Starting phenix.real_space_refine
on Tue Apr 29 19:25:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fva_50794/04_2025/9fva_50794.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fva_50794/04_2025/9fva_50794.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fva_50794/04_2025/9fva_50794.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fva_50794/04_2025/9fva_50794.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fva_50794/04_2025/9fva_50794.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fva_50794/04_2025/9fva_50794.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.009
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      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 6.02, per 1000 atoms: 0.68
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (120.36, 68.68, 135.32, 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      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      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 1.1 seconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 6 sheets defined
      62.5% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'B' and resid 15 through 20
      removed outlier: 4.502A  pdb=" N   THR B  19 " --> pdb=" O   ARG B  15 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE B  20 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 15 through 20'
    Processing helix  chain 'B' and resid 21 through 23
      No H-bonds generated for 'chain 'B' and resid 21 through 23'
    Processing helix  chain 'B' and resid 24 through 53
      removed outlier: 4.127A  pdb=" N   ILE B  28 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   VAL B  32 " --> pdb=" O   ILE B  28 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   ALA B  33 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ALA B  38 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ASP B  41 " --> pdb=" O   ASN B  37 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU B  48 " --> pdb=" O   MET B  44 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 62 through 65
    Processing helix  chain 'B' and resid 66 through 109
    Processing helix  chain 'B' and resid 123 through 164
      removed outlier: 3.650A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   GLU B 133 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 213
      Proline residue:  B 176  - end of helix
      removed outlier: 4.016A  pdb=" N   MET B 196 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   THR B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN B 209 " --> pdb=" O   THR B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
      removed outlier: 3.673A  pdb=" N   VAL B 217 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 270
      removed outlier: 3.710A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
      removed outlier: 3.567A  pdb=" N   LEU B 263 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 302
      removed outlier: 3.557A  pdb=" N   VAL B 286 " --> pdb=" O   GLY B 282 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   MET B 295 " --> pdb=" O   MET B 291 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
    Processing helix  chain 'B' and resid 303 through 322
    Processing helix  chain 'B' and resid 381 through 387
      removed outlier: 4.158A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 458
    Processing helix  chain 'B' and resid 482 through 497
    Processing helix  chain 'B' and resid 524 through 529
    Processing helix  chain 'B' and resid 538 through 544
    Processing helix  chain 'B' and resid 561 through 568
      removed outlier: 3.989A  pdb=" N   HIS B 568 " --> pdb=" O   ASP B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 580
    Processing helix  chain 'A' and resid 15 through 21
      removed outlier: 4.509A  pdb=" N   THR A  19 " --> pdb=" O   ARG A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 47
      removed outlier: 4.182A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ILE A  28 " --> pdb=" O   LYS A  24 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ASP A  41 " --> pdb=" O   ASN A  37 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   THR A  42 " --> pdb=" O   ALA A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 66 through 107
      removed outlier: 4.212A  pdb=" N   LEU A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   THR A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   MET A  98 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 116
      removed outlier: 3.925A  pdb=" N   PHE A 115 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 129
    Processing helix  chain 'A' and resid 129 through 148
    Processing helix  chain 'A' and resid 151 through 158
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 168 through 195
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 196 through 213
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 222 through 270
      removed outlier: 3.698A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.655A  pdb=" N   ILE A 258 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 259 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.620A  pdb=" N   MET A 276 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 303
      removed outlier: 4.021A  pdb=" N   THR A 285 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   MET A 295 " --> pdb=" O   MET A 291 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 4.547A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 309
      removed outlier: 3.534A  pdb=" N   GLN A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 324
      removed outlier: 3.833A  pdb=" N   ALA A 314 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 391
      removed outlier: 3.591A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 419
    Processing helix  chain 'A' and resid 433 through 437
    Processing helix  chain 'A' and resid 446 through 456
      removed outlier: 3.646A  pdb=" N   ALA A 453 " --> pdb=" O   GLN A 449 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   MET A 456 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 486
    Processing helix  chain 'A' and resid 514 through 528
      removed outlier: 3.662A  pdb=" N   LYS A 528 " --> pdb=" O   ASP A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 545
    Processing helix  chain 'A' and resid 563 through 568
      removed outlier: 3.620A  pdb=" N   GLU A 567 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   HIS A 568 " --> pdb=" O   ASP A 564 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 563 through 568'
    Processing helix  chain 'A' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'B' and resid 342 through 345
      removed outlier: 4.114A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 366 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 349
      removed outlier: 3.755A  pdb=" N   GLU B 397 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 502 through 504
      removed outlier: 6.423A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL B 372 " --> pdb=" O   SER B 532 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL B 534 " --> pdb=" O   VAL B 372 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374
      removed outlier: 7.106A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 431 through 432
      removed outlier: 3.783A  pdb=" N   ASP A 431 " --> pdb=" O   ILE A 474 " (cutoff:3.500A)

    478 hydrogen bonds defined for protein.
