Starting phenix.real_space_refine
on Wed Feb 12 20:25:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z2h_14466/02_2025/7z2h_14466.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z2h_14466/02_2025/7z2h_14466.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z2h_14466/02_2025/7z2h_14466.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z2h_14466/02_2025/7z2h_14466.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z2h_14466/02_2025/7z2h_14466.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z2h_14466/02_2025/7z2h_14466.cif"
  }
  resolution = 3.58
  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=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     P      36      5.49       5
     S      13      5.16       5
     Cl      1      4.86       5
     C    5333      2.51       5
     N    1405      2.21       5
     O    1623      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8414
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4254
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 526, 4254
          Classifications: {'peptide': 526}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 489}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 3390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 411, 3390
          Classifications: {'peptide': 411}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 380}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 741
          Classifications: {'DNA': 34, 'RNA': 2}
          Modifications used: {'rna3p': 2}
          Link IDs: {'rna3p': 35}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 6
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'2KW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.14, per 1000 atoms: 0.61
  Number of scatterers: 8414
  At special positions: 0
  Unit cell: (97, 110.58, 96.03, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      1     17.00
     S      13     16.00
     P      36     15.00
     F       3      9.00
     O    1623      8.00
     N    1405      7.00
     C    5333      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: 2.29
  Conformation dependent library (CDL) restraints added in 898.4 milliseconds
  

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1766

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 12 sheets defined
      39.7% alpha, 10.9% beta
      13 base pairs and 28 stacking pairs defined.
    Time for finding SS restraints: 2.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 44
      removed outlier: 3.558A  pdb=" N   GLU A  40 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   MET A  41 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLU A  42 " --> pdb=" O   CYS A  38 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LYS A  43 " --> pdb=" O   THR A  39 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLU A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 84
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 123 through 128
      removed outlier: 3.790A  pdb=" N   LYS A 126 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 194 through 212
      removed outlier: 3.934A  pdb=" N   TRP A 212 " --> pdb=" O   HIS A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
    Processing helix  chain 'A' and resid 254 through 268
    Processing helix  chain 'A' and resid 276 through 281
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 4.329A  pdb=" N   GLU A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 384
      removed outlier: 3.720A  pdb=" N   GLN A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 405
    Processing helix  chain 'A' and resid 473 through 488
    Processing helix  chain 'A' and resid 499 through 508
      removed outlier: 4.184A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA A 508 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'A' and resid 544 through 552
      removed outlier: 3.592A  pdb=" N   VAL A 548 " --> pdb=" O   GLY A 544 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL A 552 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 44
      removed outlier: 3.747A  pdb=" N   GLU B  36 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLU B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 91
      removed outlier: 6.508A  pdb=" N   ASP B  86 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   PHE B  87 " --> pdb=" O   ARG B  83 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TRP B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 101
      removed outlier: 3.722A  pdb=" N   LYS B 101 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 118
      removed outlier: 3.929A  pdb=" N   VAL B 118 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 127
      removed outlier: 3.746A  pdb=" N   LYS B 126 " --> pdb=" O   ASP B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.622A  pdb=" N   LYS B 138 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 175
      removed outlier: 4.288A  pdb=" N   ALA B 158 " --> pdb=" O   LYS B 154 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   SER B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   SER B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
    Processing helix  chain 'B' and resid 194 through 212
      removed outlier: 3.520A  pdb=" N   THR B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TRP B 212 " --> pdb=" O   HIS B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 239
      removed outlier: 3.729A  pdb=" N   TRP B 239 " --> pdb=" O   PRO B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 269
      removed outlier: 3.783A  pdb=" N   GLN B 269 " --> pdb=" O   ASN B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 283
    Processing helix  chain 'B' and resid 296 through 312
    Processing helix  chain 'B' and resid 364 through 383
      removed outlier: 3.561A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 402
      removed outlier: 3.770A  pdb=" N   TRP B 401 " --> pdb=" O   THR B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 406
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50
      removed outlier: 4.014A  pdb=" N   ARG A 143 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 107
    Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234
    Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 253
      removed outlier: 4.426A  pdb=" N   TRP A 252 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331
      removed outlier: 6.718A  pdb=" N   TRP A 337 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LYS A 353 " --> pdb=" O   TRP A 337 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   THR A 351 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ILE A 341 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   GLN A 343 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   LYS A 347 " --> pdb=" O   GLN A 343 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391
    Processing sheet with id=AA7, first strand: chain 'A' and resid 438 through 441
      removed outlier: 4.193A  pdb=" N   GLU A 438 " --> pdb=" O   GLU A 492 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TYR A 532 " --> pdb=" O   VAL A 493 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 444 through 445
    Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49
      removed outlier: 3.768A  pdb=" N   ILE B 142 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ILE B 132 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 110
    Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 253
      removed outlier: 4.691A  pdb=" N   TRP B 252 " --> pdb=" O   ILE B 293 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 348 through 355
      removed outlier: 3.797A  pdb=" N   TYR B 339 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU B 325 " --> pdb=" O   LYS B 388 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   LYS B 390 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA B 327 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)

    277 hydrogen bonds defined for protein.
