Starting phenix.real_space_refine
on Tue Mar 11 18:12:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e4c_27888/03_2025/8e4c_27888.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e4c_27888/03_2025/8e4c_27888.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e4c_27888/03_2025/8e4c_27888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e4c_27888/03_2025/8e4c_27888.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e4c_27888/03_2025/8e4c_27888.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e4c_27888/03_2025/8e4c_27888.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.041
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      25      5.16       5
     C    4094      2.51       5
     N    1070      2.21       5
     O    1209      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6398
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1988
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 18, 'TRANS': 234}
    Chain: "A"
      Number of atoms: 1988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1988
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 18, 'TRANS': 234}
    Chain: "C"
      Number of atoms: 1130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1130
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 12, 'TRANS': 129}
    Chain: "D"
      Number of atoms: 1222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1222
          Classifications: {'peptide': 157}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 4.44, per 1000 atoms: 0.69
  Number of scatterers: 6398
  At special positions: 0
  Unit cell: (73.04, 107.9, 156.04, 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      25     16.00
     O    1209      8.00
     N    1070      7.00
     C    4094      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 246 " - pdb=" SG  CYS B 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 353 " - pdb=" SG  CYS B 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 246 " - pdb=" SG  CYS A 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 353 " - pdb=" SG  CYS A 415 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 113 " - pdb=" SG  CYS D 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  43 " - pdb=" SG  CYS D 124 " distance=2.06
    Simple disulfide: pdb=" SG  CYS D  65 " - pdb=" SG  CYS D 120 " 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
  Links applied
    NAG-ASN
      " NAG C 401 " - " ASN C  58 "
      " NAG C 402 " - " ASN C  68 "
      " NAG D 301 " - " ASN D  68 "
      " NAG D 302 " - " ASN D  99 "
      " NAG D 303 " - " ASN D 130 "
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 831.3 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1518

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 15 sheets defined
      27.5% alpha, 30.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'B' and resid 232 through 240
      removed outlier: 3.919A  pdb=" N   ILE B 236 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 299
      removed outlier: 3.651A  pdb=" N   TRP B 297 " --> pdb=" O   CYS B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 344
    Processing helix  chain 'B' and resid 404 through 409
    Processing helix  chain 'B' and resid 444 through 476
    Processing helix  chain 'A' and resid 232 through 240
    Processing helix  chain 'A' and resid 294 through 299
    Processing helix  chain 'A' and resid 339 through 345
      removed outlier: 3.715A  pdb=" N   LEU A 345 " --> pdb=" O   GLU A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 377
      No H-bonds generated for 'chain 'A' and resid 375 through 377'
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 3.646A  pdb=" N   SER A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 476
      removed outlier: 4.176A  pdb=" N   TRP A 450 " --> pdb=" O   PHE A 446 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 96
      removed outlier: 3.631A  pdb=" N   ARG C  96 " --> pdb=" O   LYS C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 169
      Proline residue:  C 153  - end of helix
    Processing helix  chain 'D' and resid 111 through 115
    Processing helix  chain 'D' and resid 148 through 184
      removed outlier: 3.760A  pdb=" N   ARG D 152 " --> pdb=" O   ASP D 148 " (cutoff:3.500A)
      Proline residue:  D 175  - end of helix
      removed outlier: 3.639A  pdb=" N   ASP D 181 " --> pdb=" O   PHE D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 203
    Processing helix  chain 'D' and resid 208 through 213
    Processing sheet with id=AA1, first strand: chain 'B' and resid 225 through 229