    1404 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: 2.32

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2323
        1.33 -     1.45: 1499
        1.45 -     1.58: 5024
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" C   GLY A 110 "
       pdb=" N   MET A 111 "
    ideal  model  delta    sigma   weight residual
    1.327  1.392 -0.065 1.71e-02 3.42e+03 1.44e+01
  bond pdb=" N   THR B 432 "
       pdb=" CA  THR B 432 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.27e-02 6.20e+03 9.24e+00
  bond pdb=" N   VAL B 433 "
       pdb=" CA  VAL B 433 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.24e-02 6.50e+03 9.02e+00
  bond pdb=" N   ARG B  61 "
       pdb=" CA  ARG B  61 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.00e-02 1.00e+04 8.96e+00
  bond pdb=" N   ILE A 463 "
       pdb=" CA  ILE A 463 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.40e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 11759
        2.85 -     5.71: 297
        5.71 -     8.56: 29
        8.56 -    11.41: 6
       11.41 -    14.26: 1
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   ASP B 431 "
        pdb=" CA  ASP B 431 "
        pdb=" C   ASP B 431 "
      ideal   model   delta    sigma   weight residual
     109.52   99.24   10.28 1.55e+00 4.16e-01 4.40e+01
  angle pdb=" CA  ARG A 493 "
        pdb=" C   ARG A 493 "
        pdb=" O   ARG A 493 "
      ideal   model   delta    sigma   weight residual
     121.40  115.69    5.71 1.11e+00 8.12e-01 2.65e+01
  angle pdb=" N   PRO A 357 "
        pdb=" CA  PRO A 357 "
        pdb=" C   PRO A 357 "
      ideal   model   delta    sigma   weight residual
     111.14  103.45    7.69 1.56e+00 4.11e-01 2.43e+01
  angle pdb=" CA  GLU B 514 "
        pdb=" CB  GLU B 514 "
        pdb=" CG  GLU B 514 "
      ideal   model   delta    sigma   weight residual
     114.10  123.67   -9.57 2.00e+00 2.50e-01 2.29e+01
  angle pdb=" CB  MET B  44 "
        pdb=" CG  MET B  44 "
        pdb=" SD  MET B  44 "
      ideal   model   delta    sigma   weight residual
     112.70  126.96  -14.26 3.00e+00 1.11e-01 2.26e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 4690
       17.80 -    35.60: 590
       35.60 -    53.40: 145
       53.40 -    71.19: 22
       71.19 -    88.99: 7
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  GLN B 418 "
           pdb=" C   GLN B 418 "
           pdb=" N   VAL B 419 "
           pdb=" CA  VAL B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.71  -23.29     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  ARG B 416 "
           pdb=" C   ARG B 416 "
           pdb=" N   ASN B 417 "
           pdb=" CA  ASN B 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.26   22.74     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  THR B 320 "
           pdb=" C   THR B 320 "
           pdb=" N   ILE B 321 "
           pdb=" CA  ILE B 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.81   21.19     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1126
       0.055 -    0.111: 256
       0.111 -    0.166: 40
       0.166 -    0.221: 9
       0.221 -    0.277: 9
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  ASP B 431 "
            pdb=" N   ASP B 431 "
            pdb=" C   ASP B 431 "
            pdb=" CB  ASP B 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" CA  ARG A 493 "
            pdb=" N   ARG A 493 "
            pdb=" C   ARG A 493 "
            pdb=" CB  ARG A 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  ILE A 463 "
            pdb=" N   ILE A 463 "
            pdb=" C   ILE A 463 "
            pdb=" CB  ILE A 463 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.66e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 492 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.21e+00
        pdb=" C   ALA A 492 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ALA A 492 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG A 493 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 514 "   -0.013 2.00e-02 2.50e+03   2.50e-02 6.27e+00
        pdb=" C   GLU B 514 "    0.043 2.00e-02 2.50e+03
        pdb=" O   GLU B 514 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   SER B 515 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 127 "   -0.197 9.50e-02 1.11e+02   8.88e-02 5.55e+00
        pdb=" NE  ARG B 127 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 127 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 127 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 127 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1007
        2.74 -     3.28: 9856
        3.28 -     3.82: 14817
        3.82 -     4.36: 16989
