Starting phenix.real_space_refine
on Mon Jul 28 19:52:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r8a_24313/07_2025/7r8a_24313.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r8a_24313/07_2025/7r8a_24313.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2025/7r8a_24313.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2025/7r8a_24313.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2025/7r8a_24313.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r8a_24313/07_2025/7r8a_24313.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      66      5.16       5
     C    6810      2.51       5
     N    1778      2.21       5
     O    1876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10530
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4596
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 22, 'TRANS': 561}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4202
          Classifications: {'peptide': 529}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 504}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 901
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "D"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 803
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.78, per 1000 atoms: 0.64
  Number of scatterers: 10530
  At special positions: 0
  Unit cell: (117.316, 99.592, 128.288, 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      66     16.00
     O    1876      8.00
     N    1778      7.00
     C    6810      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 587 " - pdb=" SG  CYS A 600 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  41 " - pdb=" SG  CYS C 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  43 " - pdb=" SG  CYS D 108 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.70
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2468

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 9 sheets defined
      51.5% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 101
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 160 through 175
      removed outlier: 4.597A  pdb=" N   PHE A 164 " --> pdb=" O   ASN A 160 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A 175 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 208
    Processing helix  chain 'A' and resid 224 through 241
    Processing helix  chain 'A' and resid 253 through 257
      removed outlier: 3.576A  pdb=" N   LEU A 256 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 288
      removed outlier: 3.810A  pdb=" N   GLY A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 313 through 331
    Processing helix  chain 'A' and resid 332 through 347
      removed outlier: 3.917A  pdb=" N   HIS A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   HIS A 347 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 381
    Processing helix  chain 'A' and resid 382 through 404
      removed outlier: 3.613A  pdb=" N   VAL A 386 " --> pdb=" O   ASN A 382 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   ASN A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   LEU A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE A 403 " --> pdb=" O   PHE A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 453
      Proline residue:  A 431  - end of helix
      Proline residue:  A 443  - end of helix
    Processing helix  chain 'A' and resid 454 through 456
      No H-bonds generated for 'chain 'A' and resid 454 through 456'
    Processing helix  chain 'A' and resid 459 through 491
      removed outlier: 3.585A  pdb=" N   MET A 463 " --> pdb=" O   GLN A 459 " (cutoff:3.500A)
      Proline residue:  A 473  - end of helix
      removed outlier: 4.839A  pdb=" N   TRP A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 524
      Proline residue:  A 509  - end of helix
    Processing helix  chain 'A' and resid 526 through 545
    Processing helix  chain 'A' and resid 556 through 564
      removed outlier: 3.608A  pdb=" N   TYR A 564 " --> pdb=" O   LYS A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 580
      removed outlier: 4.329A  pdb=" N   TYR A 570 " --> pdb=" O   THR A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 613
      removed outlier: 3.641A  pdb=" N   PHE A 608 " --> pdb=" O   GLN A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 629
    Processing helix  chain 'A' and resid 630 through 646
      removed outlier: 3.974A  pdb=" N   LEU A 634 " --> pdb=" O   PHE A 630 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL A 635 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 120
    Processing helix  chain 'B' and resid 140 through 147
    Processing helix  chain 'B' and resid 162 through 175
    Processing helix  chain 'B' and resid 180 through 195
    Processing helix  chain 'B' and resid 214 through 227
    Processing helix  chain 'B' and resid 244 through 260
    Processing helix  chain 'B' and resid 299 through 305
    Processing helix  chain 'B' and resid 316 through 325
      removed outlier: 3.773A  pdb=" N   THR B 325 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 411
    Processing helix  chain 'B' and resid 413 through 435
    Processing helix  chain 'B' and resid 444 through 473
      removed outlier: 4.644A  pdb=" N   ILE B 459 " --> pdb=" O   ILE B 455 " (cutoff:3.500A)
      Proline residue:  B 460  - end of helix
    Processing helix  chain 'B' and resid 474 through 484
    Processing helix  chain 'B' and resid 490 through 517
      removed outlier: 4.210A  pdb=" N   PHE B 494 " --> pdb=" O   GLY B 490 " (cutoff:3.500A)
      Proline residue:  B 502  - end of helix
      Proline residue:  B 514  - end of helix
      removed outlier: 4.259A  pdb=" N   TRP B 517 " --> pdb=" O   MET B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 525 through 553
    Processing helix  chain 'B' and resid 555 through 573
    Processing helix  chain 'B' and resid 585 through 593
    Processing helix  chain 'B' and resid 594 through 609
    Processing helix  chain 'B' and resid 627 through 633
      removed outlier: 3.617A  pdb=" N   MET B 633 " --> pdb=" O   ILE B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 639 through 665
    Processing helix  chain 'C' and resid 72 through 76
    Processing helix  chain 'D' and resid 99 through 103
      removed outlier: 4.009A  pdb=" N   LEU D 103 " --> pdb=" O   SER D 100 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77
      removed outlier: 6.724A  pdb=" N   LYS A  70 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   SER A  44 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   VAL A  72 " --> pdb=" O   HIS A  42 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA A  43 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   LEU A 110 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   VAL A 113 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132
      removed outlier: 3.923A  pdb=" N   PHE A 273 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   SER A 267 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LEU A 271 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 96
      removed outlier: 7.513A  pdb=" N   PHE B  93 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   ARG B  50 " --> pdb=" O   PHE B  93 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   VAL B  95 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   GLU B  48 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151
      removed outlier: 6.373A  pdb=" N   ALA B 149 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   ASP B 237 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   VAL B 151 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   LEU B 101 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   MET B 100 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   LEU B 284 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ALA B 102 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   MET B 286 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ILE B 104 " --> pdb=" O   MET B 286 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LEU B 294 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU B 285 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26
    Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 81
      removed outlier: 4.974A  pdb=" N   TRP C  66 " --> pdb=" O   ARG C  57 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   ARG C  57 " --> pdb=" O   TRP C  66 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27
    Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 32
      removed outlier: 5.852A  pdb=" N   LEU D  31 " --> pdb=" O   GLU D 125 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE D  68 " --> pdb=" O   TRP D  55 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   GLN D  57 " --> pdb=" O   ARG D  66 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   ARG D  66 " --> pdb=" O   GLN D  57 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32
      removed outlier: 5.852A  pdb=" N   LEU D  31 " --> pdb=" O   GLU D 125 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR D 117 " --> pdb=" O   GLN D 110 " (cutoff:3.500A)

    578 hydrogen bonds defined for protein.