    756 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      36 hydrogen bonds
      72 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      28 stacking parallelities
  Total time for adding SS restraints: 2.65

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1304
        1.27 -     1.40: 2156
        1.40 -     1.54: 5045
        1.54 -     1.67: 181
        1.67 -     1.81: 24
  Bond restraints: 8710
  Sorted by residual:
  bond pdb=" C10 2KW A 601 "
       pdb=" C9  2KW A 601 "
    ideal  model  delta    sigma   weight residual
    1.354  1.522 -0.168 2.00e-02 2.50e+03 7.08e+01
  bond pdb=" C21 2KW A 601 "
       pdb=" N20 2KW A 601 "
    ideal  model  delta    sigma   weight residual
    1.356  1.500 -0.144 2.00e-02 2.50e+03 5.17e+01
  bond pdb=" C10 2KW A 601 "
       pdb=" N11 2KW A 601 "
    ideal  model  delta    sigma   weight residual
    1.355  1.489 -0.134 2.00e-02 2.50e+03 4.50e+01
  bond pdb=" C7  2KW A 601 "
       pdb=" C8  2KW A 601 "
    ideal  model  delta    sigma   weight residual
    1.359  1.485 -0.126 2.00e-02 2.50e+03 3.99e+01
  bond pdb=" C18 2KW A 601 "
       pdb=" N19 2KW A 601 "
    ideal  model  delta    sigma   weight residual
    1.287  1.402 -0.115 2.00e-02 2.50e+03 3.28e+01
  ... (remaining 8705 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.04: 11846
        3.04 -     6.08: 132
        6.08 -     9.13: 14
        9.13 -    12.17: 2
       12.17 -    15.21: 3
  Bond angle restraints: 11997
  Sorted by residual:
  angle pdb=" C   LEU A 228 "
        pdb=" CA  LEU A 228 "
        pdb=" CB  LEU A 228 "
      ideal   model   delta    sigma   weight residual
     110.24  122.50  -12.26 1.46e+00 4.69e-01 7.05e+01
  angle pdb=" N   LEU A 228 "
        pdb=" CA  LEU A 228 "
        pdb=" C   LEU A 228 "
      ideal   model   delta    sigma   weight residual
     108.13   94.42   13.71 1.72e+00 3.38e-01 6.35e+01
  angle pdb=" C   ASP A 186 "
        pdb=" CA  ASP A 186 "
        pdb=" CB  ASP A 186 "
      ideal   model   delta    sigma   weight residual
     109.33   94.12   15.21 1.97e+00 2.58e-01 5.96e+01
  angle pdb=" N   TRP B 426 "
        pdb=" CA  TRP B 426 "
        pdb=" C   TRP B 426 "
      ideal   model   delta    sigma   weight residual
     112.89  105.54    7.35 1.24e+00 6.50e-01 3.51e+01
  angle pdb=" N   ILE B 382 "
        pdb=" CA  ILE B 382 "
        pdb=" C   ILE B 382 "
      ideal   model   delta    sigma   weight residual
     110.74  116.07   -5.33 9.10e-01 1.21e+00 3.44e+01
  ... (remaining 11992 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 4338
       17.77 -    35.55: 532
       35.55 -    53.32: 171
       53.32 -    71.10: 49
       71.10 -    88.87: 11
  Dihedral angle restraints: 5101
    sinusoidal: 2367
      harmonic: 2734
  Sorted by residual:
  dihedral pdb=" C   ASP A 186 "
           pdb=" N   ASP A 186 "
           pdb=" CA  ASP A 186 "
           pdb=" CB  ASP A 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -105.98  -16.62     0      2.50e+00 1.60e-01 4.42e+01
  dihedral pdb=" C   MET A 164 "
           pdb=" N   MET A 164 "
           pdb=" CA  MET A 164 "
           pdb=" CB  MET A 164 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.65   13.05     0      2.50e+00 1.60e-01 2.73e+01
  dihedral pdb=" N   MET A 164 "
           pdb=" C   MET A 164 "
           pdb=" CA  MET A 164 "
           pdb=" CB  MET A 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.93  -12.13     0      2.50e+00 1.60e-01 2.35e+01
  ... (remaining 5098 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.123: 1279
       0.123 -    0.246: 25
       0.246 -    0.369: 4
       0.369 -    0.492: 0
       0.492 -    0.616: 2
  Chirality restraints: 1310
  Sorted by residual:
  chirality pdb=" P    DA E  -2 "
            pdb=" OP1  DA E  -2 "
            pdb=" OP2  DA E  -2 "
            pdb=" O5'  DA E  -2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.96   -0.62 2.00e-01 2.50e+01 9.47e+00
  chirality pdb=" CA  MET A 164 "
            pdb=" N   MET A 164 "
            pdb=" C   MET A 164 "
            pdb=" CB  MET A 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.53 2.00e-01 2.50e+01 6.90e+00
  chirality pdb=" C4'  DC E   3 "
            pdb=" C5'  DC E   3 "
            pdb=" O4'  DC E   3 "
            pdb=" C3'  DC E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.80    0.27 2.00e-01 2.50e+01 1.84e+00
  ... (remaining 1307 not shown)

  Planarity restraints: 1382
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 125 "   -0.565 9.50e-02 1.11e+02   2.53e-01 3.93e+01