        4.36 -     4.90: 27207
  Nonbonded interactions: 69876
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 458 "
            pdb=" NH2 ARG B 488 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" OD2 ASP A  53 "
            pdb=" OG1 THR A 280 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   MET A 160 "
            pdb=" N   SER A 164 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   ARG A  78 "
            pdb=" OG  SER A  82 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   LEU B 502 "
            pdb=" OG  SER B 532 "
     model   vdw
     2.257 3.040
  ... (remaining 69871 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 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.030
  Find NCS groups from input model:        0.290
  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:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8950  Z= 0.306
  Angle     :  1.037  14.264  12092  Z= 0.589
  Chirality :  0.052   0.277   1440
  Planarity :  0.006   0.089   1532
  Dihedral  : 16.479  88.993   3326
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.61 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 24.59 %
    Favored  : 74.69 %
  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: -1.42 (0.25), residues: 1134
  helix: -0.11 (0.20), residues: 660
  sheet: -1.93 (0.67), residues: 53
  loop : -2.07 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  17 
 HIS   0.008   0.002   HIS B 576 
 PHE   0.038   0.002   PHE A  13 
 TYR   0.013   0.001   TYR B 439 
 ARG   0.015   0.001   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15433 (  478)
  hydrogen bonds       : angle       6.43903 ( 1404)
  covalent geometry    : bond        0.00546 ( 8950)
  covalent geometry    : angle       1.03718 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 205
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 ASP cc_start: 0.7772 (t0) cc_final: 0.7567 (t0)
REVERT: B  100 MET cc_start: 0.9028 (tpp) cc_final: 0.8751 (mmp)
REVERT: B  132 SER cc_start: 0.9215 (t) cc_final: 0.8875 (p)
REVERT: B  133 GLU cc_start: 0.7868 (mp0) cc_final: 0.7445 (mp0)
REVERT: B  236 ARG cc_start: 0.8898 (mmp-170) cc_final: 0.8622 (mmp-170)
REVERT: A   98 MET cc_start: 0.8296 (tmm) cc_final: 0.7639 (tmm)
REVERT: A  126 SER cc_start: 0.9404 (m) cc_final: 0.9200 (p)
  outliers start: 7
  outliers final: 2
  residues processed: 207
  average time/residue: 0.1902
  time to fit residues: 55.1498
Evaluate side-chains
  185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    9.9990
   chunk 84 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 ASN
** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 HIS
A 436 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.113595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.090596 restraints weight = 29916.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.093384 restraints weight = 20218.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.095412 restraints weight = 15042.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8950  Z= 0.140
  Angle     :  0.655   8.391  12092  Z= 0.342
  Chirality :  0.044   0.222   1440
  Planarity :  0.005   0.046   1532
  Dihedral  :  5.239  23.265   1238
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.41 %
    Favored  : 96.38 %
  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: -0.89 (0.25), residues: 1134
  helix:  0.33 (0.20), residues: 665
  sheet: -1.16 (0.67), residues: 59
  loop : -1.98 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  91 
 HIS   0.005   0.001   HIS B 576 
 PHE   0.013   0.001   PHE A 392 
 TYR   0.016   0.001   TYR B  87 
 ARG   0.009   0.001   ARG A 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04395 (  478)
  hydrogen bonds       : angle       4.92003 ( 1404)
  covalent geometry    : bond        0.00280 ( 8950)
  covalent geometry    : angle       0.65478 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 219
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9464 (mt) cc_final: 0.9255 (mt)
REVERT: B   47 LEU cc_start: 0.9145 (mt) cc_final: 0.8876 (mt)
REVERT: B  132 SER cc_start: 0.9420 (t) cc_final: 0.9039 (p)
REVERT: B  133 GLU cc_start: 0.8058 (mp0) cc_final: 0.7519 (mp0)
REVERT: B  312 MET cc_start: 0.5323 (tpp) cc_final: 0.5078 (tpp)
REVERT: B  430 ASN cc_start: 0.7887 (p0) cc_final: 0.7571 (p0)
REVERT: B  456 MET cc_start: 0.9072 (mpp) cc_final: 0.8766 (mpp)
REVERT: A   44 MET cc_start: 0.8928 (tmm) cc_final: 0.8488 (tmm)
REVERT: A   45 LEU cc_start: 0.9416 (mt) cc_final: 0.9121 (mt)
REVERT: A  126 SER cc_start: 0.9380 (m) cc_final: 0.9088 (p)
REVERT: A  219 ILE cc_start: 0.9254 (mm) cc_final: 0.8993 (mm)
