Starting phenix.real_space_refine
on Fri Feb 14 21:01:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r8a_24313/02_2025/7r8a_24313.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r8a_24313/02_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_24313/02_2025/7r8a_24313.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r8a_24313/02_2025/7r8a_24313.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r8a_24313/02_2025/7r8a_24313.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r8a_24313/02_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.38, per 1000 atoms: 0.61
  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: 2.65
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.18
  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: 3.26

  Time building geometry restraints manager: 3.06 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:             1.360
  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:             0.000
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     25.840
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.790
-------------------------------------------------------------------------------
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  10760  Z= 0.165
  Angle     :  0.571  10.099  14569  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 

*********************** 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  : 1.230 
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: 1.2392
  time to fit residues: 345.2170
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  : 1.260 
-------------------------------------------------------------------------------
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 = 37)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.078370 restraints weight = 14780.369|
|-----------------------------------------------------------------------------|
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: 0.8908
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  10760  Z= 0.386
  Angle     :  0.709   7.895  14569  Z= 0.365
  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 

*********************** 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  : 1.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7895 (mpt180) cc_final: 0.7339 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8225 (mm-30)
REVERT: A  224 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7749 (p0)
REVERT: A  343 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8116 (tm-30)
REVERT: A  353 MET cc_start: 0.6307 (pmm) cc_final: 0.5924 (pmm)
REVERT: A  383 LYS cc_start: 0.7747 (mppt) cc_final: 0.7267 (mmtm)
REVERT: A  387 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8269 (mp)
REVERT: A  454 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7804 (mm-40)
REVERT: A  536 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8596 (tp)
REVERT: A  599 MET cc_start: 0.5319 (OUTLIER) cc_final: 0.5040 (mtm)
REVERT: B   89 GLN cc_start: 0.8832 (mt0) cc_final: 0.8347 (mt0)
REVERT: B  142 GLN cc_start: 0.8283 (pp30) cc_final: 0.7986 (tm-30)
REVERT: B  145 ARG cc_start: 0.8531 (ttm110) cc_final: 0.8325 (ttp80)
REVERT: B  397 GLN cc_start: 0.8237 (mp10) cc_final: 0.8018 (mt0)
REVERT: B  404 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8398 (mtm110)
REVERT: B  505 CYS cc_start: 0.9227 (t) cc_final: 0.8912 (m)
REVERT: B  517 TRP cc_start: 0.7924 (m100) cc_final: 0.7556 (t60)
REVERT: B  582 SER cc_start: 0.7498 (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: 0.8860 (mt) cc_final: 0.8537 (mp)
REVERT: C  103 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7910 (mm110)
REVERT: C  130 GLN cc_start: 0.8477 (mp10) cc_final: 0.8175 (pp30)
REVERT: D   37 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7711 (pm20)
REVERT: D  103 LEU cc_start: 0.8580 (tp) cc_final: 0.8372 (tt)
  outliers start: 54
  outliers final: 20
  residues processed: 190
  average time/residue: 1.3381
  time to fit residues: 272.7726
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  : 1.318 
-------------------------------------------------------------------------------
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:    3.9990
   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:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.9786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.108307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.080818 restraints weight = 14966.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.14
r_work: 0.2717 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2583 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.3800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10760  Z= 0.188
  Angle     :  0.559   6.411  14569  Z= 0.285
  Chirality :  0.041   0.184   1662
  Planarity :  0.004   0.064   1827
  Dihedral  :  4.842  53.893   1530
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 21.01 %
    Favored  : 75.43 %
  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:  0.22 (0.23), residues: 1308
  helix:  1.48 (0.20), residues: 679
  sheet: -0.05 (0.37), residues: 177
  loop : -1.87 (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   0.004   0.000   ARG A 550 

