Starting phenix.real_space_refine
on Thu Mar 13 11:19:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y94_39069/03_2025/8y94_39069.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y94_39069/03_2025/8y94_39069.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y94_39069/03_2025/8y94_39069.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y94_39069/03_2025/8y94_39069.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y94_39069/03_2025/8y94_39069.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y94_39069/03_2025/8y94_39069.cif"
  }
  resolution = 3.29
  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=   0.005 sd=   0.047
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      40      5.16       5
     C    6052      2.51       5
     N    1412      2.21       5
     O    1528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9032
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "C"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
  Time building chain proxies: 5.59, per 1000 atoms: 0.62
  Number of scatterers: 9032
  At special positions: 0
  Unit cell: (85.41, 116.07, 91.98, 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      40     16.00
     O    1528      8.00
     N    1412      7.00
     C    6052      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.31
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 0 sheets defined
      77.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 72
      removed outlier: 3.692A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 78
      removed outlier: 5.013A  pdb=" N   LEU A  76 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA A  77 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 89
    Processing helix  chain 'A' and resid 94 through 121
      Proline residue:  A 108  - end of helix
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 167
      removed outlier: 3.900A  pdb=" N   GLY A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TYR A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 204
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 220 through 224
      removed outlier: 3.570A  pdb=" N   GLU A 223 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 253
    Processing helix  chain 'A' and resid 255 through 267
      removed outlier: 3.649A  pdb=" N   SER A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE A 265 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 284
      removed outlier: 4.079A  pdb=" N   PHE A 272 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.859A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 302
      removed outlier: 3.758A  pdb=" N   LEU A 302 " --> pdb=" O   PHE A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 320
      removed outlier: 4.210A  pdb=" N   GLN A 314 " --> pdb=" O   ASP A 310 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A 316 " --> pdb=" O   ALA A 312 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 332
      removed outlier: 3.898A  pdb=" N   TYR A 332 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 372
    Processing helix  chain 'A' and resid 385 through 398
      removed outlier: 3.939A  pdb=" N   TYR A 391 " --> pdb=" O   VAL A 387 " (cutoff:3.500A)
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.623A  pdb=" N   TRP A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER A 419 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 441
      removed outlier: 4.008A  pdb=" N   ARG A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   HIS A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 436 through 441'
    Processing helix  chain 'A' and resid 441 through 457
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 3.508A  pdb=" N   THR A 462 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 494
      removed outlier: 4.045A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 509
      removed outlier: 3.501A  pdb=" N   PHE A 501 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
      removed outlier: 3.788A  pdb=" N   ALA A 527 " --> pdb=" O   PHE A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.776A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   TRP A 556 " --> pdb=" O   PRO A 552 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   MET A 566 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 579
    Processing helix  chain 'A' and resid 583 through 593
    Processing helix  chain 'A' and resid 597 through 604
      removed outlier: 3.767A  pdb=" N   VAL A 601 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN A 603 " --> pdb=" O   HIS A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 4.014A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 72
      removed outlier: 3.690A  pdb=" N   PHE C  65 " --> pdb=" O   LYS C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 78