REVERT: A  229 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8266 (ttm170)
  outliers start: 2
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2028
  time to fit residues: 61.9636
Evaluate side-chains
  177 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0270
   chunk 10 optimal weight:    0.6980
   chunk 52 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.112762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.089682 restraints weight = 30497.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.092402 restraints weight = 20939.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.094406 restraints weight = 15615.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8950  Z= 0.126
  Angle     :  0.639   9.005  12092  Z= 0.328
  Chirality :  0.042   0.211   1440
  Planarity :  0.004   0.053   1532
  Dihedral  :  5.101  22.966   1238
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.62 %
    Favored  : 96.28 %
  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: -0.68 (0.25), residues: 1134
  helix:  0.49 (0.20), residues: 663
  sheet: -0.51 (0.80), residues: 47
  loop : -1.94 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  91 
 HIS   0.005   0.001   HIS B 537 
 PHE   0.011   0.001   PHE A  23 
 TYR   0.015   0.001   TYR A 572 
 ARG   0.003   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04075 (  478)
  hydrogen bonds       : angle       4.72587 ( 1404)
  covalent geometry    : bond        0.00259 ( 8950)
  covalent geometry    : angle       0.63879 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8921 (tmm) cc_final: 0.8684 (tmm)
REVERT: B   45 LEU cc_start: 0.9451 (mt) cc_final: 0.9195 (mt)
REVERT: B   47 LEU cc_start: 0.9135 (mt) cc_final: 0.8888 (mt)
REVERT: B   75 MET cc_start: 0.9220 (ttp) cc_final: 0.8893 (ttt)
REVERT: B  132 SER cc_start: 0.9481 (t) cc_final: 0.9074 (p)
REVERT: B  133 GLU cc_start: 0.8218 (mp0) cc_final: 0.7567 (mp0)
REVERT: B  248 SER cc_start: 0.9551 (t) cc_final: 0.9338 (p)
REVERT: B  388 LEU cc_start: 0.8058 (mm) cc_final: 0.7781 (mm)
REVERT: B  430 ASN cc_start: 0.7990 (p0) cc_final: 0.7734 (p0)
REVERT: B  431 ASP cc_start: 0.7000 (t0) cc_final: 0.6778 (t0)
REVERT: B  456 MET cc_start: 0.9135 (mpp) cc_final: 0.8798 (mmm)
REVERT: A   44 MET cc_start: 0.8938 (tmm) cc_final: 0.8505 (tmm)
REVERT: A   45 LEU cc_start: 0.9418 (mt) cc_final: 0.9093 (mt)
REVERT: A  126 SER cc_start: 0.9416 (m) cc_final: 0.9157 (p)
REVERT: A  219 ILE cc_start: 0.9232 (mm) cc_final: 0.9029 (mm)
REVERT: A  229 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8208 (ttm170)
REVERT: A  248 SER cc_start: 0.9547 (t) cc_final: 0.9285 (p)
REVERT: A  449 GLN cc_start: 0.9369 (mt0) cc_final: 0.8945 (mp10)
REVERT: A  451 GLU cc_start: 0.8861 (pt0) cc_final: 0.8273 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2041
  time to fit residues: 62.2026
Evaluate side-chains
  179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 39 optimal weight:    0.2980
   chunk 16 optimal weight:    7.9990
   chunk 92 optimal weight:    8.9990
   chunk 99 optimal weight:    0.4980
   chunk 107 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.113734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.090762 restraints weight = 31434.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.093389 restraints weight = 21853.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.095373 restraints weight = 16559.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8950  Z= 0.123
  Angle     :  0.646   9.997  12092  Z= 0.331
  Chirality :  0.043   0.267   1440
  Planarity :  0.004   0.048   1532
  Dihedral  :  5.035  21.791   1238
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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 (0.26), residues: 1134
  helix:  0.48 (0.20), residues: 665
  sheet: -0.11 (0.75), residues: 52
  loop : -2.00 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  91 
 HIS   0.008   0.001   HIS B 107 
 PHE   0.015   0.001   PHE A  23 
 TYR   0.010   0.001   TYR A 572 
 ARG   0.005   0.000   ARG A 354 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  478)
  hydrogen bonds       : angle       4.65208 ( 1404)
  covalent geometry    : bond        0.00253 ( 8950)
  covalent geometry    : angle       0.64587 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9411 (mt) cc_final: 0.9141 (mt)
REVERT: B   47 LEU cc_start: 0.9071 (mt) cc_final: 0.8761 (mt)
REVERT: B  132 SER cc_start: 0.9495 (t) cc_final: 0.9206 (p)
REVERT: B  133 GLU cc_start: 0.8263 (mp0) cc_final: 0.7785 (mp0)
REVERT: B  248 SER cc_start: 0.9501 (t) cc_final: 0.9298 (p)
REVERT: B  312 MET cc_start: 0.5423 (tpp) cc_final: 0.4250 (tpp)
REVERT: B  430 ASN cc_start: 0.8103 (p0) cc_final: 0.7818 (p0)
