Starting phenix.real_space_refine
on Fri Aug 22 16:19:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tgj_41238/08_2025/8tgj_41238_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tgj_41238/08_2025/8tgj_41238.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tgj_41238/08_2025/8tgj_41238_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tgj_41238/08_2025/8tgj_41238_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tgj_41238/08_2025/8tgj_41238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tgj_41238/08_2025/8tgj_41238.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.018
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      57      5.16       5
     C    3805      2.51       5
     N     892      2.21       5
     O     966      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5720
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 2837
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 23, 'TRANS': 357}
          Chain breaks: 1
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 2839
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 21, 'TRANS': 358}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.80, per 1000 atoms: 0.31
  Number of scatterers: 5720
  At special positions: 0
  Unit cell: (74.26, 56.4, 115.62, 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      57     16.00
     O     966      8.00
     N     892      7.00
     C    3805      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 334.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1356

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      90.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 41
      removed outlier: 3.785A  pdb=" N   VAL A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 50
      removed outlier: 3.603A  pdb=" N   PHE A  48 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 144
      removed outlier: 3.877A  pdb=" N   LEU A 142 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 154
    Processing helix  chain 'A' and resid 155 through 157
      No H-bonds generated for 'chain 'A' and resid 155 through 157'
    Processing helix  chain 'A' and resid 158 through 159
      No H-bonds generated for 'chain 'A' and resid 158 through 159'
    Processing helix  chain 'A' and resid 160 through 165
    Processing helix  chain 'A' and resid 166 through 187
    Processing helix  chain 'A' and resid 189 through 219
      removed outlier: 3.943A  pdb=" N   VAL A 195 " --> pdb=" O   THR A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 254
      removed outlier: 4.602A  pdb=" N   ALA A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      Proline residue:  A 245  - end of helix
    Processing helix  chain 'A' and resid 256 through 278
      removed outlier: 4.302A  pdb=" N   PHE A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 297
      removed outlier: 3.686A  pdb=" N   LEU A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 331
      removed outlier: 3.789A  pdb=" N   LEU A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      Proline residue:  A 321  - end of helix
      Proline residue:  A 324  - end of helix
    Processing helix  chain 'A' and resid 337 through 364
      removed outlier: 3.956A  pdb=" N   PHE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
      removed outlier: 4.109A  pdb=" N   GLY A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   VAL A 358 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   ASN A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LYS A 362 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
    Processing helix  chain 'A' and resid 384 through 386
      No H-bonds generated for 'chain 'A' and resid 384 through 386'
    Processing helix  chain 'A' and resid 388 through 391
    Processing helix  chain 'A' and resid 392 through 421
      Proline residue:  A 412  - end of helix
      removed outlier: 3.991A  pdb=" N   GLY A 415 " --> pdb=" O   MET A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 455
      removed outlier: 4.207A  pdb=" N   GLY A 440 " --> pdb=" O   ALA A 436 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   PHE A 441 " --> pdb=" O   PHE A 437 " (cutoff:3.500A)
      Proline residue:  A 445  - end of helix
      removed outlier: 4.942A  pdb=" N   GLY A 449 " --> pdb=" O   PRO A 445 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 472
    Processing helix  chain 'A' and resid 473 through 480
      removed outlier: 4.167A  pdb=" N   SER A 480 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 41
      removed outlier: 3.955A  pdb=" N   VAL B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 52
    Processing helix  chain 'B' and resid 130 through 134
      removed outlier: 4.048A  pdb=" N   GLU B 133 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 164
      removed outlier: 4.554A  pdb=" N   LYS B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ALA B 147 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
      Proline residue:  B 155  - end of helix
      removed outlier: 4.502A  pdb=" N   GLY B 158 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 166 through 187
    Processing helix  chain 'B' and resid 189 through 219
      removed outlier: 3.662A  pdb=" N   LEU B 193 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   PHE B 194 " --> pdb=" O   TYR B 190 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   VAL B 195 " --> pdb=" O   THR B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 251
      removed outlier: 4.168A  pdb=" N   ARG B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU B 236 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ALA B 244 " --> pdb=" O   LEU B 240 " (cutoff:3.500A)
      Proline residue:  B 245  - end of helix
      removed outlier: 3.749A  pdb=" N   SER B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 276
      removed outlier: 4.669A  pdb=" N   PHE B 260 " --> pdb=" O   LYS B 256 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ASP B 270 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY B 271 " --> pdb=" O   ALA B 267 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU B 273 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 299 through 331
      removed outlier: 3.504A  pdb=" N   ALA B 305 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY B 315 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   VAL B 316 " --> pdb=" O   ALA B 312 " (cutoff:3.500A)
      Proline residue:  B 321  - end of helix
      Proline residue:  B 324  - end of helix
    Processing helix  chain 'B' and resid 337 through 342
      removed outlier: 3.793A  pdb=" N   PHE B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 364
      removed outlier: 3.750A  pdb=" N   TYR B 349 " --> pdb=" O   ALA B 345 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   ASN B 361 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   LYS B 362 " --> pdb=" O   VAL B 358 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   MET B 363 " --> pdb=" O   LEU B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 383
    Processing helix  chain 'B' and resid 384 through 386
      No H-bonds generated for 'chain 'B' and resid 384 through 386'
    Processing helix  chain 'B' and resid 388 through 391
    Processing helix  chain 'B' and resid 392 through 422
      removed outlier: 3.651A  pdb=" N   MET B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      Proline residue:  B 412  - end of helix
      removed outlier: 3.670A  pdb=" N   ARG B 421 " --> pdb=" O   LEU B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 455
      Proline residue:  B 445  - end of helix
      removed outlier: 3.670A  pdb=" N   ALA B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 472
      removed outlier: 3.709A  pdb=" N   LEU B 460 " --> pdb=" O   GLY B 456 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET B 461 " --> pdb=" O   PHE B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 479
      removed outlier: 3.551A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG B 479 " --> pdb=" O   TYR B 476 " (cutoff:3.500A)

    450 hydrogen bonds defined for protein.
