Starting phenix.real_space_refine
on Thu Mar 13 04:22:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jkz_36384/03_2025/8jkz_36384.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jkz_36384/03_2025/8jkz_36384.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jkz_36384/03_2025/8jkz_36384.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jkz_36384/03_2025/8jkz_36384.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jkz_36384/03_2025/8jkz_36384.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jkz_36384/03_2025/8jkz_36384.cif"
  }
  resolution = 3.6
  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=   0.002 sd=   0.027
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      33      5.16       5
     C    5404      2.51       5
     N    1443      2.21       5
     O    1562      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: 8444
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4674
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 23, 'TRANS': 560}
    Chain: "B"
      Number of atoms: 3726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3726
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 28, 'TRANS': 440}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.20, per 1000 atoms: 0.62
  Number of scatterers: 8444
  At special positions: 0
  Unit cell: (78.12, 98.28, 122.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     P       2     15.00
     O    1562      8.00
     N    1443      7.00
     C    5404      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 945.5 milliseconds
  

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1976

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 11 sheets defined
      41.5% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 16
      removed outlier: 3.550A  pdb=" N   GLN A  11 " --> pdb=" O   ASN A   7 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   HIS A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   TYR A  13 " --> pdb=" O   PHE A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 33
      removed outlier: 3.621A  pdb=" N   THR A  28 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER A  29 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG A  30 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   SER A  31 " --> pdb=" O   THR A  28 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLY A  33 " --> pdb=" O   ARG A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 49
    Processing helix  chain 'A' and resid 65 through 78
      removed outlier: 3.600A  pdb=" N   SER A  69 " --> pdb=" O   HIS A  65 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LYS A  78 " --> pdb=" O   TYR A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 98
    Processing helix  chain 'A' and resid 100 through 112
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 168 through 176
      removed outlier: 3.826A  pdb=" N   SER A 172 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 195
    Processing helix  chain 'A' and resid 198 through 217
    Processing helix  chain 'A' and resid 231 through 243
    Processing helix  chain 'A' and resid 257 through 261
    Processing helix  chain 'A' and resid 262 through 276
    Processing helix  chain 'A' and resid 286 through 297
      removed outlier: 4.075A  pdb=" N   GLN A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 310
      removed outlier: 3.547A  pdb=" N   ARG A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 366
    Processing helix  chain 'A' and resid 383 through 390
    Processing helix  chain 'A' and resid 406 through 414
      removed outlier: 3.965A  pdb=" N   SER A 410 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 431
    Processing helix  chain 'A' and resid 439 through 443
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 466
    Processing helix  chain 'A' and resid 517 through 529
    Processing helix  chain 'A' and resid 532 through 548
      removed outlier: 3.574A  pdb=" N   GLN A 538 " --> pdb=" O   GLN A 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 37
    Processing helix  chain 'B' and resid 60 through 71
      removed outlier: 3.837A  pdb=" N   LEU B  64 " --> pdb=" O   HIS B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 106
      removed outlier: 3.699A  pdb=" N   ARG B 106 " --> pdb=" O   GLU B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 119
      removed outlier: 3.948A  pdb=" N   VAL B 116 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 138
      removed outlier: 3.602A  pdb=" N   ALA B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 156
    Processing helix  chain 'B' and resid 164 through 174
    Processing helix  chain 'B' and resid 175 through 177
      No H-bonds generated for 'chain 'B' and resid 175 through 177'
    Processing helix  chain 'B' and resid 184 through 189
      removed outlier: 4.118A  pdb=" N   LEU B 188 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 209
      removed outlier: 3.547A  pdb=" N   VAL B 196 " --> pdb=" O   CYS B 192 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL B 202 " --> pdb=" O   TRP B 198 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA B 203 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 237
      No H-bonds generated for 'chain 'B' and resid 235 through 237'
    Processing helix  chain 'B' and resid 276 through 295
    Processing helix  chain 'B' and resid 312 through 321