REVERT: B  431 ASP cc_start: 0.7307 (t0) cc_final: 0.6938 (t0)
REVERT: B  456 MET cc_start: 0.9129 (mpp) cc_final: 0.8827 (mpp)
REVERT: B  474 ILE cc_start: 0.8200 (mm) cc_final: 0.7985 (mp)
REVERT: A   44 MET cc_start: 0.8920 (tmm) cc_final: 0.8576 (tmm)
REVERT: A   45 LEU cc_start: 0.9429 (mt) cc_final: 0.9092 (mt)
REVERT: A  126 SER cc_start: 0.9457 (m) cc_final: 0.9205 (p)
REVERT: A  219 ILE cc_start: 0.9245 (mm) cc_final: 0.9032 (mm)
REVERT: A  229 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8244 (ttm170)
REVERT: A  248 SER cc_start: 0.9564 (t) cc_final: 0.9322 (p)
REVERT: A  449 GLN cc_start: 0.9363 (mt0) cc_final: 0.8909 (mp10)
REVERT: A  451 GLU cc_start: 0.8899 (pt0) cc_final: 0.8318 (pp20)
REVERT: A  456 MET cc_start: 0.8206 (pmm) cc_final: 0.7996 (pmm)
REVERT: A  488 ARG cc_start: 0.8675 (ttt180) cc_final: 0.8139 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.1921
  time to fit residues: 60.3417
Evaluate side-chains
  179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 89 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 11 optimal weight:    0.3980
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0870
   chunk 60 optimal weight:    0.0570
   chunk 66 optimal weight:    0.0970
   overall best weight:    0.2474

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  37 ASN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.115738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.092339 restraints weight = 29898.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.095217 restraints weight = 20515.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.097329 restraints weight = 15307.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8950  Z= 0.119
  Angle     :  0.643   9.408  12092  Z= 0.326
  Chirality :  0.042   0.237   1440
  Planarity :  0.004   0.042   1532
  Dihedral  :  4.843  21.227   1238
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  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: 1134
  helix:  0.50 (0.20), residues: 658
  sheet: -0.40 (0.71), residues: 57
  loop : -1.97 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  91 
 HIS   0.007   0.001   HIS B 107 
 PHE   0.025   0.001   PHE B 319 
 TYR   0.012   0.001   TYR B 393 
 ARG   0.003   0.000   ARG A 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03825 (  478)
  hydrogen bonds       : angle       4.60298 ( 1404)
  covalent geometry    : bond        0.00232 ( 8950)
  covalent geometry    : angle       0.64349 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9380 (mt) cc_final: 0.9164 (mt)
REVERT: B   47 LEU cc_start: 0.8983 (mt) cc_final: 0.8595 (mt)
REVERT: B   75 MET cc_start: 0.9217 (ttp) cc_final: 0.8934 (ttt)
REVERT: B  132 SER cc_start: 0.9476 (t) cc_final: 0.9121 (p)
REVERT: B  133 GLU cc_start: 0.8286 (mp0) cc_final: 0.7782 (mp0)
REVERT: B  229 ARG cc_start: 0.8796 (ttm170) cc_final: 0.8558 (ttm170)
REVERT: B  316 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8933 (tp-100)
REVERT: B  430 ASN cc_start: 0.7799 (p0) cc_final: 0.7172 (p0)
REVERT: B  456 MET cc_start: 0.9141 (mpp) cc_final: 0.8818 (mmm)
REVERT: A   44 MET cc_start: 0.8939 (tmm) cc_final: 0.8561 (tmm)
REVERT: A   45 LEU cc_start: 0.9436 (mt) cc_final: 0.9118 (mt)
REVERT: A  126 SER cc_start: 0.9467 (m) cc_final: 0.9240 (p)
REVERT: A  157 PHE cc_start: 0.8392 (t80) cc_final: 0.8159 (t80)
REVERT: A  229 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8190 (tpp80)
REVERT: A  248 SER cc_start: 0.9560 (t) cc_final: 0.9326 (p)
REVERT: A  449 GLN cc_start: 0.9367 (mt0) cc_final: 0.8903 (mp10)
REVERT: A  451 GLU cc_start: 0.8884 (pt0) cc_final: 0.8305 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1943
  time to fit residues: 62.7659
Evaluate side-chains
  187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 4 optimal weight:    8.9990
   chunk 86 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 240 GLN
A 309 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.108061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.085103 restraints weight = 31357.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.087819 restraints weight = 21407.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.089824 restraints weight = 16004.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8950  Z= 0.179
  Angle     :  0.694   9.184  12092  Z= 0.362
  Chirality :  0.044   0.196   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  5.126  23.541   1238
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.69 %
    Favored  : 97.21 %
  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: -0.76 (0.25), residues: 1134
  helix:  0.37 (0.20), residues: 665
  sheet: -0.40 (0.74), residues: 50