    1323 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: 0.63

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 849
        1.31 -     1.43: 1551
        1.43 -     1.56: 3360
        1.56 -     1.69: 3
        1.69 -     1.81: 100
  Bond restraints: 5863
  Sorted by residual:
  bond pdb=" C31 YHR B 601 "
       pdb=" O30 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.326  1.404 -0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C17 YHR B 601 "
       pdb=" O19 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.325  1.397 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C37 YHR B 601 "
       pdb=" O39 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.342  1.409 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C13 YHR B 601 "
       pdb=" N8  YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.459  1.522 -0.063 2.00e-02 2.50e+03 9.92e+00
  bond pdb=" C10 YHR B 601 "
       pdb=" C11 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.492  1.432  0.060 2.00e-02 2.50e+03 9.15e+00
  ... (remaining 5858 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 7923
        3.66 -     7.31: 55
        7.31 -    10.97: 8
       10.97 -    14.63: 0
       14.63 -    18.29: 1
  Bond angle restraints: 7987
  Sorted by residual:
  angle pdb=" C7  YHR B 601 "
        pdb=" N8  YHR B 601 "
        pdb=" C9  YHR B 601 "
      ideal   model   delta    sigma   weight residual
     111.89  130.18  -18.29 3.00e+00 1.11e-01 3.72e+01
  angle pdb=" C   ARG B 479 "
        pdb=" N   SER B 480 "
        pdb=" CA  SER B 480 "
      ideal   model   delta    sigma   weight residual
     122.83  128.17   -5.34 1.08e+00 8.57e-01 2.44e+01
  angle pdb=" CA  ASN A 388 "
        pdb=" CB  ASN A 388 "
        pdb=" CG  ASN A 388 "
      ideal   model   delta    sigma   weight residual
     112.60  116.89   -4.29 1.00e+00 1.00e+00 1.84e+01
  angle pdb=" N   LEU A  24 "
        pdb=" CA  LEU A  24 "
        pdb=" C   LEU A  24 "
      ideal   model   delta    sigma   weight residual
     110.80  102.06    8.74 2.13e+00 2.20e-01 1.68e+01
  angle pdb=" CA  ILE A 463 "
        pdb=" CB  ILE A 463 "
        pdb=" CG1 ILE A 463 "
      ideal   model   delta    sigma   weight residual
     110.40  116.95   -6.55 1.70e+00 3.46e-01 1.48e+01
  ... (remaining 7982 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.61: 3030
       22.61 -    45.23: 356
       45.23 -    67.84: 47
       67.84 -    90.45: 8
       90.45 -   113.07: 1
  Dihedral angle restraints: 3442
    sinusoidal: 1306
      harmonic: 2136
  Sorted by residual:
  dihedral pdb=" C13 YHR B 601 "
           pdb=" C7  YHR B 601 "
           pdb=" N8  YHR B 601 "
           pdb=" C6  YHR B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.66  -55.41  113.07     1      3.00e+01 1.11e-03 1.48e+01
  dihedral pdb=" CA  VAL B 358 "
           pdb=" C   VAL B 358 "
           pdb=" N   LEU B 359 "
           pdb=" CA  LEU B 359 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.94  -19.06     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  PHE B 356 "
           pdb=" C   PHE B 356 "
           pdb=" N   GLY B 357 "
           pdb=" CA  GLY B 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.28   16.72     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 3439 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 892
       0.082 -    0.164: 62
       0.164 -    0.246: 6
       0.246 -    0.328: 0
       0.328 -    0.410: 1
  Chirality restraints: 961
  Sorted by residual:
  chirality pdb=" C13 YHR B 601 "
            pdb=" C12 YHR B 601 "
            pdb=" C14 YHR B 601 "
            pdb=" N8  YHR B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.70    0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" CA  LEU A  24 "
            pdb=" N   LEU A  24 "
            pdb=" C   LEU A  24 "
            pdb=" CB  LEU A  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  MET B 331 "
            pdb=" N   MET B 331 "
            pdb=" C   MET B 331 "
            pdb=" CB  MET B 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.54e-01
  ... (remaining 958 not shown)

  Planarity restraints: 972
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 472 "   -0.079 5.00e-02 4.00e+02   1.18e-01 2.21e+01
        pdb=" N   PRO B 473 "    0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO B 473 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO B 473 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 471 "    0.013 2.00e-02 2.50e+03   1.76e-02 6.18e+00
        pdb=" CG  TYR A 471 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 471 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 471 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 471 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 471 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 471 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 471 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 158 "    0.039 5.00e-02 4.00e+02   5.94e-02 5.65e+00
