Starting phenix.real_space_refine
on Tue Feb 11 17:51:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wox_37701/02_2025/8wox_37701.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wox_37701/02_2025/8wox_37701.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wox_37701/02_2025/8wox_37701.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wox_37701/02_2025/8wox_37701.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wox_37701/02_2025/8wox_37701.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wox_37701/02_2025/8wox_37701.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      36      5.16       5
     C    4060      2.51       5
     N    1050      2.21       5
     O    1201      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6348
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1537
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "A"
      Number of atoms: 4796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4796
          Classifications: {'peptide': 588}
          Link IDs: {'PTRANS': 25, 'TRANS': 562}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.83, per 1000 atoms: 0.92
  Number of scatterers: 6348
  At special positions: 0
  Unit cell: (93.28, 77.44, 124.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      36     16.00
     O    1201      8.00
     N    1050      7.00
     C    4060      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B 601 " - " ASN B 343 "
  Time building additional restraints: 1.42
  Conformation dependent library (CDL) restraints added in 855.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 374 "


  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1470

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      56.1% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
      removed outlier: 3.570A  pdb=" N   ASN B 343 " --> pdb=" O   GLY B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.644A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 389
      removed outlier: 3.519A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ASP B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 384 through 389'
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 417 through 422
      removed outlier: 3.539A  pdb=" N   TYR B 421 " --> pdb=" O   LYS B 417 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASN B 422 " --> pdb=" O   ILE B 418 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 417 through 422'
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.614A  pdb=" N   GLN A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ASP A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   TYR A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 80
      removed outlier: 3.674A  pdb=" N   LYS A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 103
      removed outlier: 3.732A  pdb=" N   SER A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.548A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   TYR A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 155
      removed outlier: 4.336A  pdb=" N   ASP A 149 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 172
    Processing helix  chain 'A' and resid 173 through 175
      No H-bonds generated for 'chain 'A' and resid 173 through 175'
    Processing helix  chain 'A' and resid 176 through 194
      removed outlier: 3.861A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 205 through 208
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.541A  pdb=" N   TYR A 215 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ASP A 216 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 212 through 216'
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.898A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ASP A 224 " --> pdb=" O   SER A 220 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   GLU A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLU A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE A 233 " --> pdb=" O   THR A 229 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.767A  pdb=" N   GLN A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   ASP A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ALA A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.639A  pdb=" N   TYR A 279 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 301
    Processing helix  chain 'A' and resid 303 through 317
      removed outlier: 3.613A  pdb=" N   ILE A 307 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER A 317 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 4.062A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.633A  pdb=" N   PHE A 369 " --> pdb=" O   THR A 365 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.565A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE A 407 " --> pdb=" O   ALA A 403 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.501A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.611A  pdb=" N   LYS A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.523A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.671A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 572
    Processing helix  chain 'A' and resid 581 through 588
      removed outlier: 3.566A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.643A  pdb=" N   GLU A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLN A 598 " --> pdb=" O   TRP A 594 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.614A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
      removed outlier: 3.726A  pdb=" N   TYR B 489 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.302A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.075A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)

    279 hydrogen bonds defined for protein.
    792 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: 1.61

