Starting phenix.real_space_refine
on Thu Mar  6 03:36:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sl9_25195/03_2025/7sl9_25195_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sl9_25195/03_2025/7sl9_25195.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sl9_25195/03_2025/7sl9_25195.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sl9_25195/03_2025/7sl9_25195.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sl9_25195/03_2025/7sl9_25195_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sl9_25195/03_2025/7sl9_25195_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3091      2.51       5
     N     749      2.21       5
     O     844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4712
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3763
          Classifications: {'peptide': 497}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 19, 'TRANS': 477}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 943
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'BUA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.36, per 1000 atoms: 0.71
  Number of scatterers: 4712
  At special positions: 0
  Unit cell: (91.16, 77.38, 90.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     844      8.00
     N     749      7.00
     C    3091      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 480 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 561.4 milliseconds
  

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1120

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 3 sheets defined
      64.0% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 34
      removed outlier: 3.795A  pdb=" N   SER A  25 " --> pdb=" O   MET A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 66
      removed outlier: 3.529A  pdb=" N   ALA A  58 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A  59 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A  64 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 73
      removed outlier: 3.569A  pdb=" N   LEU A  72 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 82
      removed outlier: 3.815A  pdb=" N   ARG A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 86
    Processing helix  chain 'A' and resid 87 through 102
      removed outlier: 3.502A  pdb=" N   THR A  91 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE A  93 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 110
      removed outlier: 3.776A  pdb=" N   PHE A 107 " --> pdb=" O   PHE A 103 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU A 110 " --> pdb=" O   VAL A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 123
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.721A  pdb=" N   LEU A 129 " --> pdb=" O   LYS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 159
      removed outlier: 3.689A  pdb=" N   GLY A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ILE A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      Proline residue:  A 150  - end of helix
      removed outlier: 4.035A  pdb=" N   GLN A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 175
      removed outlier: 3.880A  pdb=" N   VAL A 167 " --> pdb=" O   TRP A 163 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 172 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   CYS A 173 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 212
      removed outlier: 3.991A  pdb=" N   PHE A 191 " --> pdb=" O   TRP A 187 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   GLN A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 193 " --> pdb=" O   ASP A 189 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA A 198 " --> pdb=" O   GLY A 194 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A 201 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN A 206 " --> pdb=" O   SER A 202 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 207 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 224
      removed outlier: 4.029A  pdb=" N   ASN A 219 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   TYR A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 258
      removed outlier: 3.801A  pdb=" N   ILE A 245 " --> pdb=" O   THR A 241 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE A 251 " --> pdb=" O   ILE A 247 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   SER A 255 " --> pdb=" O   PHE A 251 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 263
    Processing helix  chain 'A' and resid 264 through 269
    Processing helix  chain 'A' and resid 272 through 305
      removed outlier: 3.652A  pdb=" N   LEU A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN A 283 " --> pdb=" O   SER A 279 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   VAL A 285 " --> pdb=" O   TYR A 281 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   CYS A 297 " --> pdb=" O   CYS A 293 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
      removed outlier: 3.510A  pdb=" N   GLN A 321 " --> pdb=" O   ALA A 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 318 through 321'
    Processing helix  chain 'A' and resid 322 through 331
      removed outlier: 3.622A  pdb=" N   LEU A 328 " --> pdb=" O   PRO A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 369
      removed outlier: 3.564A  pdb=" N   PHE A 341 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL A 342 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLY A 348 " --> pdb=" O   CYS A 344 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU A 350 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER A 354 " --> pdb=" O   LEU A 350 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL A 363 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE A 369 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 386
      removed outlier: 3.730A  pdb=" N   GLN A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 403
      removed outlier: 3.981A  pdb=" N   VAL A 390 " --> pdb=" O   GLN A 386 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 419
      removed outlier: 3.531A  pdb=" N   VAL A 416 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 433
      removed outlier: 3.846A  pdb=" N   LEU A 424 " --> pdb=" O   VAL A 420 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 427 " --> pdb=" O   PRO A 423 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   PHE A 428 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 463
      removed outlier: 3.787A  pdb=" N   VAL A 444 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLN A 461 " --> pdb=" O   GLY A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 471
    Processing helix  chain 'A' and resid 510 through 516
    Processing helix  chain 'A' and resid 525 through 533
      removed outlier: 4.139A  pdb=" N   VAL A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 543
      removed outlier: 3.690A  pdb=" N   SER A 540 " --> pdb=" O   GLY A 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 66
      removed outlier: 4.051A  pdb=" N   LYS B  66 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9
      removed outlier: 3.775A  pdb=" N   THR B  79 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41
      removed outlier: 3.741A  pdb=" N   ALA B  93 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 102
      removed outlier: 3.592A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 101 " (cutoff:3.500A)

    228 hydrogen bonds defined for protein.