        pdb=" N   PRO B 159 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 159 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 159 "    0.033 5.00e-02 4.00e+02
  ... (remaining 969 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1674
        2.81 -     3.34: 5837
        3.34 -     3.86: 9548
        3.86 -     4.38: 10360
        4.38 -     4.90: 18819
  Nonbonded interactions: 46238
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 135 "
            pdb=" NH1 ARG B 138 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   PHE A 143 "
            pdb=" NH2 ARG A 197 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" O   VAL A 375 "
            pdb=" OG  SER A 379 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" O   SER A 284 "
            pdb=" OG  SER A 284 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" OD1 ASN A 154 "
            pdb=" OG  SER A 205 "
     model   vdw
     2.422 3.040
  ... (remaining 46233 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' and (resid 19 through 278 or resid 289 through 482))
  selection = (chain 'B' and ((resid 19 and (name CA or name C or name O or name CB or name OG \ 
 )) or resid 20 through 50 or resid 136 through 482))
}

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:             2.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.580
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
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      :  0.004   0.078   5863  Z= 0.219
  Angle     :  0.780  18.286   7987  Z= 0.395
  Chirality :  0.045   0.410    961
  Planarity :  0.008   0.118    972
  Dihedral  : 18.014 113.067   2086
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 25.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 34.59 %
    Favored  : 64.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.30), residues: 751
  helix:  0.87 (0.21), residues: 593
  sheet:  None (None), residues: 0
  loop : -1.26 (0.46), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 421 
 TYR   0.043   0.002   TYR A 471 
 PHE   0.036   0.001   PHE B  28 
 TRP   0.008   0.001   TRP B 336 
 HIS   0.003   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 5863)
  covalent geometry    : angle       0.78011 ( 7987)
  hydrogen bonds       : bond        0.15863 (  450)
  hydrogen bonds       : angle       5.58577 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 159
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  190 TYR cc_start: 0.6527 (t80) cc_final: 0.5808 (t80)
REVERT: A  194 PHE cc_start: 0.8027 (t80) cc_final: 0.7420 (m-80)
REVERT: A  268 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7767 (mp)
REVERT: B  439 MET cc_start: 0.7454 (tpp) cc_final: 0.7215 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 161
  average time/residue: 0.0445
  time to fit residues: 10.1967
Evaluate side-chains
  163 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain B residue   36 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0270
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
B 154 ASN
B 274 GLN
B 329 GLN
B 337 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.140672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.127695 restraints weight = 8947.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.131555 restraints weight = 4465.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.134033 restraints weight = 2541.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.135661 restraints weight = 1592.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.136705 restraints weight = 1074.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5863  Z= 0.160
  Angle     :  0.672   9.116   7987  Z= 0.327
  Chirality :  0.044   0.139    961
  Planarity :  0.006   0.057    972
  Dihedral  :  5.753  48.838    868
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 29.18 %
    Favored  : 65.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.31), residues: 751
  helix:  1.27 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop : -1.57 (0.51), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 365 
 TYR   0.017   0.001   TYR A 471 
 PHE   0.018   0.001   PHE A 253 
 TRP   0.005   0.001   TRP B 336 
 HIS   0.002   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 5863)
  covalent geometry    : angle       0.67238 ( 7987)
  hydrogen bonds       : bond        0.04523 (  450)
  hydrogen bonds       : angle       4.30344 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLN cc_start: 0.7299 (mt0) cc_final: 0.7095 (tt0)
REVERT: A  249 VAL cc_start: 0.7881 (m) cc_final: 0.7482 (p)
REVERT: A  439 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.6006 (ttp)
REVERT: A  471 TYR cc_start: 0.8323 (t80) cc_final: 0.8013 (t80)
REVERT: A  474 LEU cc_start: 0.7835 (mt) cc_final: 0.7547 (mp)