      removed outlier: 3.532A  pdb=" N   THR B 245 " --> pdb=" O   ILE B 229 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   ASN B 243 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   VAL B 292 " --> pdb=" O   ASN B 243 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   THR B 245 " --> pdb=" O   ALA B 290 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ALA B 290 " --> pdb=" O   THR B 245 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   LEU B 247 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   GLY B 288 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   SER B 249 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA B 286 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B 274 " --> pdb=" O   LYS B 287 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 258 through 263
      removed outlier: 3.647A  pdb=" N   ILE B 320 " --> pdb=" O   PHE B 303 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   CYS B 305 " --> pdb=" O   LYS B 318 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LYS B 318 " --> pdb=" O   CYS B 305 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 332 through 336
      removed outlier: 3.791A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B 354 " --> pdb=" O   TYR B 334 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR B 352 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL B 355 " --> pdb=" O   THR B 396 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   TYR B 394 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 336
      removed outlier: 3.791A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B 354 " --> pdb=" O   TYR B 334 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR B 352 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 372 through 373
      removed outlier: 3.533A  pdb=" N   THR B 414 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   CYS B 415 " --> pdb=" O   ARG B 429 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ARG B 429 " --> pdb=" O   CYS B 415 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 228
      removed outlier: 5.807A  pdb=" N   PHE A 284 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 290 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 228
      removed outlier: 5.807A  pdb=" N   PHE A 284 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS A 274 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 263
      removed outlier: 3.775A  pdb=" N   CYS A 305 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LYS A 318 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   VAL A 307 " --> pdb=" O   GLN A 316 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN A 316 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 332 through 336
      removed outlier: 3.508A  pdb=" N   SER A 398 " --> pdb=" O   CYS A 353 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 332 through 336
      removed outlier: 5.959A  pdb=" N   TYR A 394 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 372 through 373
      removed outlier: 3.745A  pdb=" N   THR A 414 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 74 through 75
      removed outlier: 3.545A  pdb=" N   TRP C 100 " --> pdb=" O   TRP C  62 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   VAL C 103 " --> pdb=" O   LYS C 110 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LYS C 110 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 74 through 75
      removed outlier: 3.545A  pdb=" N   TRP C 100 " --> pdb=" O   TRP C  62 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY C  97 " --> pdb=" O   LEU C 117 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 54 through 55
    Processing sheet with id=AB6, first strand: chain 'D' and resid 62 through 63

    281 hydrogen bonds defined for protein.
    750 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: 1.86

  Time building geometry restraints manager: 1.80 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1415
        1.33 -     1.45: 1448
        1.45 -     1.57: 3663
        1.57 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 6557
  Sorted by residual:
  bond pdb=" CE1 HIS A 424 "
       pdb=" NE2 HIS A 424 "
    ideal  model  delta    sigma   weight residual
    1.321  1.363 -0.042 1.00e-02 1.00e+04 1.77e+01
  bond pdb=" CE1 HIS B 419 "
       pdb=" NE2 HIS B 419 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.71e+01
  bond pdb=" CE1 HIS C  95 "
       pdb=" NE2 HIS C  95 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.65e+01
  bond pdb=" CE1 HIS B 397 "
       pdb=" NE2 HIS B 397 "
    ideal  model  delta    sigma   weight residual
    1.321  1.360 -0.039 1.00e-02 1.00e+04 1.55e+01
  bond pdb=" N   ILE C  59 "
       pdb=" CA  ILE C  59 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.18e-02 7.18e+03 1.06e+01