    666 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: 1.32

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1428
        1.34 -     1.46: 1175
        1.46 -     1.58: 2183
        1.58 -     1.70: 0
        1.70 -     1.81: 43
  Bond restraints: 4829
  Sorted by residual:
  bond pdb=" C   THR A 510 "
       pdb=" N   PRO A 511 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.023 1.08e-02 8.57e+03 4.38e+00
  bond pdb=" C   SER A 317 "
       pdb=" N   ALA A 318 "
    ideal  model  delta    sigma   weight residual
    1.329  1.276  0.052 3.03e-02 1.09e+03 2.99e+00
  bond pdb=" C3  BUA A 701 "
       pdb=" C4  BUA A 701 "
    ideal  model  delta    sigma   weight residual
    1.539  1.506  0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" N   LYS A 314 "
       pdb=" CA  LYS A 314 "
    ideal  model  delta    sigma   weight residual
    1.460  1.485 -0.024 1.51e-02 4.39e+03 2.58e+00
  bond pdb=" N   VAL A 316 "
       pdb=" CA  VAL A 316 "
    ideal  model  delta    sigma   weight residual
    1.458  1.440  0.018 1.19e-02 7.06e+03 2.39e+00
  ... (remaining 4824 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 6398
        2.36 -     4.71: 153
        4.71 -     7.07: 31
        7.07 -     9.42: 8
        9.42 -    11.78: 2
  Bond angle restraints: 6592
  Sorted by residual:
  angle pdb=" N   LYS A 315 "
        pdb=" CA  LYS A 315 "
        pdb=" C   LYS A 315 "
      ideal   model   delta    sigma   weight residual
     110.35  122.13  -11.78 1.36e+00 5.41e-01 7.50e+01
  angle pdb=" N   VAL A 316 "
        pdb=" CA  VAL A 316 "
        pdb=" C   VAL A 316 "
      ideal   model   delta    sigma   weight residual
     108.12   98.81    9.31 1.44e+00 4.82e-01 4.18e+01
  angle pdb=" N   GLN A 508 "
        pdb=" CA  GLN A 508 "
        pdb=" C   GLN A 508 "
      ideal   model   delta    sigma   weight residual
     112.68  107.28    5.40 1.33e+00 5.65e-01 1.65e+01
  angle pdb=" C   PHE A 160 "
        pdb=" N   ASP A 161 "
        pdb=" CA  ASP A 161 "
      ideal   model   delta    sigma   weight residual
     121.54  129.16   -7.62 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" C   THR A 178 "
        pdb=" N   LEU A 179 "
        pdb=" CA  LEU A 179 "
      ideal   model   delta    sigma   weight residual
     124.31  130.91   -6.60 1.67e+00 3.59e-01 1.56e+01
  ... (remaining 6587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 2473
       17.66 -    35.32: 236
       35.32 -    52.98: 36
       52.98 -    70.64: 7
       70.64 -    88.30: 2
  Dihedral angle restraints: 2754
    sinusoidal: 983
      harmonic: 1771
  Sorted by residual:
  dihedral pdb=" CA  TYR B 111 "
           pdb=" C   TYR B 111 "
           pdb=" N   TYR B 112 "
           pdb=" CA  TYR B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.42  -29.58     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  LEU A 409 "
           pdb=" C   LEU A 409 "
           pdb=" N   LEU A 410 "
           pdb=" CA  LEU A 410 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.76   22.24     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  ILE A 477 "
           pdb=" C   ILE A 477 "
           pdb=" N   GLN A 478 "
           pdb=" CA  GLN A 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.94  -22.06     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 2751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 695
       0.092 -    0.184: 67
       0.184 -    0.276: 6
       0.276 -    0.368: 0
       0.368 -    0.460: 1
  Chirality restraints: 769
  Sorted by residual:
  chirality pdb=" CA  LYS A 315 "
            pdb=" N   LYS A 315 "
            pdb=" C   LYS A 315 "
            pdb=" CB  LYS A 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.29e+00
  chirality pdb=" CA  VAL A 316 "
            pdb=" N   VAL A 316 "
            pdb=" C   VAL A 316 "
            pdb=" CB  VAL A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CB  VAL A 203 "
            pdb=" CA  VAL A 203 "
            pdb=" CG1 VAL A 203 "
            pdb=" CG2 VAL A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 766 not shown)

  Planarity restraints: 813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  BUA A 701 "   -0.019 2.00e-02 2.50e+03   3.90e-02 1.52e+01
        pdb=" C4  BUA A 701 "    0.067 2.00e-02 2.50e+03
        pdb=" O1  BUA A 701 "   -0.024 2.00e-02 2.50e+03