*********************** 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
  183 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 142
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7887 (mpt180) cc_final: 0.7440 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8227 (mm-30)
REVERT: A  343 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8183 (tm-30)
REVERT: A  353 MET cc_start: 0.6323 (pmm) cc_final: 0.6063 (pmm)
REVERT: A  383 LYS cc_start: 0.7591 (mppt) cc_final: 0.7304 (mmtm)
REVERT: A  454 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7838 (mm-40)
REVERT: A  536 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8554 (tp)
REVERT: B   89 GLN cc_start: 0.8847 (mt0) cc_final: 0.8384 (mt0)
REVERT: B   94 LYS cc_start: 0.9028 (tttm) cc_final: 0.8706 (tptm)
REVERT: B  142 GLN cc_start: 0.8244 (pp30) cc_final: 0.7967 (tm-30)
REVERT: B  253 LYS cc_start: 0.9104 (mttt) cc_final: 0.8904 (mtmt)
REVERT: B  404 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8337 (mtm110)
REVERT: B  505 CYS cc_start: 0.9199 (t) cc_final: 0.8767 (m)
REVERT: B  517 TRP cc_start: 0.7926 (m100) cc_final: 0.7507 (t60)
REVERT: B  577 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.8001 (mmt)
REVERT: C   38 ARG cc_start: 0.8243 (ttp-170) cc_final: 0.7778 (mtp180)
REVERT: C   80 ASP cc_start: 0.8922 (t0) cc_final: 0.8633 (t0)
REVERT: C   99 ILE cc_start: 0.8866 (mt) cc_final: 0.8537 (mp)
REVERT: D   44 ARG cc_start: 0.8390 (ttm110) cc_final: 0.8161 (ttt90)
REVERT: D  103 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8401 (tt)
  outliers start: 41
  outliers final: 15
  residues processed: 172
  average time/residue: 1.3503
  time to fit residues: 249.5288
Evaluate side-chains
  148 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
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  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   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:    0.9980
   chunk 63 optimal weight:    9.9990
   chunk 59 optimal weight:    3.9990
   chunk 121 optimal weight:    0.0980
   chunk 100 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0170
   chunk 30 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.4818

-------------------------------------------------------------------------------
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 = 0.3307 r_free = 0.3307 target = 0.110921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.083689 restraints weight = 14763.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 2.13
r_work: 0.2772 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2641 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8798
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10760  Z= 0.139
  Angle     :  0.514   6.645  14569  Z= 0.262
  Chirality :  0.039   0.171   1662
  Planarity :  0.004   0.054   1827
  Dihedral  :  4.370  57.046   1523
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.14 %
    Favored  : 76.82 %
  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:  0.71 (0.24), residues: 1308
  helix:  1.88 (0.20), residues: 678
  sheet:  0.20 (0.38), residues: 172
  loop : -1.63 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 584 
 HIS   0.004   0.001   HIS B 531 
 PHE   0.011   0.001   PHE A 502 
 TYR   0.011   0.001   TYR A 487 
 ARG   0.003   0.000   ARG A 550 

*********************** 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
  178 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7844 (mpt180) cc_final: 0.7461 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8231 (mm-30)
REVERT: A  324 MET cc_start: 0.8409 (tmm) cc_final: 0.8033 (tmt)
REVERT: A  343 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8172 (tm-30)
REVERT: A  383 LYS cc_start: 0.7444 (mppt) cc_final: 0.7043 (mmtm)
REVERT: A  400 LEU cc_start: 0.8868 (tp) cc_final: 0.8553 (mt)
REVERT: A  454 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.7849 (mm-40)
REVERT: A  536 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8499 (tp)
REVERT: B   89 GLN cc_start: 0.8877 (mt0) cc_final: 0.8389 (mt0)
REVERT: B   94 LYS cc_start: 0.8955 (tttm) cc_final: 0.8673 (tptm)
REVERT: B  142 GLN cc_start: 0.8183 (pp30) cc_final: 0.7770 (tm-30)
REVERT: B  253 LYS cc_start: 0.9062 (mttt) cc_final: 0.8850 (mtmt)
REVERT: B  404 ARG cc_start: 0.8686 (mtp-110) cc_final: 0.8282 (mtm110)
REVERT: B  505 CYS cc_start: 0.9098 (t) cc_final: 0.8565 (m)
REVERT: B  517 TRP cc_start: 0.7898 (m100) cc_final: 0.7426 (t60)
REVERT: C   38 ARG cc_start: 0.8165 (ttp-170) cc_final: 0.7779 (mtp180)
REVERT: C   80 ASP cc_start: 0.8808 (t0) cc_final: 0.8527 (t0)
REVERT: C   90 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8050 (mm)
REVERT: C   99 ILE cc_start: 0.8853 (mt) cc_final: 0.8538 (mp)
REVERT: D   44 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8066 (ttt90)
  outliers start: 35
  outliers final: 15
  residues processed: 166
  average time/residue: 1.3490
  time to fit residues: 240.1177
Evaluate side-chains
  150 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LEU
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  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   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 D residue   94 THR
Chi-restraints excluded: chain D residue   95 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 120 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 121 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.106414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.079008 restraints weight = 14756.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 2.12
r_work: 0.2683 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2548 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8880
moved from start:          0.4094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10760  Z= 0.210
  Angle     :  0.567   7.215  14569  Z= 0.289
  Chirality :  0.041   0.197   1662
  Planarity :  0.004   0.053   1827
  Dihedral  :  4.446  54.587   1522
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 20.23 %
    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:  0.77 (0.24), residues: 1308
  helix:  1.79 (0.20), residues: 686
  sheet:  0.28 (0.36), residues: 184
  loop : -1.50 (0.30), residues: 438