        pdb=" NE  ARG A 125 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 125 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 125 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 125 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 118 "    0.063 5.00e-02 4.00e+02   9.35e-02 1.40e+01
        pdb=" N   PRO B 119 "   -0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO B 119 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 119 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 187 "    0.014 2.00e-02 2.50e+03   2.90e-02 8.43e+00
        pdb=" C   LEU A 187 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LEU A 187 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TYR A 188 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1379 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2009
        2.80 -     3.32: 7739
        3.32 -     3.85: 14183
        3.85 -     4.37: 16225
        4.37 -     4.90: 26618
  Nonbonded interactions: 66774
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 196 "
            pdb=" OG1 THR B 200 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   2KW A 601 "
            pdb=" F15 2KW A 601 "
     model   vdw
     2.293 2.990
  nonbonded pdb=" O   ARG A 277 "
            pdb=" N   SER A 280 "
     model   vdw
     2.326 3.120
  nonbonded pdb=" OG1 THR A 376 "
            pdb=" OG1 THR A 386 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" NZ  LYS A  13 "
            pdb=" O   LYS A  82 "
     model   vdw
     2.377 3.120
  ... (remaining 66769 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.080
  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:             0.020
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.170
  Set scattering table:                    0.220
  Process input model:                     24.180
  Find NCS groups from input model:        0.090
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5965
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.168   8710  Z= 0.354
  Angle     :  0.812  15.210  11997  Z= 0.463
  Chirality :  0.055   0.616   1310
  Planarity :  0.009   0.253   1382
  Dihedral  : 17.792  88.870   3335
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.34 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  0.84 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.71 (0.28), residues: 921
  helix:  0.86 (0.31), residues: 308
  sheet: -1.63 (0.42), residues: 149
  loop : -0.94 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 414 
 HIS   0.003   0.001   HIS B 208 
 PHE   0.012   0.001   PHE A 124 
 TYR   0.027   0.001   TYR A 232 
 ARG   0.003   0.000   ARG A 277 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  144 TYR cc_start: 0.7794 (m-10) cc_final: 0.7447 (m-10)
REVERT: B  180 ILE cc_start: 0.7335 (mm) cc_final: 0.6877 (tt)
REVERT: B  198 HIS cc_start: 0.4680 (t70) cc_final: 0.4389 (t70)
REVERT: B  409 THR cc_start: 0.7210 (m) cc_final: 0.6812 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 133
  average time/residue: 0.2090
  time to fit residues: 38.4233
Evaluate side-chains
  108 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ASP
Chi-restraints excluded: chain B residue   32 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 75 optimal weight:   30.0000
   chunk 29 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   overall best weight:    2.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN
B 269 GLN
B 418 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.226066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.180860 restraints weight = 9811.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.185771 restraints weight = 5985.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.188972 restraints weight = 4389.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6044
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8710  Z= 0.197
  Angle     :  0.603   8.593  11997  Z= 0.315
  Chirality :  0.043   0.189   1310
  Planarity :  0.005   0.056   1382
  Dihedral  : 16.782  74.780   1384
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.37 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  7.78 %
    Favored  : 91.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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 (0.28), residues: 921
  helix:  1.05 (0.30), residues: 319
  sheet: -1.50 (0.41), residues: 155
  loop : -0.92 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 402 
 HIS   0.003   0.001   HIS B 198 
 PHE   0.012   0.001   PHE A 124 
 TYR   0.017   0.001   TYR A 501 
 ARG   0.005   0.001   ARG A 358 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 114
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  277 ARG cc_start: 0.6123 (mmm160) cc_final: 0.5759 (tpt-90)