        pdb=" O2  BUA A 701 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 309 "   -0.040 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO A 310 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 310 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 310 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 422 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO A 423 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 423 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 423 "    0.032 5.00e-02 4.00e+02
  ... (remaining 810 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1296
        2.79 -     3.32: 4351
        3.32 -     3.84: 7690
        3.84 -     4.37: 9146
        4.37 -     4.90: 15370
  Nonbonded interactions: 37853
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 472 "
            pdb=" OH  TYR B 111 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OG1 THR B  92 "
            pdb=" O   VAL B 120 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   GLY A 224 "
            pdb=" OG  SER B  31 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   ILE A 246 "
            pdb=" OG1 THR A 250 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   THR A 250 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.312 3.040
  ... (remaining 37848 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:             0.450
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.500
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
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      :  0.005   0.060   4829  Z= 0.308
  Angle     :  0.951  11.781   6592  Z= 0.523
  Chirality :  0.058   0.460    769
  Planarity :  0.007   0.061    813
  Dihedral  : 13.950  88.296   1628
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  9.51 %
    Favored  : 90.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.01 (0.22), residues: 611
  helix: -4.33 (0.11), residues: 357
  sheet: -2.43 (0.71), residues: 45
  loop : -3.26 (0.35), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 516 
 HIS   0.004   0.002   HIS A 306 
 PHE   0.019   0.002   PHE A 160 
 TYR   0.015   0.002   TYR A 372 
 ARG   0.002   0.000   ARG A 266 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 PHE cc_start: 0.9162 (t80) cc_final: 0.8863 (t80)
REVERT: A  277 LYS cc_start: 0.8937 (mttt) cc_final: 0.8591 (mttp)
REVERT: A  383 TRP cc_start: 0.7797 (t60) cc_final: 0.7559 (t60)
REVERT: A  425 MET cc_start: 0.9033 (tmm) cc_final: 0.8483 (ttt)
REVERT: A  480 CYS cc_start: 0.5398 (t) cc_final: 0.5137 (t)
REVERT: A  514 ASP cc_start: 0.8187 (t0) cc_final: 0.7854 (m-30)
REVERT: A  515 ASN cc_start: 0.8798 (m-40) cc_final: 0.8590 (m-40)
REVERT: B    6 LEU cc_start: 0.8717 (pt) cc_final: 0.8466 (pp)
REVERT: B   21 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8850 (ttp80)
REVERT: B   39 TYR cc_start: 0.8364 (m-80) cc_final: 0.8008 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 163
  average time/residue: 0.1421
  time to fit residues: 30.1761
Evaluate side-chains
  128 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 25 optimal weight:    0.3980
   chunk 15 optimal weight:    8.9990
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 156 GLN
A 474 HIS
B   5 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.146276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.107578 restraints weight = 7544.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.111267 restraints weight = 3851.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.113632 restraints weight = 2644.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4829  Z= 0.188
  Angle     :  0.697  11.585   6592  Z= 0.356
  Chirality :  0.043   0.190    769
  Planarity :  0.005   0.042    813
  Dihedral  :  5.606  26.571    672
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.62 %
    Favored  : 78.14 %
  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: -4.08 (0.27), residues: 611
  helix: -2.44 (0.20), residues: 364
  sheet: -3.15 (0.65), residues: 47
  loop : -2.71 (0.39), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 516 
 HIS   0.002   0.001   HIS A 474 
 PHE   0.011   0.001   PHE B  69 
 TYR   0.014   0.001   TYR A 108 
 ARG   0.005   0.000   ARG B  47 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.7858 (mmt) cc_final: 0.7606 (mmm)
REVERT: A   66 MET cc_start: 0.8164 (tpp) cc_final: 0.7891 (tpp)
REVERT: A  125 LYS cc_start: 0.8888 (tptp) cc_final: 0.8486 (tptp)
REVERT: A  383 TRP cc_start: 0.7637 (t60) cc_final: 0.7345 (t60)