      removed outlier: 3.514A  pdb=" N   GLN B 317 " --> pdb=" O   GLU B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 430
      removed outlier: 4.150A  pdb=" N   THR B 421 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LYS B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 458
      removed outlier: 3.624A  pdb=" N   VAL B 447 " --> pdb=" O   PRO B 443 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLN B 458 " --> pdb=" O   ASP B 454 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184
      removed outlier: 6.404A  pdb=" N   VAL A 138 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   MET A  20 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 8.876A  pdb=" N   PHE A 139 " --> pdb=" O   MET A  20 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   TRP A  22 " --> pdb=" O   PHE A 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 252
      removed outlier: 6.546A  pdb=" N   LEU A 251 " --> pdb=" O   TYR A 280 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 580
      removed outlier: 3.610A  pdb=" N   ALA A 330 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL B 345 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338
      removed outlier: 4.550A  pdb=" N   LEU A 501 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380
      removed outlier: 3.611A  pdb=" N   CYS A 345 " --> pdb=" O   TYR A 402 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 561
      removed outlier: 3.548A  pdb=" N   ALA A 569 " --> pdb=" O   CYS A 561 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13
      removed outlier: 6.331A  pdb=" N   ILE B 303 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL B 332 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ILE B 305 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   ILE B 334 " --> pdb=" O   ILE B 305 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LYS B 307 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 13
      removed outlier: 6.331A  pdb=" N   ILE B 303 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL B 332 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ILE B 305 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   ILE B 334 " --> pdb=" O   ILE B 305 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LYS B 307 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 27
      removed outlier: 3.748A  pdb=" N   ARG B  25 " --> pdb=" O   PHE B  21 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99
      removed outlier: 6.669A  pdb=" N   VAL B  50 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   ARG B  51 " --> pdb=" O   VAL B 145 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   LEU B 147 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ALA B  53 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   TYR B 149 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   LEU B  55 " --> pdb=" O   TYR B 149 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LEU B 146 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   ILE B 183 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   VAL B 148 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 265 through 267

    346 hydrogen bonds defined for protein.
    990 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: 2.59

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1378
        1.31 -     1.43: 2382
        1.43 -     1.56: 4838
        1.56 -     1.68: 8
        1.68 -     1.81: 51
  Bond restraints: 8657
  Sorted by residual:
  bond pdb=" C2D NAD A 601 "
       pdb=" C3D NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.531  1.243  0.288 2.00e-02 2.50e+03 2.08e+02
  bond pdb=" C4B NAD A 601 "
       pdb=" O4B NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.433  1.681 -0.248 2.00e-02 2.50e+03 1.54e+02
  bond pdb=" C3B NAD A 601 "
       pdb=" C4B NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.523  1.281  0.242 2.00e-02 2.50e+03 1.46e+02
  bond pdb=" C4D NAD A 601 "
       pdb=" O4D NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.445  1.274  0.171 2.00e-02 2.50e+03 7.31e+01
  bond pdb=" C7N NAD A 601 "
       pdb=" N7N NAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.328  1.473 -0.145 2.00e-02 2.50e+03 5.25e+01
  ... (remaining 8652 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 11571
        2.64 -     5.28: 154
        5.28 -     7.93: 15
        7.93 -    10.57: 5
       10.57 -    13.21: 3
  Bond angle restraints: 11748
  Sorted by residual:
  angle pdb=" C   ILE A 390 "
        pdb=" N   PHE A 391 "
        pdb=" CA  PHE A 391 "
      ideal   model   delta    sigma   weight residual
     121.54  131.43   -9.89 1.91e+00 2.74e-01 2.68e+01
  angle pdb=" O1A NAD A 601 "
        pdb=" PA  NAD A 601 "
        pdb=" O2A NAD A 601 "
      ideal   model   delta    sigma   weight residual
     122.64  109.43   13.21 3.00e+00 1.11e-01 1.94e+01
  angle pdb=" C   ALA B   9 "
        pdb=" CA  ALA B   9 "
        pdb=" CB  ALA B   9 "
      ideal   model   delta    sigma   weight residual
     116.34  110.45    5.89 1.40e+00 5.10e-01 1.77e+01
  angle pdb=" O3  NAD A 601 "
        pdb=" PN  NAD A 601 "
        pdb=" O5D NAD A 601 "
      ideal   model   delta    sigma   weight residual
      98.00  109.75  -11.75 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" O1N NAD A 601 "
        pdb=" PN  NAD A 601 "
        pdb=" O2N NAD A 601 "