      removed outlier: 5.018A  pdb=" N   LEU C  76 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA C  77 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 89
    Processing helix  chain 'C' and resid 94 through 121
      Proline residue:  C 108  - end of helix
    Processing helix  chain 'C' and resid 131 through 133
      No H-bonds generated for 'chain 'C' and resid 131 through 133'
    Processing helix  chain 'C' and resid 134 through 167
      removed outlier: 3.894A  pdb=" N   GLY C 138 " --> pdb=" O   PHE C 134 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR C 139 " --> pdb=" O   LYS C 135 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE C 142 " --> pdb=" O   GLY C 138 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA C 145 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR C 151 " --> pdb=" O   TYR C 147 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   VAL C 154 " --> pdb=" O   PHE C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 204
    Processing helix  chain 'C' and resid 208 through 217
    Processing helix  chain 'C' and resid 220 through 224
      removed outlier: 3.570A  pdb=" N   GLU C 223 " --> pdb=" O   HIS C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 253
    Processing helix  chain 'C' and resid 255 through 267
      removed outlier: 3.652A  pdb=" N   SER C 259 " --> pdb=" O   GLY C 255 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ILE C 265 " --> pdb=" O   LYS C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 284
      removed outlier: 4.086A  pdb=" N   PHE C 272 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 295
      removed outlier: 3.860A  pdb=" N   GLY C 290 " --> pdb=" O   GLY C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 302
      removed outlier: 3.758A  pdb=" N   LEU C 302 " --> pdb=" O   PHE C 299 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 310 through 320
      removed outlier: 4.209A  pdb=" N   GLN C 314 " --> pdb=" O   ASP C 310 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE C 315 " --> pdb=" O   ALA C 311 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE C 316 " --> pdb=" O   ALA C 312 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY C 320 " --> pdb=" O   PHE C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 324 through 332
      removed outlier: 3.908A  pdb=" N   TYR C 332 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 372
    Processing helix  chain 'C' and resid 385 through 398
      removed outlier: 3.939A  pdb=" N   TYR C 391 " --> pdb=" O   VAL C 387 " (cutoff:3.500A)
      Proline residue:  C 392  - end of helix
    Processing helix  chain 'C' and resid 400 through 435
      removed outlier: 3.623A  pdb=" N   TRP C 404 " --> pdb=" O   GLY C 400 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER C 419 " --> pdb=" O   LEU C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 436 through 441
      removed outlier: 4.005A  pdb=" N   ARG C 440 " --> pdb=" O   GLN C 436 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   HIS C 441 " --> pdb=" O   VAL C 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 436 through 441'
    Processing helix  chain 'C' and resid 441 through 457
    Processing helix  chain 'C' and resid 457 through 462
      removed outlier: 3.507A  pdb=" N   THR C 462 " --> pdb=" O   LEU C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 464 through 494
      removed outlier: 4.045A  pdb=" N   VAL C 468 " --> pdb=" O   GLY C 464 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 497 through 509
      removed outlier: 3.501A  pdb=" N   PHE C 501 " --> pdb=" O   GLY C 497 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 514 through 523
    Processing helix  chain 'C' and resid 523 through 539
      removed outlier: 3.789A  pdb=" N   ALA C 527 " --> pdb=" O   PHE C 523 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 551 through 567
      removed outlier: 3.775A  pdb=" N   ASN C 555 " --> pdb=" O   PRO C 551 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TRP C 556 " --> pdb=" O   PRO C 552 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER C 565 " --> pdb=" O   ILE C 561 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   MET C 566 " --> pdb=" O   ALA C 562 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 567 through 579
    Processing helix  chain 'C' and resid 583 through 593
    Processing helix  chain 'C' and resid 597 through 604
      removed outlier: 3.761A  pdb=" N   VAL C 601 " --> pdb=" O   GLU C 597 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA C 602 " --> pdb=" O   HIS C 598 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLN C 603 " --> pdb=" O   HIS C 599 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 610 through 615
      removed outlier: 4.013A  pdb=" N   TRP C 614 " --> pdb=" O   GLN C 610 " (cutoff:3.500A)

    550 hydrogen bonds defined for protein.