REVERT: B    6 LEU cc_start: 0.8735 (pt) cc_final: 0.8514 (pp)
REVERT: B   21 ARG cc_start: 0.9105 (ttp80) cc_final: 0.8678 (ttm-80)
REVERT: B   54 ASN cc_start: 0.8957 (p0) cc_final: 0.8330 (p0)
REVERT: B   61 TYR cc_start: 0.8833 (m-80) cc_final: 0.8501 (m-80)
REVERT: B   68 ARG cc_start: 0.7481 (ptm160) cc_final: 0.6887 (ptm160)
REVERT: B   69 PHE cc_start: 0.8244 (m-10) cc_final: 0.7978 (m-80)
REVERT: B   82 LEU cc_start: 0.9476 (tt) cc_final: 0.9062 (tt)
REVERT: B   84 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7294 (mmp)
REVERT: B   91 ASP cc_start: 0.7359 (p0) cc_final: 0.7085 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 150
  average time/residue: 0.1439
  time to fit residues: 28.2065
Evaluate side-chains
  133 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 TYR
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0970
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 51 optimal weight:    0.3980
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.2982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.147408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.107729 restraints weight = 7704.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.111493 restraints weight = 4083.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.113872 restraints weight = 2855.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4829  Z= 0.266
  Angle     :  0.705  11.093   6592  Z= 0.353
  Chirality :  0.044   0.145    769
  Planarity :  0.004   0.034    813
  Dihedral  :  5.361  26.101    672
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 19.64 %
    Favored  : 74.90 %
  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: -3.01 (0.30), residues: 611
  helix: -1.40 (0.24), residues: 368
  sheet: -3.28 (0.61), residues: 47
  loop : -2.50 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 516 
 HIS   0.003   0.001   HIS A 240 
 PHE   0.011   0.001   PHE A 436 
 TYR   0.013   0.002   TYR A 176 
 ARG   0.005   0.000   ARG B  47 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.8810 (t80) cc_final: 0.8582 (t80)
REVERT: A  219 ASN cc_start: 0.8487 (t0) cc_final: 0.8048 (t0)
REVERT: A  383 TRP cc_start: 0.7769 (t60) cc_final: 0.7433 (t60)
REVERT: B   21 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8753 (ttm-80)
REVERT: B   48 GLU cc_start: 0.8232 (tt0) cc_final: 0.7753 (tt0)
REVERT: B   54 ASN cc_start: 0.8973 (p0) cc_final: 0.8392 (p0)
REVERT: B   61 TYR cc_start: 0.8869 (m-80) cc_final: 0.8488 (m-80)
REVERT: B  109 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7231 (p0)
  outliers start: 27
  outliers final: 20
  residues processed: 145
  average time/residue: 0.1508
  time to fit residues: 28.2377
Evaluate side-chains
  141 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 TYR
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0970
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0470
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.151077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.111979 restraints weight = 7672.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.115793 restraints weight = 4031.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.118281 restraints weight = 2790.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4829  Z= 0.175
  Angle     :  0.694  11.119   6592  Z= 0.340
  Chirality :  0.042   0.126    769
  Planarity :  0.004   0.039    813
  Dihedral  :  5.091  24.148    672
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 21.46 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.32), residues: 611
  helix: -0.84 (0.26), residues: 372
  sheet: -3.08 (0.64), residues: 49
  loop : -2.30 (0.44), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 516 
 HIS   0.002   0.001   HIS A 306 
 PHE   0.022   0.001   PHE A 160 
 TYR   0.011   0.001   TYR A 302 
 ARG   0.005   0.000   ARG B  47 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.8716 (t80) cc_final: 0.8494 (t80)
REVERT: A  219 ASN cc_start: 0.8440 (t0) cc_final: 0.8011 (t0)
REVERT: A  282 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8938 (mm)
REVERT: A  383 TRP cc_start: 0.7676 (t60) cc_final: 0.7401 (t60)
REVERT: B   21 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8699 (tpp80)
REVERT: B   53 ILE cc_start: 0.7806 (pt) cc_final: 0.7458 (pt)
REVERT: B   54 ASN cc_start: 0.8925 (p0) cc_final: 0.8159 (p0)
REVERT: B   82 LEU cc_start: 0.9358 (tp) cc_final: 0.8880 (tt)
REVERT: B   95 TYR cc_start: 0.8485 (m-10) cc_final: 0.8129 (m-10)