  ... (remaining 6552 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 8800
        2.90 -     5.80: 121
        5.80 -     8.69: 8
        8.69 -    11.59: 3
       11.59 -    14.49: 1
  Bond angle restraints: 8933
  Sorted by residual:
  angle pdb=" N   GLU B 443 "
        pdb=" CA  GLU B 443 "
        pdb=" CB  GLU B 443 "
      ideal   model   delta    sigma   weight residual
     110.49  124.98  -14.49 1.69e+00 3.50e-01 7.35e+01
  angle pdb=" C   PRO C  57 "
        pdb=" CA  PRO C  57 "
        pdb=" CB  PRO C  57 "
      ideal   model   delta    sigma   weight residual
     111.56  101.97    9.59 1.65e+00 3.67e-01 3.38e+01
  angle pdb=" N   ASN D 130 "
        pdb=" CA  ASN D 130 "
        pdb=" C   ASN D 130 "
      ideal   model   delta    sigma   weight residual
     108.63  101.14    7.49 1.60e+00 3.91e-01 2.19e+01
  angle pdb=" CA  PRO D  42 "
        pdb=" N   PRO D  42 "
        pdb=" CD  PRO D  42 "
      ideal   model   delta    sigma   weight residual
     112.00  105.45    6.55 1.40e+00 5.10e-01 2.19e+01
  angle pdb=" C   ASN C  58 "
        pdb=" CA  ASN C  58 "
        pdb=" CB  ASN C  58 "
      ideal   model   delta    sigma   weight residual
     109.90  116.92   -7.02 1.56e+00 4.11e-01 2.03e+01
  ... (remaining 8928 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3481
       17.92 -    35.85: 379
       35.85 -    53.77: 107
       53.77 -    71.70: 22
       71.70 -    89.62: 7
  Dihedral angle restraints: 3996
    sinusoidal: 1661
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" N   GLU B 443 "
           pdb=" C   GLU B 443 "
           pdb=" CA  GLU B 443 "
           pdb=" CB  GLU B 443 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  158.13  -35.33     0      2.50e+00 1.60e-01 2.00e+02
  dihedral pdb=" C   GLU B 443 "
           pdb=" N   GLU B 443 "
           pdb=" CA  GLU B 443 "
           pdb=" CB  GLU B 443 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -155.37   32.77     0      2.50e+00 1.60e-01 1.72e+02
  dihedral pdb=" C   PRO C  57 "
           pdb=" N   PRO C  57 "
           pdb=" CA  PRO C  57 "
           pdb=" CB  PRO C  57 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -108.74  -11.96     0      2.50e+00 1.60e-01 2.29e+01
  ... (remaining 3993 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.291: 1034
       0.291 -    0.581: 2
       0.581 -    0.872: 0
       0.872 -    1.162: 0
       1.162 -    1.453: 1
  Chirality restraints: 1037
  Sorted by residual:
  chirality pdb=" CA  GLU B 443 "
            pdb=" N   GLU B 443 "
            pdb=" C   GLU B 443 "
            pdb=" CB  GLU B 443 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.06    1.45 2.00e-01 2.50e+01 5.27e+01
  chirality pdb=" C1  NAG C 401 "
            pdb=" ND2 ASN C  58 "
            pdb=" C2  NAG C 401 "
            pdb=" O5  NAG C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.87e+00
  chirality pdb=" CA  ILE C  69 "
            pdb=" N   ILE C  69 "
            pdb=" C   ILE C  69 "
            pdb=" CB  ILE C  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.30 2.00e-01 2.50e+01 2.26e+00
  ... (remaining 1034 not shown)

  Planarity restraints: 1138
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 402 "   -0.277 2.00e-02 2.50e+03   2.37e-01 7.00e+02
        pdb=" C7  NAG C 402 "    0.067 2.00e-02 2.50e+03
        pdb=" C8  NAG C 402 "   -0.167 2.00e-02 2.50e+03
        pdb=" N2  NAG C 402 "    0.412 2.00e-02 2.50e+03
        pdb=" O7  NAG C 402 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 401 "    0.205 2.00e-02 2.50e+03   1.74e-01 3.80e+02
        pdb=" C7  NAG C 401 "   -0.040 2.00e-02 2.50e+03
        pdb=" C8  NAG C 401 "   -0.035 2.00e-02 2.50e+03
        pdb=" N2  NAG C 401 "   -0.287 2.00e-02 2.50e+03
        pdb=" O7  NAG C 401 "    0.158 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D 302 "   -0.170 2.00e-02 2.50e+03   1.45e-01 2.63e+02
        pdb=" C7  NAG D 302 "    0.032 2.00e-02 2.50e+03
        pdb=" C8  NAG D 302 "    0.033 2.00e-02 2.50e+03
        pdb=" N2  NAG D 302 "    0.238 2.00e-02 2.50e+03
        pdb=" O7  NAG D 302 "   -0.132 2.00e-02 2.50e+03
  ... (remaining 1135 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1222
        2.78 -     3.31: 6087
        3.31 -     3.84: 10132
        3.84 -     4.37: 11183
        4.37 -     4.90: 19265
  Nonbonded interactions: 47889
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 131 "
            pdb=" OG1 THR C 134 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG1 THR A 414 "
            pdb=" O   ARG A 429 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   SER A 382 "