      ideal   model   delta    sigma   weight residual
     120.02  109.43   10.59 3.00e+00 1.11e-01 1.25e+01
  ... (remaining 11743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4401
       17.98 -    35.96: 593
       35.96 -    53.95: 154
       53.95 -    71.93: 32
       71.93 -    89.91: 15
  Dihedral angle restraints: 5195
    sinusoidal: 2120
      harmonic: 3075
  Sorted by residual:
  dihedral pdb=" CA  LEU B  46 "
           pdb=" C   LEU B  46 "
           pdb=" N   PRO B  47 "
           pdb=" CA  PRO B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.47   27.53     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  TYR A 374 "
           pdb=" C   TYR A 374 "
           pdb=" N   THR A 375 "
           pdb=" CA  THR A 375 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.19   18.81     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  MET A 132 "
           pdb=" C   MET A 132 "
           pdb=" N   ASN A 133 "
           pdb=" CA  ASN A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.98  -18.02     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 5192 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1141
       0.070 -    0.140: 130
       0.140 -    0.210: 8
       0.210 -    0.280: 1
       0.280 -    0.351: 1
  Chirality restraints: 1281
  Sorted by residual:
  chirality pdb=" C3D NAD A 601 "
            pdb=" C2D NAD A 601 "
            pdb=" C4D NAD A 601 "
            pdb=" O3D NAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.38   -0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" C3B NAD A 601 "
            pdb=" C2B NAD A 601 "
            pdb=" C4B NAD A 601 "
            pdb=" O3B NAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.44   -0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C2D NAD A 601 "
            pdb=" C1D NAD A 601 "
            pdb=" C3D NAD A 601 "
            pdb=" O2D NAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.56   -2.37   -0.19 2.00e-01 2.50e+01 9.50e-01
  ... (remaining 1278 not shown)

  Planarity restraints: 1505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 206 "    0.187 9.50e-02 1.11e+02   8.39e-02 4.33e+00
        pdb=" NE  ARG A 206 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 206 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 206 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 206 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 391 "   -0.011 2.00e-02 2.50e+03   1.52e-02 4.06e+00
        pdb=" CG  PHE A 391 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 391 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 391 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 391 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 391 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 391 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 390 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.81e+00
        pdb=" C   ILE A 390 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE A 390 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 391 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1502 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1203
        2.76 -     3.29: 8017
        3.29 -     3.83: 13547
        3.83 -     4.36: 15536
        4.36 -     4.90: 27371
  Nonbonded interactions: 65674
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  83 "
            pdb=" O   ASN B 436 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OH  TYR B 277 "
            pdb=" OD2 ASP B 321 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR A 333 "
            pdb=" O   ALA A 578 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OE2 GLU B 330 "
            pdb=" NH1 ARG B 411 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" ND2 ASN B 389 "
            pdb=" OE1 GLN B 392 "
     model   vdw
     2.267 3.120
  ... (remaining 65669 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=1.00 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:             1.050
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.730
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
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   0.288   8657  Z= 0.369
  Angle     :  0.735  13.209  11748  Z= 0.398
  Chirality :  0.045   0.351   1281
  Planarity :  0.004   0.084   1505
  Dihedral  : 17.975  89.910   3219
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.01 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 26.00 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.27), residues: 1049
  helix:  0.80 (0.27), residues: 388
  sheet: -0.76 (0.40), residues: 189
  loop : -2.25 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 198 
 HIS   0.007   0.001   HIS A  52 
 PHE   0.035   0.002   PHE A 391 
 TYR   0.013   0.001   TYR B 149 
 ARG   0.006   0.000   ARG B  69 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 3
  residues processed: 92
  average time/residue: 0.2644
  time to fit residues: 32.4726
Evaluate side-chains
  78 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain B residue  257 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    0.3980
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B 317 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.156111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.116380 restraints weight = 11863.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.114200 restraints weight = 12885.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.115791 restraints weight = 15772.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8657  Z= 0.176