    1674 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: 3.78

  Time building geometry restraints manager: 3.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3340
        1.35 -     1.47: 2622
        1.47 -     1.59: 4693
        1.59 -     1.71: 0
        1.71 -     1.83: 105
  Bond restraints: 10760
  Sorted by residual:
  bond pdb=" C10 CLR A 701 "
       pdb=" C5  CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.519  1.450  0.069 2.00e-02 2.50e+03 1.18e+01
  bond pdb=" C10 CLR A 701 "
       pdb=" C19 CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.536  1.485  0.051 2.00e-02 2.50e+03 6.61e+00
  bond pdb=" C1  CLR A 701 "
       pdb=" C10 CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.544  1.498  0.046 2.00e-02 2.50e+03 5.31e+00
  bond pdb=" C13 CLR A 701 "
       pdb=" C18 CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.532  1.486  0.046 2.00e-02 2.50e+03 5.30e+00
  bond pdb=" C16 CLR A 701 "
       pdb=" C17 CLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.554  1.511  0.043 2.00e-02 2.50e+03 4.57e+00
  ... (remaining 10755 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 14383
        2.02 -     4.04: 146
        4.04 -     6.06: 28
        6.06 -     8.08: 9
        8.08 -    10.10: 3
  Bond angle restraints: 14569
  Sorted by residual:
  angle pdb=" N   GLN A 310 "
        pdb=" CA  GLN A 310 "
        pdb=" C   GLN A 310 "
      ideal   model   delta    sigma   weight residual
     114.56  108.87    5.69 1.27e+00 6.20e-01 2.01e+01
  angle pdb=" C   LEU B 458 "
        pdb=" N   ILE B 459 "
        pdb=" CA  ILE B 459 "
      ideal   model   delta    sigma   weight residual
     120.24  122.77   -2.53 6.30e-01 2.52e+00 1.62e+01
  angle pdb=" C   ILE B 459 "
        pdb=" CA  ILE B 459 "
        pdb=" CB  ILE B 459 "
      ideal   model   delta    sigma   weight residual
     114.35  110.19    4.16 1.06e+00 8.90e-01 1.54e+01
  angle pdb=" C   THR B 488 "
        pdb=" N   THR B 489 "
        pdb=" CA  THR B 489 "
      ideal   model   delta    sigma   weight residual
     121.54  128.02   -6.48 1.91e+00 2.74e-01 1.15e+01
  angle pdb=" C16 CLR A 701 "
        pdb=" C17 CLR A 701 "
        pdb=" C20 CLR A 701 "
      ideal   model   delta    sigma   weight residual
     112.02  101.92   10.10 3.00e+00 1.11e-01 1.13e+01
  ... (remaining 14564 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 5846
       17.52 -    35.04: 461
       35.04 -    52.55: 112
       52.55 -    70.07: 24
       70.07 -    87.59: 7
  Dihedral angle restraints: 6450
    sinusoidal: 2606
      harmonic: 3844
  Sorted by residual:
  dihedral pdb=" CA  THR A 358 "
           pdb=" C   THR A 358 "
           pdb=" N   LYS A 359 "
           pdb=" CA  LYS A 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.63  -16.37     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  ILE C 114 "
           pdb=" C   ILE C 114 "
           pdb=" N   TYR C 115 "
           pdb=" CA  TYR C 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.91  -16.09     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CB  GLU A 579 "
           pdb=" CG  GLU A 579 "
           pdb=" CD  GLU A 579 "
           pdb=" OE1 GLU A 579 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.59   87.59     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 6447 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1583
       0.089 -    0.178: 75
       0.178 -    0.267: 2
       0.267 -    0.356: 0
       0.356 -    0.445: 2
  Chirality restraints: 1662
  Sorted by residual:
  chirality pdb=" C13 CLR A 701 "
            pdb=" C12 CLR A 701 "
            pdb=" C14 CLR A 701 "
            pdb=" C17 CLR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.49   -0.45 2.00e-01 2.50e+01 4.95e+00
  chirality pdb=" C10 CLR A 701 "
            pdb=" C1  CLR A 701 "
            pdb=" C5  CLR A 701 "
            pdb=" C9  CLR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.45   -0.39 2.00e-01 2.50e+01 3.90e+00
  chirality pdb=" C17 CLR A 701 "
            pdb=" C13 CLR A 701 "
            pdb=" C16 CLR A 701 "
            pdb=" C20 CLR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.81   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1659 not shown)

  Planarity restraints: 1827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 490 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.44e+00
        pdb=" N   PRO B 491 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 491 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 491 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 276 "    0.022 5.00e-02 4.00e+02   3.33e-02 1.78e+00
        pdb=" N   PRO A 277 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D  78 "    0.020 5.00e-02 4.00e+02   3.07e-02 1.51e+00
        pdb=" N   PRO D  79 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO D  79 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D  79 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1824 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3300
        2.82 -     3.34: 9420
        3.34 -     3.86: 17278
        3.86 -     4.38: 19310
        4.38 -     4.90: 34751
  Nonbonded interactions: 84059
  Sorted by model distance:
  nonbonded pdb=" NE  ARG A 550 "
            pdb=" O   LEU B 434 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" ND2 ASN A 296 "
            pdb=" OD2 ASP A 299 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" O   SER A  46 "
            pdb=" OG  SER A  46 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   GLU A 315 "