    1620 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: 2.69

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2658
        1.34 -     1.46: 2276
        1.46 -     1.58: 4330
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 9326
  Sorted by residual:
  bond pdb=" C   LEU C 269 "
       pdb=" N   PRO C 270 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.013 1.28e-02 6.10e+03 1.10e+00
  bond pdb=" C   VAL A 379 "
       pdb=" O   VAL A 379 "
    ideal  model  delta    sigma   weight residual
    1.241  1.231  0.010 1.03e-02 9.43e+03 9.55e-01
  bond pdb=" C   ILE C 549 "
       pdb=" N   PHE C 550 "
    ideal  model  delta    sigma   weight residual
    1.331  1.359 -0.028 3.12e-02 1.03e+03 8.29e-01
  bond pdb=" C   ILE A 549 "
       pdb=" N   PHE A 550 "
    ideal  model  delta    sigma   weight residual
    1.331  1.359 -0.028 3.12e-02 1.03e+03 8.24e-01
  bond pdb=" C   LEU A 269 "
       pdb=" N   PRO A 270 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.012 1.28e-02 6.10e+03 8.16e-01
  ... (remaining 9321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 12326
        1.14 -     2.28: 325
        2.28 -     3.42: 59
        3.42 -     4.55: 4
        4.55 -     5.69: 12
  Bond angle restraints: 12726
  Sorted by residual:
  angle pdb=" N   ILE C 265 "
        pdb=" CA  ILE C 265 "
        pdb=" C   ILE C 265 "
      ideal   model   delta    sigma   weight residual
     111.90  109.56    2.34 8.10e-01 1.52e+00 8.34e+00
  angle pdb=" N   ILE A 265 "
        pdb=" CA  ILE A 265 "
        pdb=" C   ILE A 265 "
      ideal   model   delta    sigma   weight residual
     111.90  109.57    2.33 8.10e-01 1.52e+00 8.25e+00
  angle pdb=" C   PHE A 388 "
        pdb=" N   ILE A 389 "
        pdb=" CA  ILE A 389 "
      ideal   model   delta    sigma   weight residual
     123.08  120.24    2.84 1.01e+00 9.80e-01 7.90e+00
  angle pdb=" C   PHE C 388 "
        pdb=" N   ILE C 389 "
        pdb=" CA  ILE C 389 "
      ideal   model   delta    sigma   weight residual
     123.08  120.29    2.79 1.01e+00 9.80e-01 7.63e+00
  angle pdb=" N   GLY A 231 "
        pdb=" CA  GLY A 231 "
        pdb=" C   GLY A 231 "
      ideal   model   delta    sigma   weight residual
     111.21  113.74   -2.53 1.04e+00 9.25e-01 5.91e+00
  ... (remaining 12721 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.99: 4833
       11.99 -    23.98: 255
       23.98 -    35.97: 85
       35.97 -    47.96: 32
       47.96 -    59.95: 9
  Dihedral angle restraints: 5214
    sinusoidal: 1950
      harmonic: 3264
  Sorted by residual:
  dihedral pdb=" N   PHE A 359 "
           pdb=" CA  PHE A 359 "
           pdb=" CB  PHE A 359 "
           pdb=" CG  PHE A 359 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.95   59.95     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   PHE C 359 "
           pdb=" CA  PHE C 359 "
           pdb=" CB  PHE C 359 "
           pdb=" CG  PHE C 359 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.94   59.94     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   LEU A 190 "
           pdb=" CA  LEU A 190 "
           pdb=" CB  LEU A 190 "
           pdb=" CG  LEU A 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.24   57.24     3      1.50e+01 4.44e-03 9.43e+00
  ... (remaining 5211 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 796
       0.022 -    0.045: 360
       0.045 -    0.067: 205
       0.067 -    0.090: 36
       0.090 -    0.112: 21
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CA  PRO C 270 "
            pdb=" N   PRO C 270 "
            pdb=" C   PRO C 270 "
            pdb=" CB  PRO C 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.15e-01
  chirality pdb=" CA  ILE A 606 "
            pdb=" N   ILE A 606 "
            pdb=" C   ILE A 606 "
            pdb=" CB  ILE A 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.10e-01
  chirality pdb=" CA  ILE C 606 "
            pdb=" N   ILE C 606 "
            pdb=" C   ILE C 606 "
            pdb=" CB  ILE C 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.02e-01
  ... (remaining 1415 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 103 "    0.006 2.00e-02 2.50e+03   1.11e-02 1.24e+00
        pdb=" C   ILE C 103 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE C 103 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ILE C 104 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 103 "   -0.006 2.00e-02 2.50e+03   1.11e-02 1.24e+00
        pdb=" C   ILE A 103 "    0.019 2.00e-02 2.50e+03
        pdb=" O   ILE A 103 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ILE A 104 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 477 "    0.005 2.00e-02 2.50e+03   1.09e-02 1.20e+00
        pdb=" C   ALA C 477 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ALA C 477 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLY C 478 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2669
        2.82 -     3.34: 9057
        3.34 -     3.86: 15119
        3.86 -     4.38: 17356
        4.38 -     4.90: 29697
  Nonbonded interactions: 73898
  Sorted by model distance:
  nonbonded pdb=" O   LYS A  88 "
            pdb=" NH2 ARG A 301 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   LYS C  88 "
            pdb=" NH2 ARG C 301 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   SER C 251 "