REVERT: B  439 MET cc_start: 0.7398 (tpp) cc_final: 0.7174 (mmm)
REVERT: B  452 VAL cc_start: 0.7381 (m) cc_final: 0.7027 (p)
REVERT: B  461 MET cc_start: 0.6866 (mmm) cc_final: 0.6560 (mmt)
  outliers start: 30
  outliers final: 16
  residues processed: 178
  average time/residue: 0.0471
  time to fit residues: 11.7811
Evaluate side-chains
  178 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  479 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0980
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 223 HIS
B  35 ASN
B 154 ASN
B 337 GLN
B 468 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.140984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.128060 restraints weight = 8820.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.131846 restraints weight = 4429.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.134333 restraints weight = 2551.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.135977 restraints weight = 1609.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.136968 restraints weight = 1089.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5863  Z= 0.163
  Angle     :  0.650   8.744   7987  Z= 0.315
  Chirality :  0.043   0.139    961
  Planarity :  0.005   0.063    972
  Dihedral  :  4.868  42.196    863
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 31.48 %
    Favored  : 64.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.32), residues: 751
  helix:  1.43 (0.22), residues: 612
  sheet:  None (None), residues: 0
  loop : -1.56 (0.49), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 225 
 TYR   0.017   0.001   TYR A 476 
 PHE   0.026   0.001   PHE A 253 
 TRP   0.006   0.001   TRP B 326 
 HIS   0.002   0.001   HIS A 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 5863)
  covalent geometry    : angle       0.64955 ( 7987)
  hydrogen bonds       : bond        0.04338 (  450)
  hydrogen bonds       : angle       4.19748 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLN cc_start: 0.7318 (mt0) cc_final: 0.7112 (tt0)
REVERT: A  249 VAL cc_start: 0.7853 (m) cc_final: 0.7451 (p)
REVERT: A  299 ASP cc_start: 0.7346 (t0) cc_final: 0.7065 (m-30)
REVERT: A  439 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5963 (ttp)
REVERT: A  463 ILE cc_start: 0.7654 (mt) cc_final: 0.7230 (mp)
REVERT: A  471 TYR cc_start: 0.8325 (t80) cc_final: 0.7391 (t80)
REVERT: A  474 LEU cc_start: 0.7852 (mt) cc_final: 0.7560 (mp)
REVERT: A  476 TYR cc_start: 0.8050 (t80) cc_final: 0.7750 (t80)
REVERT: B  170 MET cc_start: 0.7084 (tpp) cc_final: 0.6720 (tpp)
REVERT: B  331 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7283 (mtm)
REVERT: B  439 MET cc_start: 0.7305 (tpp) cc_final: 0.7059 (mmm)
REVERT: B  452 VAL cc_start: 0.7350 (m) cc_final: 0.7045 (p)
REVERT: B  461 MET cc_start: 0.6863 (mmm) cc_final: 0.6609 (mmt)
  outliers start: 27
  outliers final: 16
  residues processed: 177
  average time/residue: 0.0431
  time to fit residues: 10.9010
Evaluate side-chains
  177 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  479 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0970
   chunk 33 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 74 optimal weight:    0.4980
   chunk 48 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
B 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.140477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.127519 restraints weight = 8941.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.131366 restraints weight = 4506.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.133853 restraints weight = 2588.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.135421 restraints weight = 1630.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.136554 restraints weight = 1117.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5863  Z= 0.161
  Angle     :  0.646   7.976   7987  Z= 0.312
  Chirality :  0.043   0.137    961
  Planarity :  0.005   0.065    972
  Dihedral  :  4.784  43.307    863
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 30.16 %
    Favored  : 63.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.31), residues: 751
  helix:  1.52 (0.22), residues: 610
  sheet:  None (None), residues: 0
  loop : -1.54 (0.47), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 421 
 TYR   0.015   0.001   TYR A 430 
 PHE   0.027   0.001   PHE A 253 
 TRP   0.006   0.001   TRP B 326 
 HIS   0.002   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 5863)
  covalent geometry    : angle       0.64630 ( 7987)
  hydrogen bonds       : bond        0.04263 (  450)
  hydrogen bonds       : angle       4.15818 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 170
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 GLN cc_start: 0.6857 (tt0) cc_final: 0.6604 (tt0)
REVERT: A  249 VAL cc_start: 0.7802 (m) cc_final: 0.7345 (p)
REVERT: A  250 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.6738 (mpp)
REVERT: A  299 ASP cc_start: 0.7409 (t0) cc_final: 0.7168 (m-30)