            pdb=" OG  SER A 319 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   ALA A 601 "
            pdb=" NE2 GLN A 607 "
     model   vdw
     2.315 3.120
  ... (remaining 84054 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     28.170
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:14.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
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      :  0.003   0.069  10763  Z= 0.137
  Angle     :  0.571  10.099  14575  Z= 0.313
  Chirality :  0.041   0.445   1662
  Planarity :  0.003   0.039   1827
  Dihedral  : 13.808  87.589   3973
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.59 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.58 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.21), residues: 1308
  helix: -0.04 (0.19), residues: 675
  sheet: -0.90 (0.33), residues: 185
  loop : -2.75 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 584 
 HIS   0.003   0.000   HIS A 470 
 PHE   0.007   0.001   PHE B 493 
 TYR   0.009   0.001   TYR B 507 
 ARG   0.001   0.000   ARG B 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12589 (  574)
  hydrogen bonds       : angle       4.94407 ( 1674)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       0.66554 (    6)
  covalent geometry    : bond        0.00258 (10760)
  covalent geometry    : angle       0.57105 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 229
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7153 (pt0)
REVERT: A  114 TYR cc_start: 0.8290 (m-80) cc_final: 0.6925 (m-80)
REVERT: A  118 ARG cc_start: 0.7274 (mpt180) cc_final: 0.6894 (mmt90)
REVERT: A  169 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7437 (mm-30)
REVERT: A  224 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7354 (p0)
REVERT: A  302 MET cc_start: 0.7524 (mmm) cc_final: 0.7225 (tpp)
REVERT: A  387 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7358 (mp)
REVERT: B   89 GLN cc_start: 0.8371 (mt0) cc_final: 0.7729 (mp10)
REVERT: B   94 LYS cc_start: 0.8581 (tttm) cc_final: 0.8360 (tptm)
REVERT: B  267 ILE cc_start: 0.8736 (mt) cc_final: 0.8458 (pt)
REVERT: B  281 ASP cc_start: 0.8360 (t0) cc_final: 0.8032 (t0)
REVERT: B  309 TYR cc_start: 0.8340 (m-80) cc_final: 0.8123 (m-80)
REVERT: B  404 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7232 (mtm110)
REVERT: B  459 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8028 (tp)
REVERT: B  517 TRP cc_start: 0.6979 (m100) cc_final: 0.6372 (t60)
REVERT: C   80 ASP cc_start: 0.8443 (t0) cc_final: 0.8135 (t0)
REVERT: C   99 ILE cc_start: 0.8604 (mt) cc_final: 0.8313 (mp)
REVERT: C  130 GLN cc_start: 0.8066 (mp-120) cc_final: 0.7774 (pp30)
REVERT: D   78 VAL cc_start: 0.8061 (p) cc_final: 0.7751 (t)
REVERT: D  101 GLU cc_start: 0.6566 (mp0) cc_final: 0.6044 (mp0)
  outliers start: 39
  outliers final: 3
  residues processed: 259
  average time/residue: 1.2010
  time to fit residues: 335.0820
Evaluate side-chains
  146 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain B residue  275 ASP
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  459 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:   10.0000
   chunk 99 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0070
   chunk 102 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 118 optimal weight:   10.0000
   overall best weight:    2.4006

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
A 160 ASN
A 206 GLN
A 392 GLN
A 437 ASN
A 459 GLN
A 462 GLN
A 510 HIS
A 578 ASN
A 604 GLN
A 607 GLN
B  99 GLN
B 131 GLN
B 150 HIS
B 199 GLN
B 249 HIS
B 409 ASN
B 438 HIS
B 462 ASN
C  58 GLN
C  75 ASN
C 105 ASN
C 130 GLN
D  26 GLN
D  47 GLN
D  57 GLN
D  58 GLN
D  65 GLN

Total number of N/Q/H flips: 28

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.105660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.078352 restraints weight = 14780.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 2.08
r_work: 0.2669 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2534 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8910
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  10763  Z= 0.246
  Angle     :  0.709   7.895  14575  Z= 0.366
  Chirality :  0.047   0.159   1662
  Planarity :  0.005   0.067   1827
  Dihedral  :  5.392  53.044   1533
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 19.79 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.23), residues: 1308
  helix:  0.83 (0.19), residues: 688
  sheet: -0.34 (0.36), residues: 177
  loop : -2.14 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 584 
 HIS   0.011   0.002   HIS A 510 
 PHE   0.024   0.002   PHE A 585 
 TYR   0.018   0.002   TYR A 628 
 ARG   0.009   0.001   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06717 (  574)
  hydrogen bonds       : angle       4.10886 ( 1674)
  SS BOND              : bond        0.00751 (    3)
  SS BOND              : angle       1.39184 (    6)
  covalent geometry    : bond        0.00602 (10760)
  covalent geometry    : angle       0.70875 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 149
  time to evaluate  : 1.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7894 (mpt180) cc_final: 0.7338 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8229 (mm-30)
REVERT: A  224 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7755 (p0)
REVERT: A  343 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8117 (tm-30)
REVERT: A  353 MET cc_start: 0.6309 (pmm) cc_final: 0.5928 (pmm)
REVERT: A  383 LYS cc_start: 0.7750 (mppt) cc_final: 0.7271 (mmtm)
REVERT: A  387 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8274 (mp)