            pdb=" OG1 THR C 258 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   SER A 251 "
            pdb=" OG1 THR A 258 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG1 THR C 462 "
            pdb=" N   LYS C 463 "
     model   vdw
     2.361 3.120
  ... (remaining 73893 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}

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:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.820
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6284
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      :  0.002   0.028   9326  Z= 0.110
  Angle     :  0.463   5.693  12726  Z= 0.278
  Chirality :  0.033   0.112   1418
  Planarity :  0.003   0.026   1552
  Dihedral  :  9.274  59.949   3138
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  :  6.09 %
    Favored  : 90.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.22), residues: 1126
  helix: -0.56 (0.18), residues: 732
  sheet:  None (None), residues: 0
  loop : -1.63 (0.27), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP C 235 
 HIS   0.002   0.000   HIS A 296 
 PHE   0.005   0.001   PHE A 362 
 TYR   0.008   0.001   TYR A 151 
 ARG   0.002   0.000   ARG C 607 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 352
  time to evaluate  : 1.209 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7176 (mt-10)
REVERT: A  126 THR cc_start: 0.8786 (p) cc_final: 0.8563 (p)
REVERT: A  173 TRP cc_start: 0.7971 (OUTLIER) cc_final: 0.7658 (p90)
REVERT: A  278 LEU cc_start: 0.6509 (mt) cc_final: 0.6248 (mt)
REVERT: A  332 TYR cc_start: 0.8246 (m-80) cc_final: 0.8016 (m-10)
REVERT: A  337 ASN cc_start: 0.6205 (m110) cc_final: 0.5223 (m110)
REVERT: A  480 SER cc_start: 0.8365 (m) cc_final: 0.8164 (t)
REVERT: A  559 TRP cc_start: 0.6645 (m100) cc_final: 0.5925 (t60)
REVERT: C  126 THR cc_start: 0.8757 (p) cc_final: 0.8548 (p)
REVERT: C  173 TRP cc_start: 0.7888 (OUTLIER) cc_final: 0.7582 (p90)
REVERT: C  425 GLU cc_start: 0.7237 (tt0) cc_final: 0.6953 (tt0)
REVERT: C  453 THR cc_start: 0.5477 (m) cc_final: 0.4734 (p)
REVERT: C  480 SER cc_start: 0.8374 (m) cc_final: 0.8168 (t)
REVERT: C  559 TRP cc_start: 0.6649 (m100) cc_final: 0.5894 (t60)
  outliers start: 30
  outliers final: 9
  residues processed: 372
  average time/residue: 0.2132
  time to fit residues: 110.9684
Evaluate side-chains
  229 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 218
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  173 TRP
Chi-restraints excluded: chain C residue  295 LEU
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  390 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   chunk 47 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   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  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 153 ASN
A 220 HIS
A 236 GLN
A 280 HIS
A 314 GLN
A 555 ASN
C 153 ASN
C 236 GLN
C 280 HIS
C 314 GLN
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 372 HIS
C 555 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.189908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.147957 restraints weight = 12736.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 3.07
r_work: 0.3821 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9326  Z= 0.289
  Angle     :  0.665   9.869  12726  Z= 0.339
  Chirality :  0.043   0.183   1418
  Planarity :  0.005   0.036   1552
  Dihedral  :  5.879  58.735   1238
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 16.60 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.25), residues: 1126
  helix:  0.71 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.10 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 128 
 HIS   0.013   0.002   HIS C 222 
 PHE   0.035   0.002   PHE C  82 
 TYR   0.019   0.002   TYR C 391 
 ARG   0.006   0.001   ARG A 440 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 225
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.8328 (tpp80)
REVERT: A  131 CYS cc_start: 0.8647 (t) cc_final: 0.8247 (m)
REVERT: A  246 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7027 (mp)
REVERT: A  258 THR cc_start: 0.7678 (p) cc_final: 0.7466 (p)
REVERT: A  261 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7937 (mmmt)
REVERT: A  278 LEU cc_start: 0.6823 (mt) cc_final: 0.6472 (mt)
REVERT: A  280 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.6526 (t-170)
REVERT: A  597 GLU cc_start: 0.8663 (mp0) cc_final: 0.8128 (mp0)
REVERT: A  605 ASP cc_start: 0.7966 (m-30) cc_final: 0.7692 (m-30)
REVERT: A  610 GLN cc_start: 0.8134 (mp10) cc_final: 0.7921 (mp10)
REVERT: C  121 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8291 (tpp80)
REVERT: C  131 CYS cc_start: 0.8655 (t) cc_final: 0.8200 (m)
REVERT: C  246 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7048 (mp)
REVERT: C  258 THR cc_start: 0.7635 (p) cc_final: 0.7429 (p)
REVERT: C  261 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7927 (mmmt)
REVERT: C  334 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8170 (ptmm)
REVERT: C  515 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7491 (mt)
REVERT: C  597 GLU cc_start: 0.8661 (mp0) cc_final: 0.8055 (mp0)
  outliers start: 51
  outliers final: 28
  residues processed: 258
  average time/residue: 0.2196
  time to fit residues: 80.3317