  loop : -1.92 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  91 
 HIS   0.005   0.001   HIS B 576 
 PHE   0.017   0.002   PHE B 319 
 TYR   0.012   0.002   TYR B 268 
 ARG   0.003   0.000   ARG A 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04030 (  478)
  hydrogen bonds       : angle       4.71225 ( 1404)
  covalent geometry    : bond        0.00366 ( 8950)
  covalent geometry    : angle       0.69408 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8877 (tmm) cc_final: 0.8632 (tmm)
REVERT: B   45 LEU cc_start: 0.9471 (mt) cc_final: 0.9041 (mt)
REVERT: B   47 LEU cc_start: 0.9084 (mt) cc_final: 0.8788 (mt)
REVERT: B   75 MET cc_start: 0.9285 (ttp) cc_final: 0.9056 (ttt)
REVERT: B  133 GLU cc_start: 0.8328 (mp0) cc_final: 0.7996 (mp0)
REVERT: B  229 ARG cc_start: 0.8763 (ttm170) cc_final: 0.8212 (ttm170)
REVERT: B  316 GLN cc_start: 0.9241 (tp-100) cc_final: 0.9030 (tp-100)
REVERT: B  456 MET cc_start: 0.9188 (mpp) cc_final: 0.8851 (mmm)
REVERT: B  460 MET cc_start: 0.7854 (mmt) cc_final: 0.7406 (mmp)
REVERT: A   44 MET cc_start: 0.9110 (tmm) cc_final: 0.8723 (tmm)
REVERT: A   45 LEU cc_start: 0.9464 (mt) cc_final: 0.9130 (mt)
REVERT: A   75 MET cc_start: 0.8985 (mmm) cc_final: 0.8575 (mmm)
REVERT: A  126 SER cc_start: 0.9515 (m) cc_final: 0.9301 (p)
REVERT: A  219 ILE cc_start: 0.9296 (mm) cc_final: 0.9077 (mm)
REVERT: A  229 ARG cc_start: 0.8820 (tpp80) cc_final: 0.8566 (tpp80)
REVERT: A  248 SER cc_start: 0.9596 (t) cc_final: 0.9351 (p)
REVERT: A  359 LEU cc_start: 0.7547 (mp) cc_final: 0.7313 (pt)
REVERT: A  449 GLN cc_start: 0.9375 (mt0) cc_final: 0.8991 (mp10)
  outliers start: 1
  outliers final: 1
  residues processed: 224
  average time/residue: 0.1809
  time to fit residues: 57.5439
Evaluate side-chains
  174 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0060
   overall best weight:    1.2002

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

Flipped N/Q/H residues before XYZ refinement:
B 527 GLN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.110003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.086803 restraints weight = 31953.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.089500 restraints weight = 21984.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.091497 restraints weight = 16546.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8950  Z= 0.140
  Angle     :  0.683   8.840  12092  Z= 0.353
  Chirality :  0.043   0.222   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  5.100  22.196   1238
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  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: -0.70 (0.25), residues: 1134
  helix:  0.38 (0.20), residues: 666
  sheet:  0.34 (0.84), residues: 40
  loop : -1.87 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  91 
 HIS   0.007   0.001   HIS B 107 
 PHE   0.015   0.001   PHE B 319 
 TYR   0.011   0.001   TYR A 439 
 ARG   0.004   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03907 (  478)
  hydrogen bonds       : angle       4.69892 ( 1404)
  covalent geometry    : bond        0.00293 ( 8950)
  covalent geometry    : angle       0.68313 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8837 (tmm) cc_final: 0.8602 (tmm)
REVERT: B   47 LEU cc_start: 0.8954 (mt) cc_final: 0.8695 (mt)
REVERT: B  132 SER cc_start: 0.9548 (t) cc_final: 0.9210 (p)
REVERT: B  133 GLU cc_start: 0.8380 (mp0) cc_final: 0.7809 (mp0)
REVERT: B  312 MET cc_start: 0.5863 (tpp) cc_final: 0.5491 (tpp)
REVERT: B  431 ASP cc_start: 0.7528 (t0) cc_final: 0.7000 (t0)
REVERT: B  456 MET cc_start: 0.9191 (mpp) cc_final: 0.8871 (mpp)
REVERT: B  460 MET cc_start: 0.7543 (mmt) cc_final: 0.7088 (mmp)
REVERT: A   37 ASN cc_start: 0.9440 (t0) cc_final: 0.9144 (t0)
REVERT: A   44 MET cc_start: 0.9041 (tmm) cc_final: 0.8644 (tmm)
REVERT: A   75 MET cc_start: 0.8920 (mmm) cc_final: 0.8563 (mmm)
REVERT: A  109 MET cc_start: 0.8695 (ppp) cc_final: 0.8377 (ppp)
REVERT: A  126 SER cc_start: 0.9496 (m) cc_final: 0.9274 (p)
REVERT: A  219 ILE cc_start: 0.9229 (mm) cc_final: 0.9024 (mm)
REVERT: A  229 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8376 (ttm170)
REVERT: A  248 SER cc_start: 0.9584 (t) cc_final: 0.9360 (p)
REVERT: A  449 GLN cc_start: 0.9366 (mt0) cc_final: 0.9016 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.2359
  time to fit residues: 75.1007
Evaluate side-chains
  168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 96 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0670
   chunk 99 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0020
   chunk 86 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.1530