REVERT: A  454 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7807 (mm-40)
REVERT: A  536 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8598 (tp)
REVERT: A  599 MET cc_start: 0.5322 (OUTLIER) cc_final: 0.5042 (mtm)
REVERT: B   89 GLN cc_start: 0.8831 (mt0) cc_final: 0.8348 (mt0)
REVERT: B  142 GLN cc_start: 0.8288 (pp30) cc_final: 0.7992 (tm-30)
REVERT: B  145 ARG cc_start: 0.8536 (ttm110) cc_final: 0.8331 (ttp80)
REVERT: B  397 GLN cc_start: 0.8240 (mp10) cc_final: 0.8022 (mt0)
REVERT: B  404 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8404 (mtm110)
REVERT: B  505 CYS cc_start: 0.9230 (t) cc_final: 0.8916 (m)
REVERT: B  517 TRP cc_start: 0.7928 (m100) cc_final: 0.7560 (t60)
REVERT: B  582 SER cc_start: 0.7497 (OUTLIER) cc_final: 0.7037 (p)
REVERT: C   80 ASP cc_start: 0.8941 (t0) cc_final: 0.8683 (t0)
REVERT: C   99 ILE cc_start: 0.8866 (mt) cc_final: 0.8545 (mp)
REVERT: C  103 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7911 (mm110)
REVERT: C  130 GLN cc_start: 0.8478 (mp10) cc_final: 0.8176 (pp30)
REVERT: D   37 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7714 (pm20)
REVERT: D  103 LEU cc_start: 0.8581 (tp) cc_final: 0.8374 (tt)
  outliers start: 54
  outliers final: 20
  residues processed: 190
  average time/residue: 1.2796
  time to fit residues: 260.9911
Evaluate side-chains
  161 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  112 GLU
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  214 SER
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   37 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 102 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
A 493 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.107841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.080350 restraints weight = 14966.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 2.14
r_work: 0.2695 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2559 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10763  Z= 0.138
  Angle     :  0.570   6.430  14575  Z= 0.291
  Chirality :  0.041   0.180   1662
  Planarity :  0.004   0.063   1827
  Dihedral  :  4.871  53.573   1530
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 20.83 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.23), residues: 1308
  helix:  1.44 (0.20), residues: 679
  sheet: -0.06 (0.37), residues: 177
  loop : -1.88 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 
 PHE   0.013   0.001   PHE B 493 
 TYR   0.011   0.001   TYR A 487 
 ARG   0.005   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05102 (  574)
  hydrogen bonds       : angle       3.87515 ( 1674)
  SS BOND              : bond        0.01021 (    3)
  SS BOND              : angle       1.06016 (    6)
  covalent geometry    : bond        0.00318 (10760)
  covalent geometry    : angle       0.56951 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 140
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7901 (mpt180) cc_final: 0.7447 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8237 (mm-30)
REVERT: A  343 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8185 (tm-30)
REVERT: A  353 MET cc_start: 0.6403 (pmm) cc_final: 0.6136 (pmm)
REVERT: A  383 LYS cc_start: 0.7619 (mppt) cc_final: 0.7331 (mmtm)
REVERT: A  454 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.7854 (mm-40)
REVERT: A  536 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8550 (tp)
REVERT: B   89 GLN cc_start: 0.8848 (mt0) cc_final: 0.8382 (mt0)
REVERT: B   94 LYS cc_start: 0.9048 (tttm) cc_final: 0.8726 (tptm)
REVERT: B  142 GLN cc_start: 0.8247 (pp30) cc_final: 0.7973 (tm-30)
REVERT: B  253 LYS cc_start: 0.9107 (mttt) cc_final: 0.8907 (mtmt)
REVERT: B  404 ARG cc_start: 0.8724 (mtp-110) cc_final: 0.8325 (mtm110)
REVERT: B  505 CYS cc_start: 0.9212 (t) cc_final: 0.8792 (m)
REVERT: B  517 TRP cc_start: 0.7922 (m100) cc_final: 0.7511 (t60)
REVERT: B  577 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8058 (mmt)
REVERT: C   38 ARG cc_start: 0.8238 (ttp-170) cc_final: 0.7791 (mtp180)
REVERT: C   80 ASP cc_start: 0.8919 (t0) cc_final: 0.8627 (t0)
REVERT: C   90 ILE cc_start: 0.8529 (mp) cc_final: 0.8258 (mm)
REVERT: C   99 ILE cc_start: 0.8860 (mt) cc_final: 0.8530 (mp)
REVERT: D   44 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8169 (ttt90)
REVERT: D  103 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8424 (tt)
  outliers start: 45
  outliers final: 18
  residues processed: 172
  average time/residue: 1.2508
  time to fit residues: 231.6756
Evaluate side-chains
  150 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  577 MET
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 63 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 100 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
A 393 ASN
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.107135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.079861 restraints weight = 14832.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 2.10
r_work: 0.2690 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2556 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10763  Z= 0.128
  Angle     :  0.549   6.395  14575  Z= 0.282
  Chirality :  0.041   0.154   1662
  Planarity :  0.004   0.054   1827
  Dihedral  :  4.503  54.570   1523
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.70 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.24), residues: 1308
  helix:  1.70 (0.20), residues: 680
  sheet: -0.03 (0.36), residues: 188
  loop : -1.58 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 
 PHE   0.014   0.001   PHE B 493 
 TYR   0.012   0.001   TYR A 487 