REVERT: B  180 ILE cc_start: 0.7390 (mm) cc_final: 0.6968 (tt)
REVERT: B  409 THR cc_start: 0.7219 (m) cc_final: 0.6768 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 117
  average time/residue: 0.1728
  time to fit residues: 29.7036
Evaluate side-chains
  108 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  123 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 19 optimal weight:   20.0000
   chunk 18 optimal weight:    9.9990
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 52 optimal weight:   20.0000
   chunk 22 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    4.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 HIS
** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN
B 255 ASN
** B 340 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 = 0.4635 r_free = 0.4635 target = 0.217985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.175675 restraints weight = 9953.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.174005 restraints weight = 7155.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.176192 restraints weight = 6691.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.4230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6213
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8710  Z= 0.262
  Angle     :  0.636   7.984  11997  Z= 0.332
  Chirality :  0.044   0.187   1310
  Planarity :  0.005   0.049   1382
  Dihedral  : 16.764  74.889   1382
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.65 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.42 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.66 (0.28), residues: 921
  helix:  1.10 (0.30), residues: 308
  sheet: -1.69 (0.42), residues: 141
  loop : -1.05 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 402 
 HIS   0.004   0.001   HIS A 315 
 PHE   0.018   0.002   PHE B 130 
 TYR   0.016   0.002   TYR A 457 
 ARG   0.004   0.001   ARG A 358 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  277 ARG cc_start: 0.6230 (mmm160) cc_final: 0.5907 (tpt-90)
REVERT: A  357 MET cc_start: 0.5900 (ttt) cc_final: 0.5444 (tpp)
REVERT: A  501 TYR cc_start: 0.5943 (t80) cc_final: 0.5570 (t80)
REVERT: B  180 ILE cc_start: 0.7448 (mm) cc_final: 0.6998 (tt)
  outliers start: 13
  outliers final: 9
  residues processed: 123
  average time/residue: 0.1820
  time to fit residues: 32.1519
Evaluate side-chains
  112 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  314 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 32 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 22 optimal weight:   40.0000
   chunk 84 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 40 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0370
   chunk 93 optimal weight:   20.0000
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.2860

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

Flipped N/Q/H residues before XYZ refinement:
** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.223967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.178693 restraints weight = 9759.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.183465 restraints weight = 6013.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.186517 restraints weight = 4420.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6061
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8710  Z= 0.166
  Angle     :  0.557   7.592  11997  Z= 0.290
  Chirality :  0.041   0.150   1310
  Planarity :  0.004   0.047   1382
  Dihedral  : 16.404  74.369   1382
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.15 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.22 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.33 (0.28), residues: 921
  helix:  1.46 (0.31), residues: 307
  sheet: -1.45 (0.41), residues: 155
  loop : -0.90 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 402 
 HIS   0.003   0.001   HIS A 198 
 PHE   0.008   0.001   PHE B 171 
 TYR   0.012   0.001   TYR B 354 
 ARG   0.002   0.000   ARG B 143 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 TYR cc_start: 0.7000 (m-80) cc_final: 0.6668 (m-80)
REVERT: A  281 LYS cc_start: 0.7344 (mtpt) cc_final: 0.7100 (ptmt)
REVERT: A  357 MET cc_start: 0.5786 (ttt) cc_final: 0.5353 (tpp)
REVERT: A  501 TYR cc_start: 0.6157 (t80) cc_final: 0.5864 (t80)
REVERT: B  144 TYR cc_start: 0.7841 (m-10) cc_final: 0.7448 (m-10)
REVERT: B  174 GLN cc_start: 0.6460 (mp10) cc_final: 0.5991 (mp10)
REVERT: B  180 ILE cc_start: 0.7462 (mm) cc_final: 0.7016 (tt)
  outliers start: 16
  outliers final: 14
  residues processed: 125
  average time/residue: 0.1875
  time to fit residues: 33.7172
Evaluate side-chains
  118 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  396 GLU