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   0.016   0.001   PHE B 493 
 TYR   0.012   0.001   TYR A 487 
 ARG   0.006   0.000   ARG A 550 

*********************** 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
  174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 135
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7878 (mpt180) cc_final: 0.7454 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8343 (mm-30)
REVERT: A  343 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8133 (tm-30)
REVERT: A  383 LYS cc_start: 0.7593 (mppt) cc_final: 0.7340 (mmtm)
REVERT: A  400 LEU cc_start: 0.8880 (tp) cc_final: 0.8627 (mt)
REVERT: A  454 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7898 (mm-40)
REVERT: A  536 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8538 (tp)
REVERT: B   89 GLN cc_start: 0.8930 (mt0) cc_final: 0.8506 (mt0)
REVERT: B   94 LYS cc_start: 0.9064 (tttm) cc_final: 0.8812 (tptm)
REVERT: B  142 GLN cc_start: 0.8224 (pp30) cc_final: 0.7861 (tm-30)
REVERT: B  214 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8136 (p)
REVERT: B  253 LYS cc_start: 0.9132 (mttt) cc_final: 0.8917 (mtmt)
REVERT: B  404 ARG cc_start: 0.8757 (mtp-110) cc_final: 0.8346 (mtm110)
REVERT: B  505 CYS cc_start: 0.9155 (t) cc_final: 0.8727 (m)
REVERT: B  517 TRP cc_start: 0.7949 (m100) cc_final: 0.7485 (t60)
REVERT: C   80 ASP cc_start: 0.8927 (t0) cc_final: 0.8616 (t0)
REVERT: D   44 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8152 (ttm110)
  outliers start: 39
  outliers final: 21
  residues processed: 164
  average time/residue: 1.2835
  time to fit residues: 226.5074
Evaluate side-chains
  151 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
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  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  210 VAL
Chi-restraints excluded: chain B residue  214 SER
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   96 SER
Chi-restraints excluded: chain C residue  133 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 119 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 118 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.102499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.075177 restraints weight = 14925.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2745 rms_B_bonded: 2.09
r_work: 0.2612 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2478 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10760  Z= 0.344
  Angle     :  0.651   7.533  14569  Z= 0.335
  Chirality :  0.045   0.203   1662
  Planarity :  0.004   0.055   1827
  Dihedral  :  4.735  50.046   1522
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.20 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.88 %
    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:  0.56 (0.24), residues: 1308
  helix:  1.60 (0.20), residues: 680
  sheet:  0.14 (0.36), residues: 194
  loop : -1.51 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 584 
 HIS   0.006   0.001   HIS B 531 
 PHE   0.020   0.002   PHE B 595 
 TYR   0.016   0.002   TYR A 581 
 ARG   0.007   0.001   ARG A 550 