Evaluate side-chains
  227 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 194
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  280 HIS
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  490 ILE
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  173 TRP
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  295 LEU
Chi-restraints excluded: chain C residue  334 LYS
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  472 LEU
Chi-restraints excluded: chain C residue  490 ILE
Chi-restraints excluded: chain C residue  515 LEU
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  557 VAL
Chi-restraints excluded: chain C residue  593 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS
C 280 HIS
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 HIS
C 436 GLN
C 599 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.190815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.150791 restraints weight = 13031.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 3.13
r_work: 0.3852 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9326  Z= 0.165
  Angle     :  0.542   9.436  12726  Z= 0.273
  Chirality :  0.038   0.176   1418
  Planarity :  0.004   0.037   1552
  Dihedral  :  5.638  56.853   1238
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 17.02 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.25), residues: 1126
  helix:  1.04 (0.19), residues: 756
  sheet:  None (None), residues: 0
  loop : -0.78 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 264 
 HIS   0.010   0.001   HIS A 370 
 PHE   0.032   0.001   PHE A  82 
 TYR   0.015   0.001   TYR C 548 
 ARG   0.008   0.001   ARG A 301 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 203
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.6886 (mp)
REVERT: A  274 LEU cc_start: 0.9127 (mp) cc_final: 0.8888 (mp)
REVERT: A  315 ILE cc_start: 0.5646 (OUTLIER) cc_final: 0.5436 (mp)
REVERT: A  597 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8026 (mp0)
REVERT: A  605 ASP cc_start: 0.7927 (m-30) cc_final: 0.7692 (m-30)
REVERT: A  610 GLN cc_start: 0.8192 (mp10) cc_final: 0.7964 (mp10)
REVERT: C  131 CYS cc_start: 0.8594 (t) cc_final: 0.8390 (m)
REVERT: C  246 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.6935 (mp)
REVERT: C  315 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.5372 (mp)
REVERT: C  597 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8016 (mp0)
  outliers start: 44
  outliers final: 30
  residues processed: 237
  average time/residue: 0.1888
  time to fit residues: 64.2178
Evaluate side-chains
  217 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 181
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   81 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  168 THR
Chi-restraints excluded: chain C residue  173 TRP
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  277 LEU
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  334 LYS
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  584 LEU
Chi-restraints excluded: chain C residue  593 THR
Chi-restraints excluded: chain C residue  597 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 4 optimal weight:    8.9990
   chunk 82 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 370 HIS
A 436 GLN
C 280 HIS
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 337 ASN
C 370 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.189249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.149389 restraints weight = 12944.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 3.12
r_work: 0.3830 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.4422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9326  Z= 0.169
  Angle     :  0.549   9.015  12726  Z= 0.273
  Chirality :  0.039   0.172   1418
  Planarity :  0.004   0.037   1552
  Dihedral  :  5.274  57.385   1234
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 19.01 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.25), residues: 1126
  helix:  1.28 (0.19), residues: 742
  sheet:  None (None), residues: 0
  loop : -0.66 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 264 
 HIS   0.010   0.001   HIS C 370 
 PHE   0.026   0.001   PHE C  82 
 TYR   0.014   0.001   TYR C 575 
 ARG   0.005   0.001   ARG A  81 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 207
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A  246 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.6897 (mp)
REVERT: A  261 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7848 (mmmt)
REVERT: A  597 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8028 (mp0)
REVERT: A  605 ASP cc_start: 0.7811 (m-30) cc_final: 0.7608 (m-30)
REVERT: A  610 GLN cc_start: 0.8183 (mp10) cc_final: 0.7960 (mp10)
REVERT: C  121 ARG cc_start: 0.8591 (mmm-85) cc_final: 0.8353 (mmm-85)
REVERT: C  246 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.6997 (mp)
REVERT: C  315 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5624 (mp)
REVERT: C  597 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8055 (mp0)
  outliers start: 41
  outliers final: 24
  residues processed: 237
  average time/residue: 0.1789
  time to fit residues: 61.4514
Evaluate side-chains
  212 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   81 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  173 TRP