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 91 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 2 optimal weight:   20.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN
** B 340 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 = 0.4626 r_free = 0.4626 target = 0.217090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.173839 restraints weight = 9871.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.173492 restraints weight = 7080.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.174986 restraints weight = 6379.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6236
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8710  Z= 0.268
  Angle     :  0.638   8.671  11997  Z= 0.330
  Chirality :  0.044   0.173   1310
  Planarity :  0.005   0.046   1382
  Dihedral  : 16.503  76.153   1382
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.97 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.41 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.61 (0.28), residues: 921
  helix:  1.25 (0.31), residues: 303
  sheet: -1.68 (0.41), residues: 141
  loop : -1.08 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 229 
 HIS   0.005   0.001   HIS A 315 
 PHE   0.018   0.002   PHE B 130 
 TYR   0.016   0.002   TYR B 354 
 ARG   0.005   0.001   ARG A 358 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 MET cc_start: 0.5677 (ttt) cc_final: 0.5366 (tpp)
REVERT: A  501 TYR cc_start: 0.6097 (t80) cc_final: 0.5733 (t80)
REVERT: B  174 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.6271 (mp10)
REVERT: B  180 ILE cc_start: 0.7486 (mm) cc_final: 0.7070 (tt)
  outliers start: 24
  outliers final: 14
  residues processed: 125
  average time/residue: 0.1834
  time to fit residues: 32.8993
Evaluate side-chains
  119 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  174 GLN
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 27 optimal weight:    0.5980
   chunk 83 optimal weight:    9.9990
   chunk 36 optimal weight:   20.0000
   chunk 80 optimal weight:    0.9990
   chunk 85 optimal weight:    9.9990
   chunk 60 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.218841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.173251 restraints weight = 9846.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.176662 restraints weight = 6888.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.178744 restraints weight = 5489.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6167
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8710  Z= 0.221
  Angle     :  0.600   8.548  11997  Z= 0.310
  Chirality :  0.042   0.186   1310
  Planarity :  0.004   0.044   1382
  Dihedral  : 16.354  75.619   1382
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.45 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.97 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.56 (0.28), residues: 921
  helix:  1.34 (0.31), residues: 303
  sheet: -1.55 (0.42), residues: 139
  loop : -1.13 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 398 
 HIS   0.003   0.001   HIS A 315 
 PHE   0.014   0.002   PHE B 130 
 TYR   0.014   0.002   TYR B 354 
 ARG   0.004   0.000   ARG A 358 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 MET cc_start: 0.5657 (ttt) cc_final: 0.5365 (tpp)
REVERT: A  501 TYR cc_start: 0.6246 (t80) cc_final: 0.5994 (t80)
REVERT: B  174 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6157 (mp10)
REVERT: B  180 ILE cc_start: 0.7562 (mm) cc_final: 0.7170 (tt)
REVERT: B  184 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6481 (mmt)
  outliers start: 20
  outliers final: 16
  residues processed: 122
  average time/residue: 0.1752
  time to fit residues: 30.9803
Evaluate side-chains
  126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  174 GLN
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  396 GLU
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 11 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 92 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 69 optimal weight:    9.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.218637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.171907 restraints weight = 10035.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.175248 restraints weight = 7006.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.177640 restraints weight = 5586.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6189
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8710  Z= 0.235
  Angle     :  0.616   8.822  11997  Z= 0.319
  Chirality :  0.043   0.193   1310
  Planarity :  0.005   0.043   1382
  Dihedral  : 16.338  76.715   1382