REVERT: A  439 MET cc_start: 0.6220 (OUTLIER) cc_final: 0.5956 (ttp)
REVERT: A  463 ILE cc_start: 0.7632 (mt) cc_final: 0.7297 (mm)
REVERT: A  471 TYR cc_start: 0.8274 (t80) cc_final: 0.7401 (t80)
REVERT: A  474 LEU cc_start: 0.7873 (mt) cc_final: 0.7559 (mp)
REVERT: A  476 TYR cc_start: 0.8080 (t80) cc_final: 0.7753 (t80)
REVERT: B  439 MET cc_start: 0.7286 (tpp) cc_final: 0.7049 (mmm)
REVERT: B  452 VAL cc_start: 0.7307 (m) cc_final: 0.7018 (p)
REVERT: B  461 MET cc_start: 0.6838 (mmm) cc_final: 0.6595 (mmt)
  outliers start: 36
  outliers final: 20
  residues processed: 186
  average time/residue: 0.0455
  time to fit residues: 11.9464
Evaluate side-chains
  188 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  184 PHE
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  194 PHE
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  381 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 8 optimal weight:    0.3980
   chunk 49 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 36 optimal weight:    0.3980
   chunk 53 optimal weight:    0.0980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
B 274 GLN
B 337 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.140098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.127100 restraints weight = 9079.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.131029 restraints weight = 4482.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.133525 restraints weight = 2535.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.135124 restraints weight = 1589.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.136296 restraints weight = 1085.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5863  Z= 0.153
  Angle     :  0.665   8.046   7987  Z= 0.316
  Chirality :  0.043   0.173    961
  Planarity :  0.005   0.066    972
  Dihedral  :  4.763  42.709    863
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 29.51 %
    Favored  : 64.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.31), residues: 751
  helix:  1.52 (0.22), residues: 611
  sheet:  None (None), residues: 0
  loop : -1.50 (0.46), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 365 
 TYR   0.013   0.001   TYR A 430 
 PHE   0.020   0.001   PHE A 253 
 TRP   0.008   0.001   TRP B 326 
 HIS   0.001   0.000   HIS A 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5863)
  covalent geometry    : angle       0.66456 ( 7987)
  hydrogen bonds       : bond        0.04172 (  450)
  hydrogen bonds       : angle       4.12897 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 170
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 GLN cc_start: 0.6956 (tt0) cc_final: 0.6733 (tt0)
REVERT: A  249 VAL cc_start: 0.7789 (m) cc_final: 0.7113 (p)
REVERT: A  250 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.6777 (mpp)
REVERT: A  253 PHE cc_start: 0.6995 (m-80) cc_final: 0.6786 (m-80)
REVERT: A  299 ASP cc_start: 0.7412 (t0) cc_final: 0.7196 (m-30)
REVERT: A  463 ILE cc_start: 0.7578 (mt) cc_final: 0.7129 (mm)
REVERT: A  467 ILE cc_start: 0.7958 (tt) cc_final: 0.7653 (tp)
REVERT: A  471 TYR cc_start: 0.8200 (t80) cc_final: 0.7272 (t80)
REVERT: A  474 LEU cc_start: 0.7855 (mt) cc_final: 0.7534 (mp)
REVERT: A  476 TYR cc_start: 0.8102 (t80) cc_final: 0.7705 (t80)
REVERT: B  170 MET cc_start: 0.7052 (tpp) cc_final: 0.6567 (tpp)
REVERT: B  439 MET cc_start: 0.7289 (tpp) cc_final: 0.7017 (mmm)
REVERT: B  452 VAL cc_start: 0.7351 (m) cc_final: 0.7083 (p)
REVERT: B  480 SER cc_start: 0.7538 (t) cc_final: 0.7239 (p)
  outliers start: 35
  outliers final: 23
  residues processed: 186
  average time/residue: 0.0412
  time to fit residues: 11.0384
Evaluate side-chains
  190 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  184 PHE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  381 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0870
   chunk 15 optimal weight:    0.0770
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
B 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.140969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.128313 restraints weight = 8872.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.132123 restraints weight = 4419.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.134545 restraints weight = 2526.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.136086 restraints weight = 1582.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.137242 restraints weight = 1081.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5863  Z= 0.156
  Angle     :  0.659   7.830   7987  Z= 0.315
  Chirality :  0.043   0.178    961
  Planarity :  0.005   0.065    972
  Dihedral  :  4.729  42.556    863
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 28.36 %
    Favored  : 65.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.31), residues: 751
  helix:  1.50 (0.22), residues: 609
  sheet:  None (None), residues: 0