            pdb=" OG1 THR A 396 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   VAL C 152 "
            pdb=" OG1 THR C 155 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" O   CYS D  43 "
            pdb=" OG1 THR D 132 "
     model   vdw
     2.357 3.040
  ... (remaining 47884 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.490
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.550
  Find NCS groups from input model:        0.140
  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:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4891
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   0.048   6557  Z= 0.328
  Angle     :  0.838  14.491   8933  Z= 0.513
  Chirality :  0.073   1.453   1037
  Planarity :  0.011   0.237   1133
  Dihedral  : 16.284  89.622   2454
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 22.46 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.31), residues: 793
  helix:  1.29 (0.38), residues: 196
  sheet: -0.42 (0.36), residues: 240
  loop : -0.69 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP B 450 
 HIS   0.008   0.001   HIS D  49 
 PHE   0.022   0.001   PHE D 119 
 TYR   0.014   0.001   TYR C 116 
 ARG   0.003   0.001   ARG C 118 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  297 TRP cc_start: 0.2872 (t-100) cc_final: 0.0896 (t-100)
REVERT: B  351 VAL cc_start: 0.7019 (t) cc_final: 0.6665 (m)
REVERT: B  408 ASN cc_start: 0.6788 (m-40) cc_final: 0.6554 (m110)
REVERT: B  409 SER cc_start: 0.7094 (p) cc_final: 0.6880 (m)
REVERT: B  462 LEU cc_start: 0.6787 (mp) cc_final: 0.6307 (tp)
REVERT: C   55 ARG cc_start: 0.1671 (mtt180) cc_final: 0.1106 (mmt180)
REVERT: C   71 TRP cc_start: 0.4693 (m100) cc_final: 0.4420 (m100)
REVERT: C  162 ARG cc_start: 0.2063 (ttp-110) cc_final: 0.0977 (mmt180)
REVERT: D  103 TYR cc_start: 0.5257 (m-80) cc_final: 0.4897 (m-80)
REVERT: D  144 PHE cc_start: 0.6547 (p90) cc_final: 0.6092 (p90)
  outliers start: 13
  outliers final: 5
  residues processed: 163
  average time/residue: 0.2181
  time to fit residues: 44.7377
Evaluate side-chains
  95 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain D residue  164 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    7.9990
   chunk 59 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 279 HIS
A 372 GLN
A 408 ASN
C  52 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.189782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.184953 restraints weight = 18786.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.184135 restraints weight = 27709.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.183905 restraints weight = 28783.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.4520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4385
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6557  Z= 0.205
  Angle     :  0.695   9.097   8933  Z= 0.346
  Chirality :  0.048   0.278   1037
  Planarity :  0.006   0.074   1133
  Dihedral  :  6.355  60.783    962
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 21.33 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.30), residues: 793
  helix:  1.28 (0.36), residues: 197
  sheet: -0.54 (0.34), residues: 252
  loop : -0.67 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 450 
 HIS   0.013   0.001   HIS D  49 
 PHE   0.019   0.002   PHE D 119 
 TYR   0.021   0.002   TYR B 254 
 ARG   0.004   0.001   ARG A 340 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  297 TRP cc_start: 0.3200 (t-100) cc_final: 0.1346 (t-100)
REVERT: B  351 VAL cc_start: 0.6822 (t) cc_final: 0.6602 (m)
REVERT: B  409 SER cc_start: 0.6139 (p) cc_final: 0.5780 (m)
REVERT: C   55 ARG cc_start: 0.2087 (mtt180) cc_final: 0.1401 (mmt180)
REVERT: C   71 TRP cc_start: 0.4653 (m100) cc_final: 0.4403 (m100)
REVERT: C  147 LEU cc_start: 0.7017 (tp) cc_final: 0.6596 (tp)
REVERT: C  162 ARG cc_start: 0.1522 (ttp-110) cc_final: 0.0936 (mmt180)
REVERT: D  144 PHE cc_start: 0.5694 (p90) cc_final: 0.5380 (p90)
  outliers start: 30
  outliers final: 16
  residues processed: 117
  average time/residue: 0.2084
  time to fit residues: 31.4363
Evaluate side-chains
  103 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain C residue  100 TRP
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  139 ILE
Chi-restraints excluded: chain C residue  148 PHE
Chi-restraints excluded: chain D residue  164 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    0.0050
   chunk 43 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 69 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 27 optimal weight:   20.0000
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.6800