  Angle     :  0.562   8.610  11748  Z= 0.296
  Chirality :  0.041   0.155   1281
  Planarity :  0.004   0.038   1505
  Dihedral  :  7.112  64.597   1212
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.53 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 24.12 %
    Favored  : 72.46 %
  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: -0.94 (0.27), residues: 1049
  helix:  1.15 (0.28), residues: 389
  sheet: -0.67 (0.39), residues: 186
  loop : -2.20 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 377 
 HIS   0.007   0.001   HIS A  52 
 PHE   0.030   0.001   PHE A 391 
 TYR   0.014   0.001   TYR B 366 
 ARG   0.004   0.000   ARG A 438 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.7228 (t80)
REVERT: A  112 LEU cc_start: 0.4545 (OUTLIER) cc_final: 0.4171 (tt)
REVERT: B   98 LEU cc_start: 0.9051 (tt) cc_final: 0.8664 (tt)
  outliers start: 31
  outliers final: 11
  residues processed: 111
  average time/residue: 0.2074
  time to fit residues: 32.0492
Evaluate side-chains
  88 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0770
   chunk 83 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.7342

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B  45 ASN
B 339 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.156026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.117371 restraints weight = 12048.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.115922 restraints weight = 13429.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.117303 restraints weight = 14940.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8657  Z= 0.167
  Angle     :  0.547   8.304  11748  Z= 0.286
  Chirality :  0.041   0.149   1281
  Planarity :  0.003   0.036   1505
  Dihedral  :  6.478  61.509   1209
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.34 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 24.23 %
    Favored  : 72.35 %
  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: -0.72 (0.27), residues: 1049
  helix:  1.36 (0.28), residues: 390
  sheet: -0.60 (0.40), residues: 185
  loop : -2.09 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 377 
 HIS   0.005   0.001   HIS A  52 
 PHE   0.013   0.001   PHE A 328 
 TYR   0.012   0.001   TYR B 366 
 ARG   0.005   0.000   ARG B  69 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 86
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 GLN cc_start: 0.8175 (mp10) cc_final: 0.7791 (mp10)
REVERT: A   93 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7248 (t80)
REVERT: A  112 LEU cc_start: 0.4615 (OUTLIER) cc_final: 0.4246 (tt)
REVERT: A  420 PHE cc_start: 0.8475 (t80) cc_final: 0.8006 (t80)
REVERT: B   49 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7321 (mm-40)
REVERT: B  188 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8629 (mt)
REVERT: B  197 MET cc_start: 0.9038 (mmp) cc_final: 0.8708 (mmm)
REVERT: B  373 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7713 (mp0)
  outliers start: 31
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1965
  time to fit residues: 31.6674
Evaluate side-chains
  92 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0370
   chunk 45 optimal weight:    0.0270
   chunk 79 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B 339 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.157329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.118801 restraints weight = 11809.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.116533 restraints weight = 12131.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.118110 restraints weight = 13403.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8657  Z= 0.144
  Angle     :  0.526   8.906  11748  Z= 0.273
  Chirality :  0.040   0.170   1281
  Planarity :  0.003   0.036   1505
  Dihedral  :  6.117  56.897   1209
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.06 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 25.00 %
    Favored  : 71.68 %
  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: -0.54 (0.27), residues: 1049
  helix:  1.51 (0.28), residues: 390
  sheet: -0.29 (0.41), residues: 175
  loop : -2.05 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 377 
 HIS   0.004   0.001   HIS A  52 
 PHE   0.053   0.001   PHE A 391 
 TYR   0.011   0.001   TYR B 366 
 ARG   0.004   0.000   ARG B  69 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 86
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7339 (t80)
REVERT: A  112 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.4344 (tt)
REVERT: B  197 MET cc_start: 0.9011 (mmp) cc_final: 0.8755 (mmm)
REVERT: B  411 ARG cc_start: 0.8729 (mtm180) cc_final: 0.8237 (mtm180)
  outliers start: 30
  outliers final: 18
  residues processed: 109
  average time/residue: 0.2189
  time to fit residues: 33.2385
Evaluate side-chains
  98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0170
   chunk 32 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B 339 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.156744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.118371 restraints weight = 11759.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.116006 restraints weight = 12003.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.117657 restraints weight = 13156.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8657  Z= 0.161