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.54 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.41 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.62 (0.28), residues: 921
  helix:  1.29 (0.31), residues: 303
  sheet: -1.64 (0.41), residues: 139
  loop : -1.15 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 398 
 HIS   0.004   0.001   HIS A 315 
 PHE   0.015   0.002   PHE B 130 
 TYR   0.015   0.002   TYR B 354 
 ARG   0.004   0.000   ARG A 358 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7499 (tt)
REVERT: A  282 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5955 (mt)
REVERT: A  357 MET cc_start: 0.5644 (ttt) cc_final: 0.5363 (tpp)
REVERT: A  480 GLN cc_start: 0.6051 (tt0) cc_final: 0.5644 (tt0)
REVERT: A  501 TYR cc_start: 0.6311 (t80) cc_final: 0.5819 (t80)
REVERT: B  174 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6130 (mp10)
REVERT: B  180 ILE cc_start: 0.7486 (mm) cc_final: 0.7078 (tt)
  outliers start: 25
  outliers final: 18
  residues processed: 126
  average time/residue: 0.1722
  time to fit residues: 31.8561
Evaluate side-chains
  126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  174 GLN
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  396 GLU
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 43 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 14 optimal weight:   20.0000
   chunk 89 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0050
   chunk 25 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    2.7600

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.219319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.173483 restraints weight = 10007.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.176898 restraints weight = 6931.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.178915 restraints weight = 5487.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6165
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8710  Z= 0.199
  Angle     :  0.597  10.532  11997  Z= 0.307
  Chirality :  0.042   0.182   1310
  Planarity :  0.004   0.043   1382
  Dihedral  : 16.222  76.369   1382
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.13 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.65 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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 (0.28), residues: 921
  helix:  1.35 (0.31), residues: 307
  sheet: -1.54 (0.42), residues: 139
  loop : -1.05 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 398 
 HIS   0.003   0.001   HIS A 198 
 PHE   0.012   0.001   PHE B 130 
 TYR   0.015   0.001   TYR B 354 
 ARG   0.003   0.000   ARG A 448 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7363 (tt)
REVERT: A  282 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5827 (mt)
REVERT: A  357 MET cc_start: 0.5550 (ttt) cc_final: 0.5276 (tpp)
REVERT: A  480 GLN cc_start: 0.6028 (tt0) cc_final: 0.5608 (tt0)
REVERT: A  501 TYR cc_start: 0.6213 (t80) cc_final: 0.5745 (t80)
REVERT: B  174 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6095 (mp10)
REVERT: B  180 ILE cc_start: 0.7490 (mm) cc_final: 0.7084 (tt)
  outliers start: 23
  outliers final: 18
  residues processed: 122
  average time/residue: 0.1707
  time to fit residues: 30.3895
Evaluate side-chains
  121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  174 GLN
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  396 GLU
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 51 optimal weight:   40.0000
   chunk 56 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 86 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 11 optimal weight:   30.0000
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.224507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.178911 restraints weight = 9901.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.183713 restraints weight = 6044.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.186824 restraints weight = 4406.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6064
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8710  Z= 0.166
  Angle     :  0.565  10.797  11997  Z= 0.288
  Chirality :  0.041   0.157   1310
  Planarity :  0.004   0.042   1382
  Dihedral  : 15.978  76.076   1382
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.37 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.20 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.16 (0.28), residues: 921
  helix:  1.59 (0.31), residues: 307
  sheet: -1.28 (0.42), residues: 144
  loop : -0.84 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 398 
 HIS   0.003   0.001   HIS A 198 
 PHE   0.007   0.001   PHE B 130 
 TYR   0.014   0.001   TYR B 354 