*********************** 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
  177 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 132
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7931 (mpt180) cc_final: 0.7507 (mpt-90)
REVERT: A  133 LEU cc_start: 0.9394 (mm) cc_final: 0.9193 (mt)
REVERT: A  169 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8362 (mm-30)
REVERT: A  343 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8177 (tm-30)
REVERT: A  383 LYS cc_start: 0.7816 (mppt) cc_final: 0.7348 (mmtm)
REVERT: A  387 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8306 (mp)
REVERT: A  400 LEU cc_start: 0.8970 (tp) cc_final: 0.8752 (mt)
REVERT: A  454 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.7797 (mm-40)
REVERT: A  536 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8565 (tp)
REVERT: B   89 GLN cc_start: 0.8858 (mt0) cc_final: 0.8425 (mt0)
REVERT: B   94 LYS cc_start: 0.9150 (tttm) cc_final: 0.8840 (tptm)
REVERT: B  142 GLN cc_start: 0.8256 (pp30) cc_final: 0.7912 (tm-30)
REVERT: B  404 ARG cc_start: 0.8772 (mtp-110) cc_final: 0.8391 (mtm110)
REVERT: B  429 MET cc_start: 0.8653 (ptm) cc_final: 0.7945 (mmt)
REVERT: B  505 CYS cc_start: 0.9232 (t) cc_final: 0.8908 (m)
REVERT: B  517 TRP cc_start: 0.7910 (m100) cc_final: 0.7511 (t60)
REVERT: C   80 ASP cc_start: 0.8903 (t0) cc_final: 0.8632 (t0)
REVERT: C   95 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8204 (m)
REVERT: C   99 ILE cc_start: 0.8898 (mt) cc_final: 0.8584 (mp)
REVERT: D   44 ARG cc_start: 0.8487 (ttm110) cc_final: 0.8233 (ttm110)
  outliers start: 45
  outliers final: 28
  residues processed: 167
  average time/residue: 1.3264
  time to fit residues: 237.9031
Evaluate side-chains
  158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
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  171 VAL
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  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   26 ARG
Chi-restraints excluded: chain B residue  113 SER
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  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   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   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  109 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 130 optimal weight:    2.9990
   chunk 120 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3247 r_free = 0.3247 target = 0.106802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.079762 restraints weight = 15078.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 2.12
r_work: 0.2695 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2563 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10760  Z= 0.168
  Angle     :  0.562   9.723  14569  Z= 0.285
  Chirality :  0.041   0.190   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.478  52.294   1522
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 21.01 %
    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:  0.92 (0.24), residues: 1308
  helix:  1.96 (0.20), residues: 673
  sheet:  0.23 (0.36), residues: 202
  loop : -1.42 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 
 PHE   0.013   0.001   PHE B 493 
 TYR   0.012   0.001   TYR A 487 
 ARG   0.002   0.000   ARG A 550 

*********************** 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
  171 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7894 (mpt180) cc_final: 0.7466 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8357 (mm-30)
REVERT: A  324 MET cc_start: 0.8414 (tmm) cc_final: 0.8130 (tmm)
REVERT: A  343 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8139 (tm-30)
REVERT: A  383 LYS cc_start: 0.7603 (mppt) cc_final: 0.7181 (mmtm)
REVERT: A  387 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8224 (mp)
REVERT: A  400 LEU cc_start: 0.8857 (tp) cc_final: 0.8613 (mt)
REVERT: A  454 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.7917 (mm-40)
REVERT: A  536 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8504 (tp)
REVERT: B   89 GLN cc_start: 0.8890 (mt0) cc_final: 0.8473 (mt0)
REVERT: B   94 LYS cc_start: 0.9064 (tttm) cc_final: 0.8808 (tptm)
REVERT: B  142 GLN cc_start: 0.8224 (pp30) cc_final: 0.7873 (tm-30)
REVERT: B  214 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.8094 (p)
REVERT: B  253 LYS cc_start: 0.9102 (mttt) cc_final: 0.8885 (mtmt)
REVERT: B  404 ARG cc_start: 0.8727 (mtp-110) cc_final: 0.8295 (mtm110)
REVERT: B  429 MET cc_start: 0.8475 (ptm) cc_final: 0.7798 (mmt)
REVERT: B  505 CYS cc_start: 0.9158 (t) cc_final: 0.8719 (m)
REVERT: B  517 TRP cc_start: 0.7887 (m100) cc_final: 0.7467 (t60)
REVERT: C   38 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7626 (mtp180)
REVERT: C   80 ASP cc_start: 0.8910 (t0) cc_final: 0.8618 (t0)
REVERT: D   44 ARG cc_start: 0.8422 (ttm110) cc_final: 0.8165 (ttm110)
  outliers start: 36
  outliers final: 19
  residues processed: 163
  average time/residue: 1.4178
  time to fit residues: 247.6707
Evaluate side-chains
  157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
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  613 CYS
Chi-restraints excluded: chain B residue   26 ARG
Chi-restraints excluded: chain B residue  214 SER
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   84 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  109 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:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3214 r_free = 0.3214 target = 0.104522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.077495 restraints weight = 14709.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 2.07
r_work: 0.2652 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2518 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10760  Z= 0.240
  Angle     :  0.594   8.115  14569  Z= 0.305
  Chirality :  0.042   0.184   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.556  51.337   1522
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 20.57 %
    Favored  : 75.95 %
  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:  0.92 (0.24), residues: 1308
  helix:  1.88 (0.20), residues: 678
  sheet:  0.32 (0.35), residues: 202
  loop : -1.36 (0.31), residues: 428