  Angle     :  0.531   8.076  11748  Z= 0.277
  Chirality :  0.041   0.194   1281
  Planarity :  0.003   0.035   1505
  Dihedral  :  6.006  54.179   1209
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.15 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 25.11 %
    Favored  : 71.35 %
  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: -0.49 (0.27), residues: 1049
  helix:  1.58 (0.28), residues: 389
  sheet: -0.26 (0.41), residues: 175
  loop : -2.05 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 377 
 HIS   0.004   0.001   HIS A  52 
 PHE   0.010   0.001   PHE A 328 
 TYR   0.011   0.001   TYR B 366 
 ARG   0.005   0.000   ARG B  69 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7322 (t80)
REVERT: A  112 LEU cc_start: 0.4571 (OUTLIER) cc_final: 0.4312 (tt)
REVERT: B  197 MET cc_start: 0.9025 (mmp) cc_final: 0.8819 (mmm)
  outliers start: 32
  outliers final: 21
  residues processed: 103
  average time/residue: 0.2041
  time to fit residues: 29.7755
Evaluate side-chains
  93 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 82 optimal weight:    0.3980
   chunk 3 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0270
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:   20.0000
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B 339 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.158004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.118861 restraints weight = 11823.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.116035 restraints weight = 13201.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.117922 restraints weight = 14508.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8657  Z= 0.142
  Angle     :  0.519   8.118  11748  Z= 0.269
  Chirality :  0.040   0.158   1281
  Planarity :  0.003   0.034   1505
  Dihedral  :  5.870  52.531   1209
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.96 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 25.33 %
    Favored  : 71.35 %
  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: -0.43 (0.27), residues: 1049
  helix:  1.63 (0.28), residues: 389
  sheet: -0.19 (0.41), residues: 175
  loop : -2.02 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 377 
 HIS   0.004   0.001   HIS A  46 
 PHE   0.034   0.001   PHE A 391 
 TYR   0.011   0.001   TYR B 366 
 ARG   0.004   0.000   ARG B  69 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.7331 (t80)
REVERT: A  112 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.4352 (tt)
REVERT: B  411 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8258 (mtm180)
  outliers start: 30
  outliers final: 21
  residues processed: 103
  average time/residue: 0.2000
  time to fit residues: 29.1358
Evaluate side-chains
  95 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B 339 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.156110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.117415 restraints weight = 11878.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.114694 restraints weight = 13824.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.116685 restraints weight = 13212.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8657  Z= 0.182
  Angle     :  0.558   8.188  11748  Z= 0.289
  Chirality :  0.041   0.171   1281
  Planarity :  0.003   0.035   1505
  Dihedral  :  5.906  51.491   1209
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.53 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 25.33 %
    Favored  : 71.13 %
  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: -0.51 (0.27), residues: 1049
  helix:  1.58 (0.28), residues: 388
  sheet: -0.35 (0.41), residues: 185
  loop : -2.05 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 377 
 HIS   0.005   0.001   HIS A  52 
 PHE   0.010   0.001   PHE B 143 
 TYR   0.018   0.001   TYR A 402 
 ARG   0.005   0.000   ARG B  69 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7279 (t80)
REVERT: A  112 LEU cc_start: 0.4494 (OUTLIER) cc_final: 0.4239 (tt)
REVERT: A  372 LEU cc_start: 0.8798 (mt) cc_final: 0.8390 (mp)
REVERT: B  373 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7820 (mp0)
  outliers start: 32
  outliers final: 24
  residues processed: 105
  average time/residue: 0.1878
  time to fit residues: 28.2623
Evaluate side-chains
  101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 101 optimal weight:    0.4980
   chunk 28 optimal weight:    0.6980
   chunk 37 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.154690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.115906 restraints weight = 11949.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.112608 restraints weight = 13906.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.113794 restraints weight = 16347.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8657  Z= 0.210
  Angle     :  0.566   8.047  11748  Z= 0.292
  Chirality :  0.042   0.155   1281
  Planarity :  0.003   0.035   1505
  Dihedral  :  6.031  51.932   1209
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 25.22 %
    Favored  : 71.13 %
  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: -0.57 (0.27), residues: 1049
  helix:  1.52 (0.28), residues: 389
  sheet: -0.42 (0.40), residues: 187
  loop : -2.07 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 377 