 ARG   0.005   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04837 (  574)
  hydrogen bonds       : angle       3.80695 ( 1674)
  SS BOND              : bond        0.00410 (    3)
  SS BOND              : angle       1.84400 (    6)
  covalent geometry    : bond        0.00292 (10760)
  covalent geometry    : angle       0.54786 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 139
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7853 (mpt180) cc_final: 0.7463 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8245 (mm-30)
REVERT: A  343 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8145 (tm-30)
REVERT: A  353 MET cc_start: 0.6403 (pmm) cc_final: 0.6189 (pmm)
REVERT: A  383 LYS cc_start: 0.7576 (mppt) cc_final: 0.7161 (mmtm)
REVERT: A  387 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8299 (mp)
REVERT: A  400 LEU cc_start: 0.8887 (tp) cc_final: 0.8594 (mt)
REVERT: A  454 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7906 (mm-40)
REVERT: A  536 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8553 (tp)
REVERT: B   89 GLN cc_start: 0.8921 (mt0) cc_final: 0.8498 (mt0)
REVERT: B   94 LYS cc_start: 0.9066 (tttm) cc_final: 0.8802 (tptm)
REVERT: B  142 GLN cc_start: 0.8265 (pp30) cc_final: 0.7884 (tm-30)
REVERT: B  253 LYS cc_start: 0.9121 (mttt) cc_final: 0.8920 (mtmt)
REVERT: B  397 GLN cc_start: 0.8223 (mp10) cc_final: 0.8014 (mt0)
REVERT: B  404 ARG cc_start: 0.8755 (mtp-110) cc_final: 0.8348 (mtm110)
REVERT: B  505 CYS cc_start: 0.9159 (t) cc_final: 0.8721 (m)
REVERT: B  517 TRP cc_start: 0.7941 (m100) cc_final: 0.7508 (t60)
REVERT: C   38 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7791 (mtp180)
REVERT: C   80 ASP cc_start: 0.8923 (t0) cc_final: 0.8615 (t0)
REVERT: C   90 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8238 (mm)
REVERT: C   99 ILE cc_start: 0.8871 (mt) cc_final: 0.8554 (mp)
REVERT: D   44 ARG cc_start: 0.8407 (ttm110) cc_final: 0.8104 (ttt90)
REVERT: D  103 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8583 (tt)
  outliers start: 47
  outliers final: 23
  residues processed: 170
  average time/residue: 1.3842
  time to fit residues: 253.1524
Evaluate side-chains
  158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  311 SER
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain B residue  609 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  103 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0670
   chunk 73 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 121 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.4124

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.104761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.077594 restraints weight = 14749.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 2.08
r_work: 0.2649 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2512 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8914
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10763  Z= 0.158
  Angle     :  0.584   7.041  14575  Z= 0.301
  Chirality :  0.042   0.191   1662
  Planarity :  0.004   0.064   1827
  Dihedral  :  4.613  52.651   1523
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.18 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.24), residues: 1308
  helix:  1.66 (0.20), residues: 680
  sheet:  0.04 (0.35), residues: 194
  loop : -1.47 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 584 
 HIS   0.006   0.001   HIS B 531 
 PHE   0.017   0.001   PHE B 493 
 TYR   0.013   0.001   TYR A 581 
 ARG   0.005   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05462 (  574)
  hydrogen bonds       : angle       3.87748 ( 1674)
  SS BOND              : bond        0.00691 (    3)
  SS BOND              : angle       1.86685 (    6)
  covalent geometry    : bond        0.00376 (10760)
  covalent geometry    : angle       0.58256 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 135
  time to evaluate  : 1.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7942 (mpt180) cc_final: 0.7526 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8292 (mm-30)
REVERT: A  324 MET cc_start: 0.8417 (tmm) cc_final: 0.8140 (tmm)
REVERT: A  343 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8187 (tm-30)
REVERT: A  383 LYS cc_start: 0.7698 (mppt) cc_final: 0.7278 (mmtm)
REVERT: A  387 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8309 (mp)
REVERT: A  454 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.7911 (mm-40)
REVERT: A  536 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8554 (tp)
REVERT: B   89 GLN cc_start: 0.8890 (mt0) cc_final: 0.8470 (mt0)
REVERT: B   94 LYS cc_start: 0.9100 (tttm) cc_final: 0.8840 (tptm)
REVERT: B  142 GLN cc_start: 0.8262 (pp30) cc_final: 0.7897 (tm-30)
REVERT: B  253 LYS cc_start: 0.9158 (mttt) cc_final: 0.8941 (mtmt)
REVERT: B  404 ARG cc_start: 0.8758 (mtp-110) cc_final: 0.8375 (mtm110)
REVERT: B  505 CYS cc_start: 0.9208 (t) cc_final: 0.8815 (m)
REVERT: B  517 TRP cc_start: 0.7912 (m100) cc_final: 0.7514 (t60)
REVERT: C   38 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7823 (mtp180)
REVERT: C   80 ASP cc_start: 0.8919 (t0) cc_final: 0.8634 (t0)
REVERT: C   90 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8275 (mm)
REVERT: C   95 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8001 (m)
REVERT: D   44 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8160 (ttm110)
REVERT: D  103 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8680 (tt)
  outliers start: 47
  outliers final: 27
  residues processed: 170
  average time/residue: 1.2223
  time to fit residues: 224.0837
Evaluate side-chains