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

Flipped N/Q/H residues before XYZ refinement:
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  95 HIS
C 165 ASN
D  64 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.187036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.180806 restraints weight = 19283.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.180618 restraints weight = 27220.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.180605 restraints weight = 25490.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4557
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   6557  Z= 0.299
  Angle     :  0.764  14.010   8933  Z= 0.382
  Chirality :  0.048   0.240   1037
  Planarity :  0.006   0.064   1133
  Dihedral  :  6.657  54.884    961
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 21.19 %
    Favored  : 72.03 %
  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: -0.80 (0.29), residues: 793
  helix:  0.65 (0.35), residues: 200
  sheet: -0.88 (0.33), residues: 249
  loop : -0.83 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 100 
 HIS   0.012   0.002   HIS D  49 
 PHE   0.029   0.003   PHE B 303 
 TYR   0.019   0.002   TYR B 254 
 ARG   0.006   0.001   ARG C  55 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 104
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0532 (OUTLIER) cc_final: 0.0209 (pt)
REVERT: B  297 TRP cc_start: 0.3364 (t-100) cc_final: 0.2295 (t60)
REVERT: B  351 VAL cc_start: 0.6889 (t) cc_final: 0.6687 (m)
REVERT: B  364 SER cc_start: 0.6504 (OUTLIER) cc_final: 0.6240 (t)
REVERT: B  409 SER cc_start: 0.5834 (p) cc_final: 0.5630 (m)
REVERT: A  276 MET cc_start: 0.4766 (mmp) cc_final: 0.4297 (mmp)
REVERT: A  476 LYS cc_start: 0.3954 (tptp) cc_final: 0.2427 (ptmm)
REVERT: C  147 LEU cc_start: 0.7297 (tp) cc_final: 0.7042 (tp)
REVERT: D  118 TYR cc_start: 0.6303 (m-80) cc_final: 0.6018 (m-10)
REVERT: D  144 PHE cc_start: 0.5730 (p90) cc_final: 0.5467 (p90)
  outliers start: 48
  outliers final: 25
  residues processed: 135
  average time/residue: 0.2002
  time to fit residues: 35.0879
Evaluate side-chains
  116 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  110 ILE
Chi-restraints excluded: chain D residue  174 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 GLN
A 440 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.187700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.179177 restraints weight = 19381.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.178573 restraints weight = 29308.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.178724 restraints weight = 27700.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.4453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4689
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6557  Z= 0.233
  Angle     :  0.710  11.668   8933  Z= 0.355
  Chirality :  0.046   0.263   1037
  Planarity :  0.006   0.065   1133
  Dihedral  :  6.640  55.822    958
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.55 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 23.02 %
    Favored  : 70.90 %
  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: -0.65 (0.30), residues: 793
  helix:  0.76 (0.35), residues: 198
  sheet: -0.86 (0.33), residues: 260
  loop : -0.65 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 450 
 HIS   0.009   0.001   HIS D  49 
 PHE   0.029   0.002   PHE A 456 
 TYR   0.020   0.001   TYR B 254 
 ARG   0.003   0.000   ARG A 340 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 98
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  297 TRP cc_start: 0.3293 (t-100) cc_final: 0.2123 (t60)
REVERT: B  351 VAL cc_start: 0.7006 (t) cc_final: 0.6784 (m)
REVERT: B  409 SER cc_start: 0.6180 (p) cc_final: 0.5925 (m)
REVERT: B  443 GLU cc_start: 0.5997 (pp20) cc_final: 0.5747 (pp20)
REVERT: A  276 MET cc_start: 0.4805 (mmp) cc_final: 0.4418 (mmp)
REVERT: A  440 ASN cc_start: 0.5329 (OUTLIER) cc_final: 0.5112 (t0)
REVERT: A  476 LYS cc_start: 0.4078 (tptp) cc_final: 0.2281 (ptmm)
REVERT: D  144 PHE cc_start: 0.5995 (p90) cc_final: 0.5641 (p90)
  outliers start: 43
  outliers final: 32
  residues processed: 124
  average time/residue: 0.1951
  time to fit residues: 31.6615
Evaluate side-chains
  118 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  457 ILE
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  105 GLU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  174 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0770
   chunk 8 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0970
   chunk 69 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0870
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8316