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  277 LEU
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  334 LYS
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  584 LEU
Chi-restraints excluded: chain C residue  593 THR
Chi-restraints excluded: chain C residue  597 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 111 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A 370 HIS
A 436 GLN
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.187068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.147256 restraints weight = 13136.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 3.05
r_work: 0.3808 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.4711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9326  Z= 0.197
  Angle     :  0.569  10.826  12726  Z= 0.281
  Chirality :  0.039   0.152   1418
  Planarity :  0.004   0.037   1552
  Dihedral  :  5.053  57.672   1230
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 20.48 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1126
  helix:  1.30 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop : -0.54 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 494 
 HIS   0.010   0.001   HIS A 370 
 PHE   0.027   0.001   PHE C  82 
 TYR   0.019   0.001   TYR C  87 
 ARG   0.005   0.001   ARG C  81 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 200
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  246 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7026 (mp)
REVERT: A  261 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7849 (mmmt)
REVERT: A  597 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8087 (mp0)
REVERT: C  121 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8276 (mmm-85)
REVERT: C  246 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7107 (mp)
REVERT: C  315 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5919 (mp)
REVERT: C  528 PHE cc_start: 0.7192 (t80) cc_final: 0.6947 (m-10)
REVERT: C  597 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8090 (mp0)
  outliers start: 41
  outliers final: 27
  residues processed: 227
  average time/residue: 0.1839
  time to fit residues: 60.0182
Evaluate side-chains
  207 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 175
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   81 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  173 TRP
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  277 LEU
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  334 LYS
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  584 LEU
Chi-restraints excluded: chain C residue  593 THR
Chi-restraints excluded: chain C residue  597 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 103 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 46 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 87 optimal weight:   10.0000
   chunk 21 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
A 436 GLN
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.186392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.146563 restraints weight = 13091.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 3.10
r_work: 0.3799 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9326  Z= 0.195
  Angle     :  0.564  12.102  12726  Z= 0.282
  Chirality :  0.040   0.175   1418
  Planarity :  0.004   0.037   1552
  Dihedral  :  5.059  57.350   1230
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 21.22 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.11 (0.25), residues: 1126
  helix:  1.41 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop : -0.57 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 494 
 HIS   0.011   0.001   HIS C 370 
 PHE   0.034   0.001   PHE C  82 
 TYR   0.034   0.002   TYR A  87 
 ARG   0.007   0.001   ARG A 121 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 186
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: A  246 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7240 (mp)
REVERT: A  597 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8133 (mp0)
REVERT: C  126 THR cc_start: 0.8904 (p) cc_final: 0.8666 (p)
REVERT: C  246 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7257 (mp)
REVERT: C  315 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.6037 (mp)
REVERT: C  528 PHE cc_start: 0.7242 (t80) cc_final: 0.6992 (m-10)
REVERT: C  597 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8146 (mp0)
  outliers start: 43
  outliers final: 33
  residues processed: 214
  average time/residue: 0.1703
  time to fit residues: 53.8073
Evaluate side-chains
  211 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 173
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   81 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  167 PHE
Chi-restraints excluded: chain C residue  173 TRP
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  277 LEU
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  334 LYS
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  584 LEU
Chi-restraints excluded: chain C residue  593 THR
Chi-restraints excluded: chain C residue  597 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.186287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.146703 restraints weight = 13166.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 3.12