  164 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   90 ILE
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   46 SER
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 119 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 114 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 118 optimal weight:    0.0370
   chunk 76 optimal weight:    6.9990
   overall best weight:    1.7262

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.103511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.076495 restraints weight = 14900.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 2.07
r_work: 0.2629 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2492 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8924
moved from start:          0.4433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10763  Z= 0.181
  Angle     :  0.614   8.588  14575  Z= 0.315
  Chirality :  0.043   0.174   1662
  Planarity :  0.004   0.055   1827
  Dihedral  :  4.698  51.030   1523
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 18.84 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.24), residues: 1308
  helix:  1.62 (0.20), residues: 681
  sheet:  0.10 (0.36), residues: 194
  loop : -1.48 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 584 
 HIS   0.006   0.001   HIS B 531 
 PHE   0.018   0.002   PHE B 493 
 TYR   0.013   0.001   TYR A 487 
 ARG   0.005   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05764 (  574)
  hydrogen bonds       : angle       3.94170 ( 1674)
  SS BOND              : bond        0.00661 (    3)
  SS BOND              : angle       1.75284 (    6)
  covalent geometry    : bond        0.00440 (10760)
  covalent geometry    : angle       0.61279 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 131
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7908 (mpt180) cc_final: 0.7468 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8350 (mm-30)
REVERT: A  324 MET cc_start: 0.8407 (tmm) cc_final: 0.8133 (tmm)
REVERT: A  343 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8189 (tm-30)
REVERT: A  383 LYS cc_start: 0.7737 (mppt) cc_final: 0.7293 (mmtm)
REVERT: A  387 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8297 (mp)
REVERT: A  454 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.7870 (mm-40)
REVERT: A  536 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8527 (tp)
REVERT: B   89 GLN cc_start: 0.8885 (mt0) cc_final: 0.8463 (mt0)
REVERT: B   94 LYS cc_start: 0.9137 (tttm) cc_final: 0.8834 (tptm)
REVERT: B  142 GLN cc_start: 0.8247 (pp30) cc_final: 0.7889 (tm-30)
REVERT: B  404 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8359 (mtm110)
REVERT: B  505 CYS cc_start: 0.9210 (t) cc_final: 0.8828 (m)
REVERT: B  517 TRP cc_start: 0.7914 (m100) cc_final: 0.7488 (t60)
REVERT: C   80 ASP cc_start: 0.8908 (t0) cc_final: 0.8641 (t0)
REVERT: C   95 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8154 (m)
REVERT: D  103 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8728 (tt)
  outliers start: 55
  outliers final: 30
  residues processed: 170
  average time/residue: 1.2857
  time to fit residues: 234.5799
Evaluate side-chains
  159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 124
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue   46 SER
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   chunk 120 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.104801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.077572 restraints weight = 15053.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.2789 rms_B_bonded: 2.10
r_work: 0.2657 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2522 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10763  Z= 0.145
  Angle     :  0.585   8.694  14575  Z= 0.300
  Chirality :  0.042   0.165   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.613  51.813   1523
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 20.05 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.24), residues: 1308
  helix:  1.74 (0.20), residues: 680
  sheet:  0.15 (0.35), residues: 202
  loop : -1.41 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 
 PHE   0.016   0.001   PHE B 493 
 TYR   0.013   0.001   TYR A 487 
 ARG   0.004   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05195 (  574)
  hydrogen bonds       : angle       3.89196 ( 1674)
  SS BOND              : bond        0.00599 (    3)
  SS BOND              : angle       1.52271 (    6)
  covalent geometry    : bond        0.00340 (10760)
  covalent geometry    : angle       0.58426 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 129
  time to evaluate  : 1.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7893 (mpt180) cc_final: 0.7544 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8388 (mm-30)
REVERT: A  324 MET cc_start: 0.8394 (tmm) cc_final: 0.8108 (tmm)
REVERT: A  343 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8158 (tm-30)
REVERT: A  383 LYS cc_start: 0.7669 (mppt) cc_final: 0.7253 (mmtm)
REVERT: A  387 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8278 (mp)
REVERT: A  454 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.7905 (mm-40)
REVERT: A  536 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8511 (tp)
REVERT: B   89 GLN cc_start: 0.8891 (mt0) cc_final: 0.8472 (mt0)
REVERT: B   94 LYS cc_start: 0.9119 (tttm) cc_final: 0.8857 (tptm)
REVERT: B  142 GLN cc_start: 0.8221 (pp30) cc_final: 0.7862 (tm-30)
REVERT: B  404 ARG cc_start: 0.8737 (mtp-110) cc_final: 0.8341 (mtm110)
REVERT: B  429 MET cc_start: 0.8614 (ptm) cc_final: 0.7813 (mmt)