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

Flipped N/Q/H residues before XYZ refinement:
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.187745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.181508 restraints weight = 19320.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.180730 restraints weight = 25609.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.180491 restraints weight = 27650.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4575
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6557  Z= 0.204
  Angle     :  0.679  11.493   8933  Z= 0.334
  Chirality :  0.045   0.256   1037
  Planarity :  0.005   0.065   1133
  Dihedral  :  6.226  55.139    958
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 24.01 %
    Favored  : 70.90 %
  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: -0.58 (0.30), residues: 793
  helix:  0.83 (0.35), residues: 198
  sheet: -0.94 (0.32), residues: 270
  loop : -0.45 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 100 
 HIS   0.011   0.001   HIS D  49 
 PHE   0.023   0.002   PHE A 456 
 TYR   0.020   0.001   TYR B 254 
 ARG   0.013   0.001   ARG D  51 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 90
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0600 (OUTLIER) cc_final: 0.0259 (pt)
REVERT: B  297 TRP cc_start: 0.3245 (t-100) cc_final: 0.2050 (t60)
REVERT: A  276 MET cc_start: 0.4835 (mmp) cc_final: 0.4413 (mmp)
REVERT: A  476 LYS cc_start: 0.4091 (tptp) cc_final: 0.2354 (ptmm)
REVERT: C   55 ARG cc_start: 0.2493 (mtt90) cc_final: 0.1206 (mmt180)
REVERT: D  118 TYR cc_start: 0.6378 (m-80) cc_final: 0.5942 (m-10)
REVERT: D  144 PHE cc_start: 0.5802 (p90) cc_final: 0.5508 (p90)
  outliers start: 36
  outliers final: 26
  residues processed: 113
  average time/residue: 0.1899
  time to fit residues: 28.1224
Evaluate side-chains
  109 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  148 PHE
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  141 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0870
   chunk 13 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 6 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0970
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 GLN
** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 129 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.189523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.180258 restraints weight = 19178.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.179503 restraints weight = 24191.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.179740 restraints weight = 21620.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.4458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4684
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6557  Z= 0.181
  Angle     :  0.659  11.750   8933  Z= 0.323
  Chirality :  0.045   0.243   1037
  Planarity :  0.005   0.066   1133
  Dihedral  :  5.989  57.257    958
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 25.00 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.30), residues: 793
  helix:  0.99 (0.35), residues: 198
  sheet: -0.86 (0.32), residues: 270
  loop : -0.34 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.001   TRP B 450 
 HIS   0.010   0.001   HIS D  49 
 PHE   0.020   0.001   PHE D 119 
 TYR   0.020   0.001   TYR B 254 
 ARG   0.005   0.000   ARG D  51 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 84
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  297 TRP cc_start: 0.3257 (t-100) cc_final: 0.2010 (t60)
REVERT: A  276 MET cc_start: 0.4759 (mmp) cc_final: 0.4394 (mmp)
REVERT: A  456 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.7115 (t80)
REVERT: A  476 LYS cc_start: 0.4074 (tptp) cc_final: 0.2270 (ptmm)
REVERT: C   55 ARG cc_start: 0.2203 (mtt90) cc_final: 0.1400 (mmt90)
REVERT: D  118 TYR cc_start: 0.6423 (m-80) cc_final: 0.5995 (m-10)
REVERT: D  144 PHE cc_start: 0.5944 (p90) cc_final: 0.5597 (p90)
  outliers start: 35
  outliers final: 24
  residues processed: 109
  average time/residue: 0.1863
  time to fit residues: 26.8041
Evaluate side-chains
  105 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  141 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 41 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.188051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.183459 restraints weight = 18806.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.182863 restraints weight = 27081.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.183016 restraints weight = 24476.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.4520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4483