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.109128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.086321 restraints weight = 31156.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.088914 restraints weight = 21556.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.090865 restraints weight = 16242.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8950  Z= 0.138
  Angle     :  0.691   8.397  12092  Z= 0.355
  Chirality :  0.043   0.222   1440
  Planarity :  0.004   0.040   1532
  Dihedral  :  5.095  24.347   1238
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: 1134
  helix:  0.43 (0.20), residues: 666
  sheet:  0.40 (0.85), residues: 40
  loop : -1.85 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  91 
 HIS   0.008   0.001   HIS B 107 
 PHE   0.013   0.002   PHE A 220 
 TYR   0.009   0.001   TYR B 268 
 ARG   0.006   0.000   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03871 (  478)
  hydrogen bonds       : angle       4.66086 ( 1404)
  covalent geometry    : bond        0.00288 ( 8950)
  covalent geometry    : angle       0.69138 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 1.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8795 (tmm) cc_final: 0.8559 (tmm)
REVERT: B   45 LEU cc_start: 0.9452 (mt) cc_final: 0.9002 (mt)
REVERT: B   47 LEU cc_start: 0.9059 (mt) cc_final: 0.8743 (mt)
REVERT: B  132 SER cc_start: 0.9520 (t) cc_final: 0.9161 (p)
REVERT: B  133 GLU cc_start: 0.8384 (mp0) cc_final: 0.7813 (mp0)
REVERT: B  312 MET cc_start: 0.5736 (tpp) cc_final: 0.5320 (tpp)
REVERT: B  431 ASP cc_start: 0.7644 (t0) cc_final: 0.7064 (t0)
REVERT: B  456 MET cc_start: 0.9259 (mpp) cc_final: 0.8897 (mpp)
REVERT: B  460 MET cc_start: 0.7701 (mmt) cc_final: 0.7246 (mmp)
REVERT: A   37 ASN cc_start: 0.9461 (t0) cc_final: 0.9147 (t0)
REVERT: A   44 MET cc_start: 0.9091 (tmm) cc_final: 0.8690 (tmm)
REVERT: A   75 MET cc_start: 0.8987 (mmm) cc_final: 0.8575 (mmm)
REVERT: A  109 MET cc_start: 0.8849 (ppp) cc_final: 0.8540 (ppp)
REVERT: A  126 SER cc_start: 0.9521 (m) cc_final: 0.9313 (p)
REVERT: A  157 PHE cc_start: 0.8595 (t80) cc_final: 0.8362 (t80)
REVERT: A  216 GLU cc_start: 0.8673 (tp30) cc_final: 0.8450 (tp30)
REVERT: A  219 ILE cc_start: 0.9329 (mm) cc_final: 0.9078 (mm)
REVERT: A  229 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8346 (ttm170)
REVERT: A  248 SER cc_start: 0.9591 (t) cc_final: 0.9358 (p)
REVERT: A  449 GLN cc_start: 0.9388 (mt0) cc_final: 0.9054 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.1978
  time to fit residues: 62.8856
Evaluate side-chains
  179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.109437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.086384 restraints weight = 30434.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.089102 restraints weight = 20544.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.091130 restraints weight = 15288.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8950  Z= 0.132
  Angle     :  0.688   8.405  12092  Z= 0.350
  Chirality :  0.043   0.215   1440
  Planarity :  0.004   0.039   1532
  Dihedral  :  5.025  23.782   1238
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  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: -0.55 (0.25), residues: 1134
  helix:  0.49 (0.20), residues: 664
  sheet:  1.42 (1.00), residues: 30
  loop : -1.84 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  91 
 HIS   0.006   0.001   HIS B 576 
 PHE   0.011   0.001   PHE A 220 
 TYR   0.008   0.001   TYR A 572 
 ARG   0.006   0.000   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03763 (  478)
  hydrogen bonds       : angle       4.58245 ( 1404)
  covalent geometry    : bond        0.00279 ( 8950)
  covalent geometry    : angle       0.68812 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8768 (tmm) cc_final: 0.8536 (tmm)
REVERT: B   45 LEU cc_start: 0.9416 (mt) cc_final: 0.8970 (mt)
REVERT: B   47 LEU cc_start: 0.9025 (mt) cc_final: 0.8696 (mt)
REVERT: B   75 MET cc_start: 0.8607 (ttm) cc_final: 0.8355 (ttp)
REVERT: B  132 SER cc_start: 0.9523 (t) cc_final: 0.9191 (p)
REVERT: B  133 GLU cc_start: 0.8376 (mp0) cc_final: 0.7840 (mp0)
REVERT: B  312 MET cc_start: 0.5777 (tpp) cc_final: 0.5336 (tpp)
REVERT: B  430 ASN cc_start: 0.8016 (p0) cc_final: 0.7599 (p0)
REVERT: B  431 ASP cc_start: 0.7589 (t0) cc_final: 0.7120 (t0)
REVERT: B  456 MET cc_start: 0.9281 (mpp) cc_final: 0.8915 (mpp)
REVERT: B  460 MET cc_start: 0.7632 (mmt) cc_final: 0.7179 (mmp)
REVERT: B  474 ILE cc_start: 0.8313 (mp) cc_final: 0.8046 (mm)
REVERT: A   37 ASN cc_start: 0.9441 (t0) cc_final: 0.9135 (t0)
REVERT: A   44 MET cc_start: 0.9093 (tmm) cc_final: 0.8698 (tmm)
REVERT: A   75 MET cc_start: 0.8981 (mmm) cc_final: 0.8563 (mmm)