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   0.017   0.001   PHE B 493 
 TYR   0.012   0.001   TYR A 487 
 ARG   0.002   0.000   ARG A 550 

*********************** 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  : 1.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7887 (mpt180) cc_final: 0.7536 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8420 (mm-30)
REVERT: A  324 MET cc_start: 0.8421 (tmm) cc_final: 0.8134 (tmm)
REVERT: A  343 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8146 (tm-30)
REVERT: A  383 LYS cc_start: 0.7713 (mppt) cc_final: 0.7288 (mmtm)
REVERT: A  387 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8321 (mp)
REVERT: A  400 LEU cc_start: 0.8941 (tp) cc_final: 0.8701 (mt)
REVERT: A  454 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7887 (mm-40)
REVERT: A  536 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8539 (tp)
REVERT: B   89 GLN cc_start: 0.8894 (mt0) cc_final: 0.8481 (mt0)
REVERT: B   94 LYS cc_start: 0.9118 (tttm) cc_final: 0.8837 (tptm)
REVERT: B  142 GLN cc_start: 0.8247 (pp30) cc_final: 0.7914 (tm-30)
REVERT: B  214 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8168 (p)
REVERT: B  404 ARG cc_start: 0.8764 (mtp-110) cc_final: 0.8375 (mtm110)
REVERT: B  429 MET cc_start: 0.8490 (ptm) cc_final: 0.7856 (mmt)
REVERT: B  505 CYS cc_start: 0.9195 (t) cc_final: 0.8796 (m)
REVERT: B  517 TRP cc_start: 0.7895 (m100) cc_final: 0.7509 (t60)
REVERT: C   38 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7588 (mtp180)
REVERT: C   80 ASP cc_start: 0.8900 (t0) cc_final: 0.8615 (t0)
REVERT: D   44 ARG cc_start: 0.8467 (ttm110) cc_final: 0.8246 (ttt180)
  outliers start: 40
  outliers final: 26
  residues processed: 159
  average time/residue: 1.3131
  time to fit residues: 224.6716
Evaluate side-chains
  157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
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  171 VAL
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  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  214 SER
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   84 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  103 GLN
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  109 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0170
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.2022

-------------------------------------------------------------------------------
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 = 0.3229 r_free = 0.3229 target = 0.105475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.078341 restraints weight = 14875.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 2.09
r_work: 0.2675 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2541 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8907
moved from start:          0.4467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10760  Z= 0.220
  Angle     :  0.595  11.400  14569  Z= 0.302
  Chirality :  0.042   0.182   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.530  50.990   1522
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.18 %
    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:  1.00 (0.24), residues: 1308
  helix:  1.95 (0.20), residues: 674
  sheet:  0.42 (0.35), residues: 202
  loop : -1.33 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 584 
 HIS   0.005   0.001   HIS B 531 
 PHE   0.016   0.001   PHE B 493 
 TYR   0.012   0.001   TYR A 487 
 ARG   0.002   0.000   ARG A 550 

*********************** 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
  163 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7905 (mpt180) cc_final: 0.7532 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8410 (mm-30)
REVERT: A  324 MET cc_start: 0.8393 (tmm) cc_final: 0.8104 (tmm)
REVERT: A  383 LYS cc_start: 0.7695 (mppt) cc_final: 0.7278 (mmtm)
REVERT: A  387 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8275 (mp)
REVERT: A  400 LEU cc_start: 0.8942 (tp) cc_final: 0.8706 (mt)
REVERT: A  454 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7881 (mm-40)
REVERT: A  536 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8556 (tp)
REVERT: B   89 GLN cc_start: 0.8896 (mt0) cc_final: 0.8485 (mt0)
REVERT: B   94 LYS cc_start: 0.9093 (tttm) cc_final: 0.8843 (tptm)
REVERT: B  121 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6863 (mpt180)
REVERT: B  142 GLN cc_start: 0.8247 (pp30) cc_final: 0.7916 (tm-30)
REVERT: B  214 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8144 (p)
REVERT: B  404 ARG cc_start: 0.8761 (mtp-110) cc_final: 0.8337 (mtm110)
REVERT: B  429 MET cc_start: 0.8513 (ptm) cc_final: 0.7881 (mmt)
REVERT: B  505 CYS cc_start: 0.9192 (t) cc_final: 0.8782 (m)
REVERT: B  517 TRP cc_start: 0.7886 (m100) cc_final: 0.7509 (t60)
REVERT: C   38 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7611 (mtp180)
REVERT: C   80 ASP cc_start: 0.8941 (t0) cc_final: 0.8675 (t0)
REVERT: D   44 ARG cc_start: 0.8470 (ttm110) cc_final: 0.8253 (ttt180)
  outliers start: 34
  outliers final: 26
  residues processed: 158
  average time/residue: 1.3103
  time to fit residues: 222.9287
Evaluate side-chains
  158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 127
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  339 LEU
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  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  214 SER
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   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  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 127 optimal weight:    0.0030
   chunk 10 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 96 optimal weight:    0.2980
   chunk 11 optimal weight:    0.7980
   chunk 126 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.6192