r_work: 0.3807 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.5141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9326  Z= 0.182
  Angle     :  0.568  12.242  12726  Z= 0.281
  Chirality :  0.039   0.161   1418
  Planarity :  0.004   0.037   1552
  Dihedral  :  5.024  56.842   1230
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 21.74 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1126
  helix:  1.40 (0.19), residues: 766
  sheet:  None (None), residues: 0
  loop : -0.55 (0.35), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 494 
 HIS   0.011   0.001   HIS C 370 
 PHE   0.027   0.001   PHE C  82 
 TYR   0.021   0.001   TYR A  87 
 ARG   0.009   0.001   ARG C 121 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 194
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 THR cc_start: 0.8838 (p) cc_final: 0.8541 (p)
REVERT: A  261 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7534 (mttt)
REVERT: A  597 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8185 (mp0)
REVERT: C  126 THR cc_start: 0.8882 (p) cc_final: 0.8608 (p)
REVERT: C  401 SER cc_start: 0.9018 (p) cc_final: 0.8352 (t)
REVERT: C  597 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8144 (mp0)
  outliers start: 41
  outliers final: 29
  residues processed: 219
  average time/residue: 0.1688
  time to fit residues: 54.2605
Evaluate side-chains
  206 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 175
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  167 PHE
Chi-restraints excluded: chain C residue  173 TRP
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  277 LEU
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  593 THR
Chi-restraints excluded: chain C residue  597 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 93 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.183571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.143898 restraints weight = 13318.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 3.06
r_work: 0.3781 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.5401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9326  Z= 0.226
  Angle     :  0.605  13.388  12726  Z= 0.302
  Chirality :  0.041   0.259   1418
  Planarity :  0.004   0.037   1552
  Dihedral  :  5.063  56.002   1230
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 21.74 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.25), residues: 1126
  helix:  1.30 (0.19), residues: 766
  sheet:  None (None), residues: 0
  loop : -0.55 (0.35), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 494 
 HIS   0.012   0.001   HIS C 370 
 PHE   0.029   0.001   PHE C  82 
 TYR   0.028   0.002   TYR C  87 
 ARG   0.007   0.001   ARG C 121 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 186
  time to evaluate  : 1.036 
Fit side-chains
REVERT: A   87 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6757 (m-80)
REVERT: A  126 THR cc_start: 0.8889 (p) cc_final: 0.8615 (p)
REVERT: A  190 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8002 (tp)
REVERT: A  261 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7586 (mttt)
REVERT: A  597 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8179 (mp0)
REVERT: C  126 THR cc_start: 0.8934 (p) cc_final: 0.8653 (p)
REVERT: C  315 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6294 (mp)
REVERT: C  401 SER cc_start: 0.9018 (p) cc_final: 0.8366 (t)
REVERT: C  597 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8178 (mp0)
  outliers start: 45
  outliers final: 33
  residues processed: 213
  average time/residue: 0.1642
  time to fit residues: 52.3882
Evaluate side-chains
  215 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 177
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  173 TRP
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  277 LEU
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  557 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  584 LEU
Chi-restraints excluded: chain C residue  593 THR
Chi-restraints excluded: chain C residue  597 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 27 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 56 optimal weight:   20.0000
   chunk 75 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.180715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.141105 restraints weight = 13278.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 3.09
r_work: 0.3740 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.5722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9326  Z= 0.253
  Angle     :  0.637  14.995  12726  Z= 0.318
  Chirality :  0.042   0.162   1418
  Planarity :  0.004   0.041   1552
  Dihedral  :  5.066  54.505   1228
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 22.48 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.25), residues: 1126
  helix:  1.02 (0.18), residues: 774
  sheet:  None (None), residues: 0
  loop : -0.72 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP C 494 
 HIS   0.012   0.001   HIS C 370 
 PHE   0.032   0.001   PHE C  82 
 TYR   0.027   0.002   TYR C  87 
 ARG   0.007   0.001   ARG C 121 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 191
  time to evaluate  : 0.943 
Fit side-chains
REVERT: A   87 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6993 (m-80)
REVERT: A  126 THR cc_start: 0.8888 (p) cc_final: 0.8608 (p)