REVERT: B  109 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7087 (p0)
  outliers start: 22
  outliers final: 15
  residues processed: 147
  average time/residue: 0.1445
  time to fit residues: 27.7929
Evaluate side-chains
  148 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
B  29 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.149422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.109878 restraints weight = 7805.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.113637 restraints weight = 4115.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.116095 restraints weight = 2869.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4829  Z= 0.216
  Angle     :  0.709  11.152   6592  Z= 0.347
  Chirality :  0.043   0.131    769
  Planarity :  0.004   0.036    813
  Dihedral  :  5.110  24.979    672
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 21.05 %
    Favored  : 73.68 %
  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: -1.97 (0.33), residues: 611
  helix: -0.52 (0.26), residues: 370
  sheet: -3.03 (0.68), residues: 49
  loop : -2.14 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 187 
 HIS   0.002   0.001   HIS A 306 
 PHE   0.015   0.001   PHE A 160 
 TYR   0.023   0.001   TYR B  61 
 ARG   0.007   0.000   ARG B  68 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8995 (tptp) cc_final: 0.8552 (tptp)
REVERT: A  219 ASN cc_start: 0.8424 (t0) cc_final: 0.8037 (t0)
REVERT: A  383 TRP cc_start: 0.7679 (t60) cc_final: 0.7399 (t60)
REVERT: A  436 PHE cc_start: 0.7776 (p90) cc_final: 0.7412 (p90)
REVERT: A  514 ASP cc_start: 0.8098 (t0) cc_final: 0.7892 (m-30)
REVERT: B   21 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8798 (tpp80)
REVERT: B   54 ASN cc_start: 0.8895 (p0) cc_final: 0.8225 (p0)
REVERT: B   68 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7457 (ptm160)
REVERT: B   69 PHE cc_start: 0.8667 (m-80) cc_final: 0.7862 (m-80)
REVERT: B   82 LEU cc_start: 0.9333 (tp) cc_final: 0.8863 (tt)
REVERT: B   91 ASP cc_start: 0.7327 (p0) cc_final: 0.6852 (p0)
REVERT: B  109 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7113 (p0)
  outliers start: 26
  outliers final: 20
  residues processed: 152
  average time/residue: 0.1523
  time to fit residues: 30.1705
Evaluate side-chains
  149 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    0.0030
   chunk 35 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 60 optimal weight:    0.5980
   chunk 47 optimal weight:    0.4980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.151310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.111813 restraints weight = 7639.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.115562 restraints weight = 4053.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.118055 restraints weight = 2824.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4829  Z= 0.187
  Angle     :  0.704   9.830   6592  Z= 0.344
  Chirality :  0.043   0.130    769
  Planarity :  0.004   0.035    813
  Dihedral  :  5.010  23.946    672
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 22.67 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.34), residues: 611
  helix: -0.31 (0.27), residues: 370
  sheet: -2.96 (0.72), residues: 47
  loop : -2.12 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 306 
 PHE   0.016   0.001   PHE A 160 
 TYR   0.012   0.001   TYR A  32 
 ARG   0.005   0.000   ARG B  68 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8943 (tptp) cc_final: 0.8482 (tptp)
REVERT: A  219 ASN cc_start: 0.8462 (t0) cc_final: 0.8031 (t0)
REVERT: A  282 ILE cc_start: 0.9069 (mm) cc_final: 0.8860 (mm)
REVERT: A  383 TRP cc_start: 0.7639 (t60) cc_final: 0.7366 (t60)
REVERT: A  436 PHE cc_start: 0.7782 (p90) cc_final: 0.7474 (p90)
REVERT: B   54 ASN cc_start: 0.8918 (p0) cc_final: 0.8250 (p0)
REVERT: B   69 PHE cc_start: 0.8681 (m-80) cc_final: 0.8440 (m-10)
REVERT: B   91 ASP cc_start: 0.7216 (p0) cc_final: 0.6753 (p0)
REVERT: B  109 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6974 (p0)
  outliers start: 25
  outliers final: 21
  residues processed: 150
  average time/residue: 0.1465
  time to fit residues: 28.7813
Evaluate side-chains
  149 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0370
   chunk 28 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
B   5 GLN
B  78 ASN