moved from start:          0.5028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6557  Z= 0.216
  Angle     :  0.691  12.294   8933  Z= 0.342
  Chirality :  0.046   0.258   1037
  Planarity :  0.005   0.065   1133
  Dihedral  :  5.788  53.953    956
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 23.73 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.30), residues: 793
  helix:  0.77 (0.36), residues: 198
  sheet: -0.80 (0.32), residues: 266
  loop : -0.45 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.070   0.002   TRP B 450 
 HIS   0.012   0.002   HIS D  49 
 PHE   0.021   0.002   PHE D 119 
 TYR   0.009   0.001   TYR C  99 
 ARG   0.004   0.000   ARG A 346 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 83
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  456 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.7093 (t80)
REVERT: A  476 LYS cc_start: 0.4293 (tptp) cc_final: 0.2364 (ptmm)
REVERT: C   55 ARG cc_start: 0.2452 (mtt90) cc_final: 0.1168 (mmt180)
REVERT: D  144 PHE cc_start: 0.5776 (p90) cc_final: 0.5482 (p90)
  outliers start: 43
  outliers final: 32
  residues processed: 114
  average time/residue: 0.1912
  time to fit residues: 28.7548
Evaluate side-chains
  112 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  427 THR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  141 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 28 optimal weight:   20.0000
   chunk 16 optimal weight:    0.0670
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.9924

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.188189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.182097 restraints weight = 19455.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.181587 restraints weight = 27999.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.181781 restraints weight = 26961.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.4488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4615
moved from start:          0.5334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6557  Z= 0.220
  Angle     :  0.698  12.365   8933  Z= 0.344
  Chirality :  0.046   0.264   1037
  Planarity :  0.005   0.069   1133
  Dihedral  :  5.916  54.026    956
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 23.73 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.30), residues: 793
  helix:  0.60 (0.36), residues: 198
  sheet: -0.78 (0.31), residues: 266
  loop : -0.55 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.080   0.002   TRP B 450 
 HIS   0.013   0.001   HIS D  49 
 PHE   0.027   0.002   PHE B 319 
 TYR   0.009   0.001   TYR C  99 
 ARG   0.015   0.001   ARG A 346 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 80
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0500 (OUTLIER) cc_final: 0.0175 (pt)
REVERT: A  276 MET cc_start: 0.4548 (OUTLIER) cc_final: 0.4102 (mmp)
REVERT: A  456 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.7055 (t80)
REVERT: C   55 ARG cc_start: 0.2289 (mtt90) cc_final: 0.1020 (mmt180)
REVERT: C  162 ARG cc_start: 0.1833 (ttp-110) cc_final: 0.0659 (mmt180)
REVERT: D  118 TYR cc_start: 0.6213 (m-80) cc_final: 0.6012 (m-10)
REVERT: D  144 PHE cc_start: 0.6030 (p90) cc_final: 0.5638 (p90)
  outliers start: 45
  outliers final: 32
  residues processed: 110
  average time/residue: 0.2013
  time to fit residues: 29.2097
Evaluate side-chains
  111 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 76
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  397 HIS
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  141 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 29 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 59 optimal weight:    7.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 ASN
** D 108 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 = 0.4593 r_free = 0.4593 target = 0.189090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.181184 restraints weight = 19551.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.180687 restraints weight = 27137.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.180849 restraints weight = 26025.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.4472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4667
moved from start:          0.5472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6557  Z= 0.200
  Angle     :  0.688  13.515   8933  Z= 0.336
  Chirality :  0.046   0.269   1037
  Planarity :  0.005   0.071   1133
  Dihedral  :  5.862  56.586    956
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 23.87 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.30), residues: 793
  helix:  0.70 (0.36), residues: 198
  sheet: -0.77 (0.31), residues: 269
