (m-10)
REVERT: B  225 HIS cc_start: 0.7413 (m-70) cc_final: 0.7034 (m-70)
REVERT: B  289 TYR cc_start: 0.8152 (m-10) cc_final: 0.7826 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1609
  time to fit residues: 45.4066
Evaluate side-chains
  156 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 52 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0030
   chunk 40 optimal weight:   20.0000
   chunk 87 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    2.9396

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

Flipped N/Q/H residues before XYZ refinement:
C 241 ASN
** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.139948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.110269 restraints weight = 65388.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113317 restraints weight = 53413.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.114405 restraints weight = 20068.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3504
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.5597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   8047  Z= 0.345
  Angle     :  0.761  10.234  10906  Z= 0.398
  Chirality :  0.048   0.180   1252
  Planarity :  0.005   0.078   1381
  Dihedral  :  5.199  23.556   1092
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 19.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.42 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.05 %
    Favored  : 98.83 %
  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: -0.87 (0.27), residues: 993
  helix:  0.51 (0.23), residues: 461
  sheet: -1.28 (0.39), residues: 179
  loop : -1.53 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP B 297 
 HIS   0.007   0.002   HIS C 325 
 PHE   0.029   0.002   PHE B 234 
 TYR   0.044   0.003   TYR C  71 
 ARG   0.005   0.001   ARG B  49 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  173 HIS cc_start: 0.7989 (m-70) cc_final: 0.7611 (m90)
REVERT: C  247 LEU cc_start: 0.9284 (mm) cc_final: 0.8974 (mt)
REVERT: C  359 TYR cc_start: 0.7832 (m-10) cc_final: 0.7287 (m-80)
REVERT: A   53 MET cc_start: 0.8792 (mmm) cc_final: 0.8338 (mpp)
REVERT: A  188 HIS cc_start: 0.8048 (m-70) cc_final: 0.7370 (t70)
REVERT: A  289 GLU cc_start: 0.7914 (pm20) cc_final: 0.7375 (tm-30)
REVERT: A  305 CYS cc_start: 0.8546 (m) cc_final: 0.7984 (t)
REVERT: B   45 MET cc_start: 0.8086 (mmm) cc_final: 0.7776 (mmm)
REVERT: B   57 LYS cc_start: 0.8999 (mtmt) cc_final: 0.8700 (mtmm)
REVERT: B  211 TRP cc_start: 0.8536 (m100) cc_final: 0.7593 (m100)
REVERT: B  225 HIS cc_start: 0.7356 (m-70) cc_final: 0.6896 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1664
  time to fit residues: 48.3054
Evaluate side-chains
  150 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0770
   chunk 19 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   chunk 92 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 30 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.3342

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

Flipped N/Q/H residues before XYZ refinement:
C 211 GLN
** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 325 HIS ** 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 = 0.3939 r_free = 0.3939 target = 0.144397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.121019 restraints weight = 49720.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.123274 restraints weight = 49783.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.126660 restraints weight = 15569.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3661 r_free = 0.3661    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3661 r_free = 0.3661    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.5756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   8047  Z= 0.236
  Angle     :  0.708  10.726  10906  Z= 0.368
  Chirality :  0.046   0.195   1252
  Planarity :  0.004   0.075   1381
  Dihedral  :  5.010  19.835   1092
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.19 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.12 %
    Favored  : 99.77 %
  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: -0.74 (0.27), residues: 993
  helix:  0.66 (0.24), residues: 461
  sheet: -1.27 (0.38), residues: 190
  loop : -1.49 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 297 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.036   0.002   PHE A 189 
 TYR   0.042   0.002   TYR C  71 
 ARG   0.005   0.000   ARG C 327 

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

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

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1986 Ramachandran restraints generated.
    993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 MET cc_start: 0.7751 (tpt) cc_final: 0.6724 (tpt)
REVERT: C  173 HIS cc_start: 0.7808 (m-70) cc_final: 0.7587 (m-70)
REVERT: C  204 MET cc_start: 0.8538 (tpp) cc_final: 0.8161 (tpt)
REVERT: C  359 TYR cc_start: 0.7706 (m-10) cc_final: 0.7231 (m-80)
REVERT: A   53 MET cc_start: 0.8623 (mmm) cc_final: 0.8257 (mpp)
REVERT: A  119 MET cc_start: -0.0256 (ptt) cc_final: -0.2786 (tpt)
REVERT: A  289 GLU cc_start: 0.7809 (pm20) cc_final: 0.7269 (tm-30)
REVERT: A  304 GLN cc_start: 0.8719 (tt0) cc_final: 0.8342 (tt0)
REVERT: A  305 CYS cc_start: 0.8414 (m) cc_final: 0.7838 (t)
REVERT: A  339 VAL cc_start: 0.8812 (t) cc_final: 0.8532 (t)
REVERT: B   45 MET cc_start: 0.8204 (mmm) cc_final: 0.7841 (mmm)
REVERT: B   57 LYS cc_start: 0.9010 (mtmt) cc_final: 0.8592 (mtmm)
REVERT: B  251 ARG cc_start: 0.7196 (mtt90) cc_final: 0.6772 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1604
  time to fit residues: 45.1011
Evaluate side-chains
  157 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 89 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 149 ASN
** B 225 HIS ** 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 = 0.3955 r_free = 0.3955 target = 0.145764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.122190 restraints weight = 58115.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.124166 restraints weight = 54469.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.129339 restraints weight = 16354.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.5865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   8047  Z= 0.208
  Angle     :  0.683  10.981  10906  Z= 0.358
  Chirality :  0.045   0.173   1252
  Planarity :  0.004   0.074   1381
  Dihedral  :  4.898  20.016   1092
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.30 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.58 %
    Favored  : 99.30 %
  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: -0.64 (0.27), residues: 993
  helix:  0.75 (0.24), residues: 462
  sheet: -1.10 (0.39), residues: 185
  loop : -1.54 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 135 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.032   0.002   PHE A 189 
 TYR   0.038   0.002   TYR C  71 
 ARG   0.005   0.000   ARG C 327 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3122.79 seconds
wall clock time: 56 minutes 21.61 seconds (3381.61 seconds total)