 ARG   0.003   0.000   ARG A 448 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.5641 (tmtt) cc_final: 0.5209 (tmtt)
REVERT: A  228 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7084 (tt)
REVERT: A  232 TYR cc_start: 0.6824 (m-80) cc_final: 0.6369 (m-80)
REVERT: A  357 MET cc_start: 0.5478 (ttt) cc_final: 0.5259 (tpp)
REVERT: A  501 TYR cc_start: 0.6405 (t80) cc_final: 0.6008 (t80)
REVERT: B  174 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.6046 (mp10)
REVERT: B  180 ILE cc_start: 0.7611 (mm) cc_final: 0.7223 (tt)
REVERT: B  184 MET cc_start: 0.6954 (mmt) cc_final: 0.6492 (mmp)
  outliers start: 18
  outliers final: 12
  residues processed: 126
  average time/residue: 0.1888
  time to fit residues: 34.0468
Evaluate side-chains
  119 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  174 GLN
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  396 GLU
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 95 optimal weight:   20.0000
   chunk 60 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   chunk 78 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 258 GLN
A 519 ASN
B 182 GLN
B 407 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.218813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.176008 restraints weight = 9850.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.175092 restraints weight = 7335.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.177149 restraints weight = 6332.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8710  Z= 0.242
  Angle     :  0.620  10.487  11997  Z= 0.319
  Chirality :  0.043   0.193   1310
  Planarity :  0.005   0.042   1382
  Dihedral  : 16.140  77.922   1382
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.10 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.16 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.39 (0.28), residues: 921
  helix:  1.35 (0.31), residues: 307
  sheet: -1.34 (0.44), residues: 134
  loop : -0.99 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 398 
 HIS   0.005   0.001   HIS B 208 
 PHE   0.041   0.002   PHE A 160 
 TYR   0.017   0.002   TYR B 354 
 ARG   0.007   0.001   ARG B 211 

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.5697 (tmtt) cc_final: 0.5234 (tmtt)
REVERT: A  228 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7246 (tt)
REVERT: A  357 MET cc_start: 0.5539 (ttt) cc_final: 0.5310 (tpp)
REVERT: A  480 GLN cc_start: 0.6040 (tt0) cc_final: 0.5621 (tt0)
REVERT: A  501 TYR cc_start: 0.6278 (t80) cc_final: 0.5858 (t80)
REVERT: B  174 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6133 (mp10)
REVERT: B  180 ILE cc_start: 0.7409 (mm) cc_final: 0.7033 (tt)
REVERT: B  184 MET cc_start: 0.7050 (mmt) cc_final: 0.6646 (mmt)
  outliers start: 16
  outliers final: 14
  residues processed: 116
  average time/residue: 0.2036
  time to fit residues: 33.5686
Evaluate side-chains
  119 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   32 LYS
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  174 GLN
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  396 GLU
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 95 optimal weight:   20.0000
   chunk 40 optimal weight:    0.7980
   chunk 14 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 77 optimal weight:    0.2980
   chunk 29 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 94 optimal weight:   10.0000
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 182 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.220889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.175034 restraints weight = 9921.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.178651 restraints weight = 6832.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.180959 restraints weight = 5363.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6123
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8710  Z= 0.186
  Angle     :  0.587  10.816  11997  Z= 0.302
  Chirality :  0.042   0.170   1310
  Planarity :  0.004   0.041   1382
  Dihedral  : 16.029  76.651   1382
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.13 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 19.52 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.27 (0.28), residues: 921
  helix:  1.44 (0.31), residues: 306
  sheet: -1.24 (0.42), residues: 144
  loop : -0.90 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 398 
 HIS   0.004   0.001   HIS A 198 
 PHE   0.032   0.002   PHE A 160 
 TYR   0.013   0.001   TYR B 354 
 ARG   0.003   0.000   ARG A 448 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2427.61 seconds
wall clock time: 44 minutes 25.93 seconds (2665.93 seconds total)