  loop : -0.58 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP B 450 
 HIS   0.013   0.001   HIS D  49 
 PHE   0.022   0.002   PHE D 119 
 TYR   0.009   0.001   TYR C  99 
 ARG   0.011   0.001   ARG A 346 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 78
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.0384 (OUTLIER) cc_final: 0.0107 (pt)
REVERT: A  276 MET cc_start: 0.4582 (OUTLIER) cc_final: 0.4142 (mmp)
REVERT: A  456 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.7089 (t80)
REVERT: C   55 ARG cc_start: 0.2322 (mtt90) cc_final: 0.1036 (mmt180)
REVERT: C  162 ARG cc_start: 0.1688 (ttp-110) cc_final: 0.0510 (mmt180)
REVERT: D  118 TYR cc_start: 0.6244 (m-80) cc_final: 0.5943 (m-10)
REVERT: D  144 PHE cc_start: 0.6083 (p90) cc_final: 0.5592 (p90)
  outliers start: 41
  outliers final: 31
  residues processed: 107
  average time/residue: 0.2100
  time to fit residues: 28.7950
Evaluate side-chains
  105 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 71
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  396 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 16 optimal weight:    0.2980
   chunk 1 optimal weight:    0.4980
   chunk 67 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0870
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 ASN
C 136 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.188368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.178177 restraints weight = 18255.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.177497 restraints weight = 28075.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.177865 restraints weight = 24628.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4711
moved from start:          0.5617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6557  Z= 0.197
  Angle     :  0.698  13.551   8933  Z= 0.341
  Chirality :  0.046   0.275   1037
  Planarity :  0.005   0.071   1133
  Dihedral  :  5.769  57.358    956
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 25.85 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.31), residues: 793
  helix:  0.80 (0.37), residues: 198
  sheet: -0.67 (0.32), residues: 269
  loop : -0.53 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP B 450 
 HIS   0.012   0.001   HIS D  49 
 PHE   0.021   0.002   PHE D 119 
 TYR   0.008   0.001   TYR D  66 
 ARG   0.009   0.001   ARG A 346 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 72
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.7056 (t80)
REVERT: C   55 ARG cc_start: 0.2218 (mtt90) cc_final: 0.0941 (mmt180)
REVERT: C  162 ARG cc_start: 0.1822 (ttp-110) cc_final: 0.0509 (mmt180)
REVERT: D  118 TYR cc_start: 0.6231 (m-80) cc_final: 0.5925 (m-10)
REVERT: D  144 PHE cc_start: 0.6066 (p90) cc_final: 0.5634 (p90)
  outliers start: 34
  outliers final: 32
  residues processed: 96
  average time/residue: 0.2045
  time to fit residues: 25.7688
Evaluate side-chains
  103 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 70
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  387 GLU
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   chunk 24 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 71 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN
** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 440 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.188350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.175908 restraints weight = 18691.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 125)---------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.173703 restraints weight = 22568.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.173498 restraints weight = 20012.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.4392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4980
moved from start:          0.5626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.128   6557  Z= 0.312
  Angle     :  1.115  59.014   8933  Z= 0.645
  Chirality :  0.046   0.276   1037
  Planarity :  0.006   0.072   1133
  Dihedral  :  5.817  57.359    956
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.80 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 25.42 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.30), residues: 793
  helix:  0.78 (0.36), residues: 198
  sheet: -0.64 (0.32), residues: 269
  loop : -0.54 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.004   TRP B 450 
 HIS   0.012   0.001   HIS D  49 
 PHE   0.021   0.002   PHE D 119 
 TYR   0.009   0.001   TYR D  66 
 ARG   0.033   0.001   ARG D 153 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2270.88 seconds
wall clock time: 40 minutes 14.72 seconds (2414.72 seconds total)