 HIS   0.006   0.001   HIS A  52 
 PHE   0.040   0.001   PHE A 391 
 TYR   0.012   0.001   TYR B 366 
 ARG   0.006   0.000   ARG B  69 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 74
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7761 (mp10)
REVERT: A   93 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7331 (t80)
REVERT: A  112 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.4173 (tt)
REVERT: A  372 LEU cc_start: 0.8811 (mt) cc_final: 0.8405 (mp)
REVERT: B  373 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7762 (mp0)
  outliers start: 33
  outliers final: 21
  residues processed: 103
  average time/residue: 0.2125
  time to fit residues: 31.1722
Evaluate side-chains
  94 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 100 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 93 optimal weight:    0.3980
   chunk 50 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0670
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS
B  45 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.157093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.118662 restraints weight = 11985.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.116765 restraints weight = 13781.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.118559 restraints weight = 13691.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8657  Z= 0.154
  Angle     :  0.558   9.037  11748  Z= 0.286
  Chirality :  0.041   0.218   1281
  Planarity :  0.003   0.034   1505
  Dihedral  :  5.886  54.295   1209
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 26.00 %
    Favored  : 71.02 %
  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: -0.50 (0.27), residues: 1049
  helix:  1.56 (0.28), residues: 388
  sheet: -0.26 (0.41), residues: 175
  loop : -2.02 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 377 
 HIS   0.004   0.001   HIS A  52 
 PHE   0.009   0.001   PHE B 143 
 TYR   0.014   0.001   TYR A 402 
 ARG   0.005   0.000   ARG B  69 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7335 (t80)
REVERT: A  112 LEU cc_start: 0.4356 (OUTLIER) cc_final: 0.4135 (tt)
REVERT: A  372 LEU cc_start: 0.8777 (mt) cc_final: 0.8355 (mp)
  outliers start: 27
  outliers final: 20
  residues processed: 103
  average time/residue: 0.2055
  time to fit residues: 29.7846
Evaluate side-chains
  96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.155539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.116798 restraints weight = 11879.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.114868 restraints weight = 14007.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.116527 restraints weight = 15465.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8657  Z= 0.189
  Angle     :  0.571   7.970  11748  Z= 0.293
  Chirality :  0.041   0.151   1281
  Planarity :  0.003   0.035   1505
  Dihedral  :  5.939  54.634   1209
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.53 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 26.11 %
    Favored  : 71.13 %
  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: -0.52 (0.27), residues: 1049
  helix:  1.59 (0.28), residues: 388
  sheet: -0.41 (0.40), residues: 185
  loop : -2.05 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 377 
 HIS   0.005   0.001   HIS A  52 
 PHE   0.039   0.001   PHE A 391 
 TYR   0.012   0.001   TYR B 366 
 ARG   0.006   0.000   ARG B  69 

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7397 (t80)
REVERT: A  112 LEU cc_start: 0.4147 (OUTLIER) cc_final: 0.3900 (tt)
REVERT: A  372 LEU cc_start: 0.8781 (mt) cc_final: 0.8366 (mp)
  outliers start: 25
  outliers final: 20
  residues processed: 98
  average time/residue: 0.2120
  time to fit residues: 29.3079
Evaluate side-chains
  97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLN
Chi-restraints excluded: chain A residue   46 HIS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  374 TYR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  467 PHE
Chi-restraints excluded: chain A residue  541 ASP
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  373 GLU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 0 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 2 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.156250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.117905 restraints weight = 12059.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.115339 restraints weight = 13387.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.116758 restraints weight = 15489.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8657  Z= 0.168
  Angle     :  0.564   8.572  11748  Z= 0.290
  Chirality :  0.041   0.212   1281
  Planarity :  0.003   0.034   1505
  Dihedral  :  5.898  55.569   1209
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.15 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 26.44 %
    Favored  : 71.13 %
  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: -0.49 (0.27), residues: 1049
  helix:  1.61 (0.28), residues: 388
  sheet: -0.41 (0.40), residues: 185
  loop : -2.02 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 377 
 HIS   0.005   0.001   HIS A  52 
 PHE   0.010   0.001   PHE B 143 
 TYR   0.012   0.001   TYR B 366 
 ARG   0.006   0.000   ARG B  69 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2389.19 seconds
wall clock time: 42 minutes 27.94 seconds (2547.94 seconds total)