  loop : -1.52 (0.46), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 479 
 TYR   0.013   0.001   TYR A 430 
 PHE   0.020   0.001   PHE A 253 
 TRP   0.005   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 5863)
  covalent geometry    : angle       0.65873 ( 7987)
  hydrogen bonds       : bond        0.04126 (  450)
  hydrogen bonds       : angle       4.11620 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 172
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLN cc_start: 0.7241 (tm-30) cc_final: 0.6810 (tm-30)
REVERT: A  249 VAL cc_start: 0.7776 (m) cc_final: 0.7065 (p)
REVERT: A  250 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.6779 (mpp)
REVERT: A  253 PHE cc_start: 0.6972 (m-80) cc_final: 0.6739 (m-80)
REVERT: A  299 ASP cc_start: 0.7386 (t0) cc_final: 0.7175 (m-30)
REVERT: A  463 ILE cc_start: 0.7570 (mt) cc_final: 0.7105 (mm)
REVERT: A  467 ILE cc_start: 0.7975 (tt) cc_final: 0.7768 (tt)
REVERT: A  471 TYR cc_start: 0.8179 (t80) cc_final: 0.7258 (t80)
REVERT: A  474 LEU cc_start: 0.7833 (mt) cc_final: 0.7501 (mp)
REVERT: A  476 TYR cc_start: 0.8121 (t80) cc_final: 0.7658 (t80)
REVERT: B  170 MET cc_start: 0.7072 (tpp) cc_final: 0.6626 (tpp)
REVERT: B  452 VAL cc_start: 0.7315 (m) cc_final: 0.7082 (p)
REVERT: B  480 SER cc_start: 0.7563 (t) cc_final: 0.7241 (p)
  outliers start: 39
  outliers final: 24
  residues processed: 187
  average time/residue: 0.0463
  time to fit residues: 12.5326
Evaluate side-chains
  194 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 169
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  184 PHE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  387 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   chunk 60 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 64 optimal weight:    0.1980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
B 337 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.138312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.124976 restraints weight = 9062.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.128895 restraints weight = 4525.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.131396 restraints weight = 2601.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.132987 restraints weight = 1651.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.134179 restraints weight = 1151.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5863  Z= 0.160
  Angle     :  0.682   7.846   7987  Z= 0.323
  Chirality :  0.043   0.161    961
  Planarity :  0.005   0.066    972
  Dihedral  :  4.745  43.979    863
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  6.23 %
    Allowed  : 30.00 %
    Favored  : 63.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.31), residues: 751
  helix:  1.47 (0.22), residues: 608
  sheet:  None (None), residues: 0
  loop : -1.53 (0.46), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 479 
 TYR   0.014   0.001   TYR A 430 
 PHE   0.018   0.001   PHE A 253 
 TRP   0.005   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 5863)
  covalent geometry    : angle       0.68169 ( 7987)
  hydrogen bonds       : bond        0.04147 (  450)
  hydrogen bonds       : angle       4.14484 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 168
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6830 (tm-30)
REVERT: A  249 VAL cc_start: 0.7802 (m) cc_final: 0.7064 (p)
REVERT: A  250 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.6800 (mpp)
REVERT: A  253 PHE cc_start: 0.7052 (m-80) cc_final: 0.6789 (m-80)
REVERT: A  463 ILE cc_start: 0.7523 (mt) cc_final: 0.7097 (mm)
REVERT: A  467 ILE cc_start: 0.7986 (tt) cc_final: 0.7775 (tt)
REVERT: A  471 TYR cc_start: 0.8150 (t80) cc_final: 0.7255 (t80)
REVERT: A  474 LEU cc_start: 0.7824 (mt) cc_final: 0.7494 (mp)
REVERT: A  476 TYR cc_start: 0.8156 (t80) cc_final: 0.7696 (t80)
REVERT: B  170 MET cc_start: 0.7016 (tpp) cc_final: 0.6569 (tpp)
REVERT: B  439 MET cc_start: 0.7406 (tpp) cc_final: 0.6816 (mpp)
REVERT: B  452 VAL cc_start: 0.7381 (m) cc_final: 0.7159 (p)
REVERT: B  480 SER cc_start: 0.7587 (t) cc_final: 0.7190 (p)
  outliers start: 38
  outliers final: 25
  residues processed: 186
  average time/residue: 0.0438
  time to fit residues: 11.7202
Evaluate side-chains
  189 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  184 PHE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  479 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    0.0470
   chunk 62 optimal weight:    0.0970
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0870
   chunk 66 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 38 optimal weight:    0.3980
   chunk 35 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.2454

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

Flipped N/Q/H residues before XYZ refinement:
B 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.140900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.128460 restraints weight = 8860.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.132262 restraints weight = 4416.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.134671 restraints weight = 2524.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.136282 restraints weight = 1568.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.137368 restraints weight = 1047.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5863  Z= 0.136
  Angle     :  0.691  11.783   7987  Z= 0.323
  Chirality :  0.043   0.196    961
  Planarity :  0.005   0.065    972
  Dihedral  :  4.754  42.862    863
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 30.82 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.31), residues: 751
  helix:  1.52 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -1.44 (0.46), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 197 
 TYR   0.012   0.001   TYR A 430 
 PHE   0.017   0.001   PHE B 356 
 TRP   0.006   0.001   TRP B 326 
 HIS   0.001   0.000   HIS B 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5863)
  covalent geometry    : angle       0.69109 ( 7987)
  hydrogen bonds       : bond        0.03966 (  450)
  hydrogen bonds       : angle       4.09128 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 168
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLN cc_start: 0.7295 (tm-30) cc_final: 0.6850 (tm-30)
REVERT: A  249 VAL cc_start: 0.7749 (m) cc_final: 0.7040 (p)
REVERT: A  250 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.6765 (mpp)
REVERT: A  253 PHE cc_start: 0.6963 (m-80) cc_final: 0.6715 (m-80)
REVERT: A  463 ILE cc_start: 0.7525 (mt) cc_final: 0.7074 (mm)
REVERT: A  467 ILE cc_start: 0.7923 (tt) cc_final: 0.7604 (tp)
REVERT: A  471 TYR cc_start: 0.8091 (t80) cc_final: 0.7192 (t80)
REVERT: A  474 LEU cc_start: 0.7818 (mt) cc_final: 0.7474 (mp)
REVERT: A  476 TYR cc_start: 0.8138 (t80) cc_final: 0.7679 (t80)
REVERT: B  170 MET cc_start: 0.6919 (tpp) cc_final: 0.6570 (tpp)
REVERT: B  452 VAL cc_start: 0.7297 (m) cc_final: 0.7079 (p)
REVERT: B  480 SER cc_start: 0.7562 (t) cc_final: 0.7153 (p)
  outliers start: 30
  outliers final: 22
  residues processed: 181
  average time/residue: 0.0462
  time to fit residues: 12.0411
Evaluate side-chains
  187 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 164
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  184 PHE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  381 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0870
   chunk 38 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
B 337 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.139025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.125674 restraints weight = 9063.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.129611 restraints weight = 4530.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.132107 restraints weight = 2605.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.133789 restraints weight = 1653.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.134900 restraints weight = 1133.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5863  Z= 0.170
  Angle     :  0.718  11.749   7987  Z= 0.338
  Chirality :  0.044   0.222    961
  Planarity :  0.005   0.066    972
  Dihedral  :  4.763  43.429    863
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 30.82 %
    Favored  : 64.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.31), residues: 751
  helix:  1.42 (0.22), residues: 608
  sheet:  None (None), residues: 0
  loop : -1.38 (0.47), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 479 
 TYR   0.014   0.001   TYR A 430 
 PHE   0.016   0.001   PHE B 356 
 TRP   0.004   0.001   TRP B 366 
 HIS   0.002   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 5863)
  covalent geometry    : angle       0.71834 ( 7987)
  hydrogen bonds       : bond        0.04195 (  450)
  hydrogen bonds       : angle       4.15482 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLN cc_start: 0.7388 (tm-30) cc_final: 0.6919 (tm-30)
REVERT: A   37 LEU cc_start: 0.8451 (tp) cc_final: 0.8186 (tt)
REVERT: A  249 VAL cc_start: 0.7802 (m) cc_final: 0.7070 (p)
REVERT: A  250 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.6823 (mpp)
REVERT: A  253 PHE cc_start: 0.7047 (m-80) cc_final: 0.6778 (m-80)
REVERT: A  463 ILE cc_start: 0.7521 (mt) cc_final: 0.7085 (mm)
REVERT: A  467 ILE cc_start: 0.7973 (tt) cc_final: 0.7757 (tt)
REVERT: A  471 TYR cc_start: 0.8062 (t80) cc_final: 0.7157 (t80)
REVERT: A  474 LEU cc_start: 0.7837 (mt) cc_final: 0.7496 (mp)
REVERT: A  476 TYR cc_start: 0.8188 (t80) cc_final: 0.7751 (t80)
REVERT: B  170 MET cc_start: 0.6923 (tpp) cc_final: 0.6452 (tpp)
REVERT: B  302 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7523 (mt)
REVERT: B  452 VAL cc_start: 0.7372 (m) cc_final: 0.7150 (p)
REVERT: B  480 SER cc_start: 0.7592 (t) cc_final: 0.7193 (p)
  outliers start: 29
  outliers final: 23
  residues processed: 176