REVERT: B  505 CYS cc_start: 0.9196 (t) cc_final: 0.8792 (m)
REVERT: B  517 TRP cc_start: 0.7891 (m100) cc_final: 0.7486 (t60)
REVERT: C   80 ASP cc_start: 0.8897 (t0) cc_final: 0.8614 (t0)
REVERT: C   95 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8155 (m)
REVERT: D  103 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8712 (tt)
  outliers start: 44
  outliers final: 28
  residues processed: 162
  average time/residue: 1.9180
  time to fit residues: 334.7037
Evaluate side-chains
  160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   46 SER
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  103 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   chunk 94 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0570
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.3100

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.104399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.077305 restraints weight = 14746.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.2781 rms_B_bonded: 2.09
r_work: 0.2647 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2510 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8904
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10763  Z= 0.152
  Angle     :  0.592   8.434  14575  Z= 0.304
  Chirality :  0.042   0.161   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.614  51.518   1523
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 20.49 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.24), residues: 1308
  helix:  1.75 (0.20), residues: 680
  sheet:  0.25 (0.36), residues: 194
  loop : -1.37 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 584 
 HIS   0.006   0.001   HIS B 531 
 PHE   0.016   0.001   PHE B 493 
 TYR   0.013   0.001   TYR A 487 
 ARG   0.002   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05289 (  574)
  hydrogen bonds       : angle       3.88446 ( 1674)
  SS BOND              : bond        0.00613 (    3)
  SS BOND              : angle       1.50279 (    6)
  covalent geometry    : bond        0.00361 (10760)
  covalent geometry    : angle       0.59119 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 2.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7892 (mpt180) cc_final: 0.7547 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8408 (mm-30)
REVERT: A  324 MET cc_start: 0.8400 (tmm) cc_final: 0.8109 (tmm)
REVERT: A  343 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8159 (tm-30)
REVERT: A  383 LYS cc_start: 0.7679 (mppt) cc_final: 0.7265 (mmtm)
REVERT: A  387 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8287 (mp)
REVERT: A  454 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.7884 (mm-40)
REVERT: A  536 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8495 (tp)
REVERT: B   89 GLN cc_start: 0.8895 (mt0) cc_final: 0.8479 (mt0)
REVERT: B   94 LYS cc_start: 0.9123 (tttm) cc_final: 0.8833 (tptm)
REVERT: B  121 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6990 (mpt180)
REVERT: B  142 GLN cc_start: 0.8226 (pp30) cc_final: 0.7881 (tm-30)
REVERT: B  404 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8311 (mtm110)
REVERT: B  429 MET cc_start: 0.8528 (ptm) cc_final: 0.7805 (mmt)
REVERT: B  505 CYS cc_start: 0.9202 (t) cc_final: 0.8797 (m)
REVERT: B  517 TRP cc_start: 0.7908 (m100) cc_final: 0.7493 (t60)
REVERT: C   80 ASP cc_start: 0.8900 (t0) cc_final: 0.8618 (t0)
REVERT: C   95 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8180 (m)
REVERT: D  103 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8720 (tt)
  outliers start: 40
  outliers final: 28
  residues processed: 159
  average time/residue: 1.4204
  time to fit residues: 243.0294
Evaluate side-chains
  160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 89 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.106856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.079819 restraints weight = 14906.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.10
r_work: 0.2700 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2567 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.4356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10763  Z= 0.120
  Angle     :  0.553   8.913  14575  Z= 0.283
  Chirality :  0.041   0.162   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.456  52.139   1523
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.57 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.24), residues: 1308
  helix:  1.96 (0.20), residues: 679
  sheet:  0.32 (0.36), residues: 202
  loop : -1.31 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 
 PHE   0.013   0.001   PHE C  89 
 TYR   0.012   0.001   TYR A 487 
 ARG   0.001   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  574)
  hydrogen bonds       : angle       3.77378 ( 1674)
  SS BOND              : bond        0.00533 (    3)
  SS BOND              : angle       1.24124 (    6)
  covalent geometry    : bond        0.00270 (10760)
  covalent geometry    : angle       0.55266 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7284 (tt0)
REVERT: A  114 TYR cc_start: 0.8627 (m-80) cc_final: 0.8370 (m-80)
REVERT: A  118 ARG cc_start: 0.7879 (mpt180) cc_final: 0.7546 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8402 (mm-30)
REVERT: A  324 MET cc_start: 0.8417 (tmm) cc_final: 0.8114 (tmm)
REVERT: A  343 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8153 (tm-30)
REVERT: A  383 LYS cc_start: 0.7587 (mppt) cc_final: 0.7211 (mmtm)
REVERT: A  454 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7917 (mm-40)
REVERT: A  536 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8524 (tp)