REVERT: A  109 MET cc_start: 0.8827 (ppp) cc_final: 0.8545 (ppp)
REVERT: A  126 SER cc_start: 0.9550 (m) cc_final: 0.9345 (p)
REVERT: A  157 PHE cc_start: 0.8614 (t80) cc_final: 0.8377 (t80)
REVERT: A  229 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8397 (ttm170)
REVERT: A  248 SER cc_start: 0.9584 (t) cc_final: 0.9356 (p)
REVERT: A  449 GLN cc_start: 0.9376 (mt0) cc_final: 0.9045 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1704
  time to fit residues: 53.5909
Evaluate side-chains
  175 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 95 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 88 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 579 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.107621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.084605 restraints weight = 30508.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.087290 restraints weight = 20577.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.089230 restraints weight = 15253.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.4404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8950  Z= 0.150
  Angle     :  0.698   8.424  12092  Z= 0.358
  Chirality :  0.044   0.233   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  5.201  24.117   1238
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.25), residues: 1134
  helix:  0.49 (0.20), residues: 660
  sheet: -0.33 (0.79), residues: 50
  loop : -1.82 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  91 
 HIS   0.006   0.001   HIS B 576 
 PHE   0.019   0.002   PHE B  23 
 TYR   0.012   0.001   TYR A 268 
 ARG   0.007   0.000   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03844 (  478)
  hydrogen bonds       : angle       4.65590 ( 1404)
  covalent geometry    : bond        0.00314 ( 8950)
  covalent geometry    : angle       0.69843 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9423 (mt) cc_final: 0.8979 (mt)
REVERT: B   47 LEU cc_start: 0.9058 (mt) cc_final: 0.8755 (mt)
REVERT: B   75 MET cc_start: 0.8549 (ttm) cc_final: 0.8349 (ppp)
REVERT: B  132 SER cc_start: 0.9563 (t) cc_final: 0.9220 (p)
REVERT: B  133 GLU cc_start: 0.8456 (mp0) cc_final: 0.7938 (mp0)
REVERT: B  460 MET cc_start: 0.7889 (mmt) cc_final: 0.7450 (mmp)
REVERT: B  474 ILE cc_start: 0.8408 (mp) cc_final: 0.8114 (mm)
REVERT: A   37 ASN cc_start: 0.9469 (t0) cc_final: 0.9159 (t0)
REVERT: A   44 MET cc_start: 0.9113 (tmm) cc_final: 0.8706 (tmm)
REVERT: A   75 MET cc_start: 0.9000 (mmm) cc_final: 0.8566 (mmm)
REVERT: A   98 MET cc_start: 0.8350 (tmm) cc_final: 0.7851 (tmm)
REVERT: A  109 MET cc_start: 0.8902 (ppp) cc_final: 0.8611 (ppp)
REVERT: A  157 PHE cc_start: 0.8629 (t80) cc_final: 0.8373 (t80)
REVERT: A  229 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8663 (tpp80)
REVERT: A  248 SER cc_start: 0.9595 (t) cc_final: 0.9360 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1765
  time to fit residues: 55.7491
Evaluate side-chains
  175 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 40 optimal weight:    0.2980
   chunk 53 optimal weight:    6.9990
   chunk 86 optimal weight:    0.8980
   chunk 54 optimal weight:    8.9990
   chunk 111 optimal weight:    9.9990
   chunk 102 optimal weight:    0.0270
   chunk 84 optimal weight:    1.9990
   chunk 87 optimal weight:    0.4980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 GLN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 579 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.110456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.086962 restraints weight = 30163.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.089744 restraints weight = 20401.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.091828 restraints weight = 15107.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8950  Z= 0.127
  Angle     :  0.701   9.185  12092  Z= 0.354
  Chirality :  0.043   0.246   1440
  Planarity :  0.004   0.039   1532
  Dihedral  :  5.026  22.738   1238
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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: -0.49 (0.25), residues: 1134
  helix:  0.56 (0.20), residues: 660
  sheet:  0.44 (0.90), residues: 40
  loop : -1.78 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  91 
 HIS   0.005   0.001   HIS B 576 
 PHE   0.023   0.001   PHE B  23 
 TYR   0.010   0.001   TYR B 439 
 ARG   0.003   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03766 (  478)
  hydrogen bonds       : angle       4.55811 ( 1404)
  covalent geometry    : bond        0.00264 ( 8950)
  covalent geometry    : angle       0.70140 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3376.12 seconds
wall clock time: 59 minutes 58.26 seconds (3598.26 seconds total)