-------------------------------------------------------------------------------
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 = 0.3274 r_free = 0.3274 target = 0.108580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.081710 restraints weight = 14757.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 2.08
r_work: 0.2729 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2595 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10760  Z= 0.157
  Angle     :  0.558  10.426  14569  Z= 0.283
  Chirality :  0.040   0.176   1662
  Planarity :  0.004   0.056   1827
  Dihedral  :  4.377  52.153   1522
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.09 %
    Favored  : 75.95 %
  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:  1.21 (0.24), residues: 1308
  helix:  2.14 (0.20), residues: 677
  sheet:  0.73 (0.37), residues: 192
  loop : -1.37 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 584 
 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 A 344 

********************** 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
  173 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.7891 (mpt180) cc_final: 0.7504 (mpt-90)
REVERT: A  169 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8438 (mm-30)
REVERT: A  324 MET cc_start: 0.8397 (tmm) cc_final: 0.8107 (tmm)
REVERT: A  383 LYS cc_start: 0.7605 (mppt) cc_final: 0.7203 (mmtm)
REVERT: A  387 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8243 (mp)
REVERT: A  400 LEU cc_start: 0.8884 (tp) cc_final: 0.8608 (mt)
REVERT: A  454 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.7905 (mm-40)
REVERT: A  536 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8554 (tp)
REVERT: B   89 GLN cc_start: 0.8937 (mt0) cc_final: 0.8491 (mt0)
REVERT: B   94 LYS cc_start: 0.9000 (tttm) cc_final: 0.8787 (tptm)
REVERT: B  121 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6873 (mpt180)
REVERT: B  142 GLN cc_start: 0.8225 (pp30) cc_final: 0.7900 (tm-30)
REVERT: B  404 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8307 (mtm110)
REVERT: B  429 MET cc_start: 0.8454 (ptm) cc_final: 0.7856 (mmt)
REVERT: B  505 CYS cc_start: 0.9132 (t) cc_final: 0.8647 (m)
REVERT: B  517 TRP cc_start: 0.7891 (m100) cc_final: 0.7446 (t60)
REVERT: C   38 ARG cc_start: 0.8124 (ttp-170) cc_final: 0.7661 (mtp180)
REVERT: C   80 ASP cc_start: 0.8919 (t0) cc_final: 0.8642 (t0)
  outliers start: 34
  outliers final: 26
  residues processed: 165
  average time/residue: 1.3686
  time to fit residues: 241.8751
Evaluate side-chains
  161 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
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  339 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  387 ILE
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   90 ILE
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  103 GLN
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0270
   chunk 122 optimal weight:    7.9990
   chunk 111 optimal weight:    0.0070
   chunk 60 optimal weight:    2.9990
   chunk 128 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.5860

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.104621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.077367 restraints weight = 14740.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.2788 rms_B_bonded: 2.07
r_work: 0.2657 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2523 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8922
moved from start:          0.4554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10760  Z= 0.265
  Angle     :  0.617   9.714  14569  Z= 0.314
  Chirality :  0.043   0.173   1662
  Planarity :  0.004   0.055   1827
  Dihedral  :  4.553  50.626   1522
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.44 %
    Favored  : 75.69 %
  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:  1.06 (0.24), residues: 1308
  helix:  1.94 (0.20), residues: 679
  sheet:  0.59 (0.37), residues: 194
  loop : -1.27 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 584 
 HIS   0.006   0.001   HIS B 531 
 PHE   0.018   0.002   PHE B 493 
 TYR   0.012   0.001   TYR A 487 
 ARG   0.003   0.000   ARG A 550 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7648.87 seconds
wall clock time: 135 minutes 31.90 seconds (8131.90 seconds total)