** B  83 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 = 0.3942 r_free = 0.3942 target = 0.152035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.113481 restraints weight = 7609.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.117137 restraints weight = 4038.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.119567 restraints weight = 2812.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4829  Z= 0.180
  Angle     :  0.704   9.100   6592  Z= 0.344
  Chirality :  0.042   0.131    769
  Planarity :  0.004   0.033    813
  Dihedral  :  4.951  27.453    672
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 23.48 %
    Favored  : 70.85 %
  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: -1.62 (0.34), residues: 611
  helix: -0.16 (0.27), residues: 370
  sheet: -3.01 (0.68), residues: 49
  loop : -2.17 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.018   0.001   PHE A 160 
 TYR   0.016   0.001   TYR A  32 
 ARG   0.005   0.001   ARG B  21 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 0.525 
Fit side-chains
REVERT: A  219 ASN cc_start: 0.8414 (t0) cc_final: 0.7958 (t0)
REVERT: A  282 ILE cc_start: 0.9031 (mm) cc_final: 0.8792 (mm)
REVERT: A  290 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8981 (tp)
REVERT: A  383 TRP cc_start: 0.7652 (t60) cc_final: 0.7380 (t60)
REVERT: A  436 PHE cc_start: 0.7815 (p90) cc_final: 0.7526 (p90)
REVERT: B   20 LEU cc_start: 0.8752 (tt) cc_final: 0.8511 (mm)
REVERT: B   21 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8171 (tpp80)
REVERT: B   54 ASN cc_start: 0.8892 (p0) cc_final: 0.8254 (p0)
REVERT: B   95 TYR cc_start: 0.8288 (m-10) cc_final: 0.7908 (m-10)
REVERT: B  109 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6948 (p0)
  outliers start: 28
  outliers final: 23
  residues processed: 146
  average time/residue: 0.1512
  time to fit residues: 28.7103
Evaluate side-chains
  149 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 6 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0470
   chunk 54 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 47 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
B   5 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.151025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.111725 restraints weight = 7677.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.115446 restraints weight = 4096.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.117888 restraints weight = 2868.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4829  Z= 0.183
  Angle     :  0.709   8.995   6592  Z= 0.351
  Chirality :  0.043   0.130    769
  Planarity :  0.004   0.039    813
  Dihedral  :  4.891  25.235    672
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 24.09 %
    Favored  : 70.45 %
  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: -1.60 (0.34), residues: 611
  helix: -0.16 (0.27), residues: 374
  sheet: -2.91 (0.62), residues: 54
  loop : -2.15 (0.45), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.034   0.001   PHE A  65 
 TYR   0.017   0.001   TYR A  32 
 ARG   0.009   0.001   ARG B  68 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8900 (tptp) cc_final: 0.8444 (tptp)
REVERT: A  219 ASN cc_start: 0.8384 (t0) cc_final: 0.7965 (t0)
REVERT: A  282 ILE cc_start: 0.9052 (mm) cc_final: 0.8795 (mm)
REVERT: A  290 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8855 (tt)
REVERT: A  383 TRP cc_start: 0.7694 (t60) cc_final: 0.7409 (t60)
REVERT: A  436 PHE cc_start: 0.7857 (p90) cc_final: 0.7596 (p90)
REVERT: B   20 LEU cc_start: 0.8607 (tt) cc_final: 0.8379 (mm)
REVERT: B   54 ASN cc_start: 0.8942 (p0) cc_final: 0.8240 (p0)
REVERT: B   95 TYR cc_start: 0.8330 (m-10) cc_final: 0.8011 (m-10)
REVERT: B  109 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6982 (p0)
  outliers start: 27
  outliers final: 21
  residues processed: 143
  average time/residue: 0.1517
  time to fit residues: 28.4265
Evaluate side-chains
  145 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 31 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B   5 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.149398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.109565 restraints weight = 7724.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.113232 restraints weight = 4140.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.115572 restraints weight = 2901.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4829  Z= 0.264
  Angle     :  0.746   8.732   6592  Z= 0.371
  Chirality :  0.045   0.145    769
  Planarity :  0.004   0.045    813