REVERT: A  190 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8026 (tp)
REVERT: A  261 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7585 (mttt)
REVERT: A  597 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8182 (mp0)
REVERT: C   87 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6530 (m-80)
REVERT: C  126 THR cc_start: 0.8923 (p) cc_final: 0.8639 (p)
REVERT: C  261 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7616 (mttt)
REVERT: C  401 SER cc_start: 0.8992 (p) cc_final: 0.8337 (t)
  outliers start: 43
  outliers final: 30
  residues processed: 220
  average time/residue: 0.1600
  time to fit residues: 52.4263
Evaluate side-chains
  215 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 181
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   87 TYR
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  173 TRP
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  246 ILE
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  557 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  584 LEU
Chi-restraints excluded: chain C residue  593 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 105 optimal weight:    0.0570
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 107 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6700

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

Flipped N/Q/H residues before XYZ refinement:
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 HIS
C  89 ASN
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.183822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.144139 restraints weight = 13251.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 3.14
r_work: 0.3789 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.5714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9326  Z= 0.182
  Angle     :  0.625  14.495  12726  Z= 0.306
  Chirality :  0.041   0.197   1418
  Planarity :  0.004   0.037   1552
  Dihedral  :  5.013  54.491   1228
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 24.26 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1126
  helix:  1.13 (0.19), residues: 778
  sheet:  None (None), residues: 0
  loop : -0.63 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP C 494 
 HIS   0.013   0.001   HIS A 370 
 PHE   0.025   0.001   PHE C  82 
 TYR   0.059   0.002   TYR A 391 
 ARG   0.006   0.001   ARG C 121 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 197
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.7016 (m-80)
REVERT: A  126 THR cc_start: 0.8872 (p) cc_final: 0.8564 (p)
REVERT: A  190 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8008 (tp)
REVERT: A  261 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7569 (mttt)
REVERT: A  370 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.7054 (m170)
REVERT: A  597 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8193 (mp0)
REVERT: C   87 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6667 (m-80)
REVERT: C  120 ASN cc_start: 0.8238 (m110) cc_final: 0.7900 (m110)
REVERT: C  126 THR cc_start: 0.8930 (p) cc_final: 0.8613 (p)
REVERT: C  261 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7619 (mttt)
REVERT: C  368 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7512 (mtm)
REVERT: C  401 SER cc_start: 0.8947 (p) cc_final: 0.8282 (t)
REVERT: C  494 TRP cc_start: 0.8932 (m100) cc_final: 0.8704 (m100)
REVERT: C  597 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8194 (mp0)
  outliers start: 31
  outliers final: 18
  residues processed: 218
  average time/residue: 0.1666
  time to fit residues: 54.0435
Evaluate side-chains
  215 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue   87 TYR
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  359 PHE
Chi-restraints excluded: chain C residue  368 MET
Chi-restraints excluded: chain C residue  557 VAL
Chi-restraints excluded: chain C residue  580 THR
Chi-restraints excluded: chain C residue  584 LEU
Chi-restraints excluded: chain C residue  593 THR
Chi-restraints excluded: chain C residue  597 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 102 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0370
   chunk 99 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.7462

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A 337 ASN
A 370 HIS
** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.184916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.145157 restraints weight = 13207.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 3.10
r_work: 0.3801 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.5764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9326  Z= 0.189
  Angle     :  0.630  14.830  12726  Z= 0.311
  Chirality :  0.041   0.232   1418
  Planarity :  0.004   0.037   1552
  Dihedral  :  4.849  54.425   1226
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 24.79 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1126
  helix:  1.14 (0.19), residues: 774
  sheet:  None (None), residues: 0
  loop : -0.61 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP C 494 
 HIS   0.018   0.001   HIS A 370 
 PHE   0.027   0.001   PHE C  82 
 TYR   0.058   0.002   TYR C 391 
 ARG   0.006   0.001   ARG C 121 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4398.91 seconds
wall clock time: 77 minutes 9.99 seconds (4629.99 seconds total)