REVERT: B   89 GLN cc_start: 0.8919 (mt0) cc_final: 0.8466 (mt0)
REVERT: B   94 LYS cc_start: 0.9062 (tttm) cc_final: 0.8840 (tptm)
REVERT: B  121 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6976 (mpt180)
REVERT: B  142 GLN cc_start: 0.8216 (pp30) cc_final: 0.7893 (tm-30)
REVERT: B  404 ARG cc_start: 0.8742 (mtp-110) cc_final: 0.8316 (mtm110)
REVERT: B  429 MET cc_start: 0.8480 (ptm) cc_final: 0.7840 (mmt)
REVERT: B  505 CYS cc_start: 0.9177 (t) cc_final: 0.8735 (m)
REVERT: B  517 TRP cc_start: 0.7899 (m100) cc_final: 0.7451 (t60)
REVERT: C   80 ASP cc_start: 0.8902 (t0) cc_final: 0.8615 (t0)
REVERT: D  103 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8731 (tt)
  outliers start: 37
  outliers final: 25
  residues processed: 165
  average time/residue: 1.6009
  time to fit residues: 282.9276
Evaluate side-chains
  159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 127 optimal weight:    0.4980
   chunk 10 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0770
   chunk 11 optimal weight:    0.5980
   chunk 126 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
B 249 HIS
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.108403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.081536 restraints weight = 14780.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 2.09
r_work: 0.2732 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2599 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10763  Z= 0.110
  Angle     :  0.546  10.539  14575  Z= 0.278
  Chirality :  0.040   0.161   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.359  52.814   1523
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.53 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.24), residues: 1308
  helix:  2.15 (0.20), residues: 676
  sheet:  0.61 (0.36), residues: 192
  loop : -1.34 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 536 
 HIS   0.005   0.001   HIS B 531 
 PHE   0.012   0.001   PHE A 502 
 TYR   0.012   0.001   TYR A 487 
 ARG   0.002   0.000   ARG D  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04169 (  574)
  hydrogen bonds       : angle       3.70204 ( 1674)
  SS BOND              : bond        0.00475 (    3)
  SS BOND              : angle       1.06323 (    6)
  covalent geometry    : bond        0.00242 (10760)
  covalent geometry    : angle       0.54553 (14569)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 1.617 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7328 (tt0)
REVERT: A  114 TYR cc_start: 0.8623 (m-80) cc_final: 0.8311 (m-80)
REVERT: A  118 ARG cc_start: 0.7900 (mpt180) cc_final: 0.7570 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8476 (mm-30)
REVERT: A  324 MET cc_start: 0.8427 (tmm) cc_final: 0.8115 (tmm)
REVERT: A  343 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8113 (tm-30)
REVERT: A  454 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.7892 (mm-40)
REVERT: A  536 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8519 (tp)
REVERT: B   89 GLN cc_start: 0.8961 (mt0) cc_final: 0.8522 (mt0)
REVERT: B  121 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6827 (mpt180)
REVERT: B  142 GLN cc_start: 0.8202 (pp30) cc_final: 0.7996 (tm-30)
REVERT: B  253 LYS cc_start: 0.9119 (mttt) cc_final: 0.8912 (mtmt)
REVERT: B  404 ARG cc_start: 0.8720 (mtp-110) cc_final: 0.8302 (mtm110)
REVERT: B  429 MET cc_start: 0.8461 (ptm) cc_final: 0.7807 (mmt)
REVERT: B  505 CYS cc_start: 0.9123 (t) cc_final: 0.8628 (m)
REVERT: B  517 TRP cc_start: 0.7910 (m100) cc_final: 0.7429 (t60)
REVERT: C   80 ASP cc_start: 0.8854 (t0) cc_final: 0.8587 (t0)
REVERT: D  103 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8708 (tt)
  outliers start: 30
  outliers final: 23
  residues processed: 167
  average time/residue: 1.4368
  time to fit residues: 257.2571
Evaluate side-chains
  160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 2.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 64 optimal weight:    0.0670
   chunk 6 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 111 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 128 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.3924

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.105608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.078479 restraints weight = 14776.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 2.08
r_work: 0.2674 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2540 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
moved from start:          0.4438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10763  Z= 0.155
  Angle     :  0.586   9.799  14575  Z= 0.300
  Chirality :  0.042   0.205   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.423  51.974   1522
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.79 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.24), residues: 1308
  helix:  2.02 (0.20), residues: 680
  sheet:  0.48 (0.36), residues: 202
  loop : -1.26 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 584 
 HIS   0.006   0.001   HIS B 531 
 PHE   0.015   0.001   PHE B 493 
 TYR   0.012   0.001   TYR A 487 
 ARG   0.003   0.000   ARG D  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05053 (  574)
  hydrogen bonds       : angle       3.79137 ( 1674)
  SS BOND              : bond        0.00611 (    3)
  SS BOND              : angle       1.40162 (    6)
  covalent geometry    : bond        0.00373 (10760)
  covalent geometry    : angle       0.58575 (14569)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8592.66 seconds
wall clock time: 151 minutes 22.20 seconds (9082.20 seconds total)