  Dihedral  :  5.042  25.448    672
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 25.10 %
    Favored  : 69.64 %
  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: -1.57 (0.34), residues: 611
  helix: -0.17 (0.27), residues: 373
  sheet: -2.82 (0.62), residues: 49
  loop : -2.12 (0.45), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 311 
 HIS   0.002   0.001   HIS A 240 
 PHE   0.035   0.002   PHE A 160 
 TYR   0.018   0.001   TYR A 176 
 ARG   0.007   0.001   ARG B  68 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8897 (tptp) cc_final: 0.8471 (tptp)
REVERT: A  219 ASN cc_start: 0.8343 (t0) cc_final: 0.7953 (t0)
REVERT: A  277 LYS cc_start: 0.8954 (mttt) cc_final: 0.8720 (mttp)
REVERT: A  282 ILE cc_start: 0.9161 (mm) cc_final: 0.8934 (mm)
REVERT: A  383 TRP cc_start: 0.7704 (t60) cc_final: 0.7404 (t60)
REVERT: A  436 PHE cc_start: 0.7904 (p90) cc_final: 0.7617 (p90)
REVERT: B   20 LEU cc_start: 0.8528 (tt) cc_final: 0.8313 (mm)
REVERT: B   54 ASN cc_start: 0.8930 (p0) cc_final: 0.8219 (p0)
REVERT: B  109 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7191 (p0)
  outliers start: 26
  outliers final: 20
  residues processed: 142
  average time/residue: 0.1488
  time to fit residues: 27.6994
Evaluate side-chains
  141 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    0.1980
   chunk 48 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0980
   chunk 26 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
B   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.151856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.112788 restraints weight = 7608.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.116620 restraints weight = 4077.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.119128 restraints weight = 2839.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.4217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4829  Z= 0.189
  Angle     :  0.766   9.939   6592  Z= 0.377
  Chirality :  0.043   0.138    769
  Planarity :  0.004   0.057    813
  Dihedral  :  4.975  24.139    672
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 27.53 %
    Favored  : 69.03 %
  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: -1.45 (0.34), residues: 611
  helix: -0.09 (0.27), residues: 372
  sheet: -2.74 (0.61), residues: 53
  loop : -2.02 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.032   0.001   PHE A 160 
 TYR   0.013   0.001   TYR A  32 
 ARG   0.004   0.000   ARG B  21 

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8803 (tptp) cc_final: 0.8442 (tptp)
REVERT: A  219 ASN cc_start: 0.8408 (t0) cc_final: 0.8003 (t0)
REVERT: A  282 ILE cc_start: 0.9118 (mm) cc_final: 0.8849 (mm)
REVERT: A  383 TRP cc_start: 0.7621 (t60) cc_final: 0.7357 (t60)
REVERT: A  436 PHE cc_start: 0.7787 (p90) cc_final: 0.7517 (p90)
REVERT: B   54 ASN cc_start: 0.8908 (p0) cc_final: 0.8184 (p0)
REVERT: B   69 PHE cc_start: 0.8429 (m-80) cc_final: 0.7787 (m-80)
REVERT: B   95 TYR cc_start: 0.8354 (m-10) cc_final: 0.8140 (m-10)
REVERT: B  109 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7040 (p0)
  outliers start: 17
  outliers final: 15
  residues processed: 135
  average time/residue: 0.1481
  time to fit residues: 26.1426
Evaluate side-chains
  139 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 48 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.151837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.112639 restraints weight = 7774.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.116494 restraints weight = 4130.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118977 restraints weight = 2870.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.4313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4829  Z= 0.202
  Angle     :  0.757   9.761   6592  Z= 0.373
  Chirality :  0.044   0.146    769
  Planarity :  0.004   0.067    813
  Dihedral  :  4.962  23.452    672
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 27.33 %
    Favored  : 69.23 %
  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: -1.47 (0.34), residues: 611
  helix: -0.09 (0.27), residues: 372
  sheet: -2.72 (0.59), residues: 49
  loop : -2.07 (0.45), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.031   0.001   PHE A 160 
 TYR   0.021   0.001   TYR A 176 
 ARG   0.008   0.001   ARG B  68 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1914.28 seconds
wall clock time: 33 minutes 47.39 seconds (2027.39 seconds total)