  average time/residue: 0.0443
  time to fit residues: 11.2047
Evaluate side-chains
  188 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  184 PHE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  479 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0870
   chunk 15 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
B 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.138193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.125139 restraints weight = 9176.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.129009 restraints weight = 4502.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.131575 restraints weight = 2558.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.133267 restraints weight = 1604.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.134414 restraints weight = 1075.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5863  Z= 0.175
  Angle     :  0.722  10.157   7987  Z= 0.340
  Chirality :  0.045   0.219    961
  Planarity :  0.005   0.066    972
  Dihedral  :  4.771  43.177    863
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 31.31 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.31), residues: 751
  helix:  1.39 (0.22), residues: 608
  sheet:  None (None), residues: 0
  loop : -1.37 (0.47), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 479 
 TYR   0.015   0.001   TYR A 430 
 PHE   0.017   0.001   PHE B 356 
 TRP   0.006   0.001   TRP B 326 
 HIS   0.002   0.001   HIS B 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5863)
  covalent geometry    : angle       0.72222 ( 7987)
  hydrogen bonds       : bond        0.04231 (  450)
  hydrogen bonds       : angle       4.18988 ( 1323)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 GLN cc_start: 0.7378 (tm-30) cc_final: 0.6912 (tm-30)
REVERT: A   37 LEU cc_start: 0.8469 (tp) cc_final: 0.8220 (tt)
REVERT: A   39 THR cc_start: 0.8341 (t) cc_final: 0.8111 (t)
REVERT: A  150 GLN cc_start: 0.7005 (tt0) cc_final: 0.6728 (tt0)
REVERT: A  177 MET cc_start: 0.7441 (ttp) cc_final: 0.7222 (ttp)
REVERT: A  249 VAL cc_start: 0.7792 (m) cc_final: 0.7065 (p)
REVERT: A  250 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.6826 (mpp)
REVERT: A  253 PHE cc_start: 0.7032 (m-80) cc_final: 0.6772 (m-80)
REVERT: A  463 ILE cc_start: 0.7519 (mt) cc_final: 0.7083 (mm)
REVERT: A  467 ILE cc_start: 0.7960 (tt) cc_final: 0.7740 (tt)
REVERT: A  471 TYR cc_start: 0.8047 (t80) cc_final: 0.7144 (t80)
REVERT: A  474 LEU cc_start: 0.7832 (mt) cc_final: 0.7495 (mp)
REVERT: A  476 TYR cc_start: 0.8192 (t80) cc_final: 0.7770 (t80)
REVERT: B  170 MET cc_start: 0.7035 (tpp) cc_final: 0.6568 (tpp)
REVERT: B  302 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7527 (mt)
REVERT: B  452 VAL cc_start: 0.7370 (m) cc_final: 0.7150 (p)
REVERT: B  480 SER cc_start: 0.7584 (t) cc_final: 0.7236 (p)
  outliers start: 27
  outliers final: 21
  residues processed: 177
  average time/residue: 0.0421
  time to fit residues: 10.7428
Evaluate side-chains
  186 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  184 PHE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  314 MET
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  381 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 54 optimal weight:    0.1980
   chunk 24 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 73 optimal weight:    0.2980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
B 337 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.138620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.125640 restraints weight = 8964.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.129511 restraints weight = 4469.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.131899 restraints weight = 2569.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.133605 restraints weight = 1646.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.134741 restraints weight = 1123.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5863  Z= 0.172
  Angle     :  0.732  14.908   7987  Z= 0.343
  Chirality :  0.045   0.214    961
  Planarity :  0.005   0.066    972
  Dihedral  :  4.795  43.102    863
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 31.80 %
    Favored  : 63.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.31), residues: 751
  helix:  1.36 (0.22), residues: 607
  sheet:  None (None), residues: 0
  loop : -1.37 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 479 
 TYR   0.014   0.001   TYR A 430 
 PHE   0.017   0.001   PHE B 356 
 TRP   0.005   0.001   TRP B 326 
 HIS   0.002   0.001   HIS B 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 5863)
  covalent geometry    : angle       0.73182 ( 7987)
  hydrogen bonds       : bond        0.04272 (  450)
  hydrogen bonds       : angle       4.20416 ( 1323)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 835.02 seconds
wall clock time: 15 minutes 8.37 seconds (908.37 seconds total)