  Time building geometry restraints manager: 1.68 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2036
        1.34 -     1.46: 1680
        1.46 -     1.58: 2749
        1.58 -     1.70: 0
        1.70 -     1.82: 57
  Bond restraints: 6522
  Sorted by residual:
  bond pdb=" C   ASP A 499 "
       pdb=" N   PRO A 500 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 1.28e-02 6.10e+03 1.57e+00
  bond pdb=" C3  NAG B 601 "
       pdb=" O3  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.84e-01
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.425 -0.019 2.00e-02 2.50e+03 9.12e-01
  bond pdb=" C   GLU A  35 "
       pdb=" O   GLU A  35 "
    ideal  model  delta    sigma   weight residual
    1.237  1.248 -0.011 1.19e-02 7.06e+03 8.59e-01
  bond pdb=" C5  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.431 -0.018 2.00e-02 2.50e+03 8.10e-01
  ... (remaining 6517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 8554
        1.23 -     2.46: 240
        2.46 -     3.69: 38
        3.69 -     4.92: 21
        4.92 -     6.15: 3
  Bond angle restraints: 8856
  Sorted by residual:
  angle pdb=" CA  ILE A 513 "
        pdb=" C   ILE A 513 "
        pdb=" N   ARG A 514 "
      ideal   model   delta    sigma   weight residual
     118.48  115.70    2.78 1.01e+00 9.80e-01 7.58e+00
  angle pdb=" CA  CYS B 525 "
        pdb=" CB  CYS B 525 "
        pdb=" SG  CYS B 525 "
      ideal   model   delta    sigma   weight residual
     114.40  120.55   -6.15 2.30e+00 1.89e-01 7.16e+00
  angle pdb=" N   ILE A 513 "
        pdb=" CA  ILE A 513 "
        pdb=" C   ILE A 513 "
      ideal   model   delta    sigma   weight residual
     113.07  109.44    3.63 1.37e+00 5.33e-01 7.01e+00
  angle pdb=" CA  CYS B 391 "
        pdb=" CB  CYS B 391 "
        pdb=" SG  CYS B 391 "
      ideal   model   delta    sigma   weight residual
     114.40  119.83   -5.43 2.30e+00 1.89e-01 5.57e+00
  angle pdb=" C   TRP A 459 "
        pdb=" N   ARG A 460 "
        pdb=" CA  ARG A 460 "
      ideal   model   delta    sigma   weight residual
     120.29  117.04    3.25 1.42e+00 4.96e-01 5.23e+00
  ... (remaining 8851 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.13: 3626
       22.13 -    44.26: 204
       44.26 -    66.39: 21
       66.39 -    88.53: 10
       88.53 -   110.66: 4
  Dihedral angle restraints: 3865
    sinusoidal: 1573
      harmonic: 2292
  Sorted by residual:
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.68  -80.32     1      1.00e+01 1.00e-02 7.99e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.94   58.06     1      1.00e+01 1.00e-02 4.52e+01
  dihedral pdb=" CA  VAL B 524 "
           pdb=" C   VAL B 524 "
           pdb=" N   CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.41   19.59     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 3862 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 479
       0.027 -    0.054: 294
       0.054 -    0.080: 96
       0.080 -    0.107: 44
       0.107 -    0.134: 16
  Chirality restraints: 929
  Sorted by residual:
  chirality pdb=" CA  ILE A 468 "
            pdb=" N   ILE A 468 "
            pdb=" C   ILE A 468 "
            pdb=" CB  ILE A 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.80e-01
  chirality pdb=" CA  CYS B 525 "
            pdb=" N   CYS B 525 "
            pdb=" C   CYS B 525 "
            pdb=" CB  CYS B 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.78e-01
  ... (remaining 926 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 468 "   -0.037 5.00e-02 4.00e+02   5.58e-02 4.99e+00
        pdb=" N   PRO A 469 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 469 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 469 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 414 "    0.025 5.00e-02 4.00e+02   3.78e-02 2.28e+00
        pdb=" N   PRO A 415 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 415 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 415 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 611 "   -0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO A 612 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 612 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 612 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 64
        2.66 -     3.22: 5695
        3.22 -     3.78: 9181
        3.78 -     4.34: 12136
        4.34 -     4.90: 20582
  Nonbonded interactions: 47658
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.099 2.230
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.100 2.230
  nonbonded pdb=" OG  SER A 563 "
            pdb=" OE1 GLU A 564 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OG  SER A 331 "
            pdb=" O   ILE A 358 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" NH1 ARG A 177 "
            pdb=" O   GLU A 495 "
     model   vdw
     2.250 3.120
  ... (remaining 47653 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.930
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.830
  Find NCS groups from input model:        0.060
  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:11.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6522  Z= 0.199
  Angle     :  0.530   6.152   8856  Z= 0.292
  Chirality :  0.041   0.134    929
  Planarity :  0.004   0.056   1144
  Dihedral  : 13.941 110.656   2377
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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:  0.02 (0.31), residues: 776
  helix:  0.85 (0.29), residues: 366
  sheet:  2.45 (0.76), residues: 44
  loop : -1.18 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.016   0.001   PHE A 400 
 TYR   0.013   0.001   TYR A 587 
 ARG   0.002   0.000   ARG A 514 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.736 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.7578 (tp30) cc_final: 0.7172 (tp30)
REVERT: A   75 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7388 (tm-30)
REVERT: A  126 ILE cc_start: 0.8350 (tt) cc_final: 0.8005 (tt)
REVERT: A  224 ASP cc_start: 0.7668 (m-30) cc_final: 0.7395 (m-30)
REVERT: A  334 THR cc_start: 0.8472 (t) cc_final: 0.8247 (m)
REVERT: A  335 GLU cc_start: 0.7697 (tp30) cc_final: 0.7047 (mm-30)
REVERT: A  338 ASP cc_start: 0.7256 (p0) cc_final: 0.6853 (p0)
REVERT: A  341 LYS cc_start: 0.7911 (mttt) cc_final: 0.7709 (mttt)
REVERT: A  376 MET cc_start: 0.8691 (tpp) cc_final: 0.8388 (mmt)
REVERT: A  470 LYS cc_start: 0.8152 (tppp) cc_final: 0.7880 (tppp)
REVERT: A  509 ASP cc_start: 0.7027 (p0) cc_final: 0.6639 (p0)
REVERT: A  597 GLU cc_start: 0.7990 (tp30) cc_final: 0.7753 (mm-30)
  outliers start: 0
  outliers final: 1
  residues processed: 199
  average time/residue: 1.1552
  time to fit residues: 241.2110
Evaluate side-chains
  169 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0970
   chunk 19 optimal weight:    0.0980
   chunk 39 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN
B 481 ASN
A  42 GLN
A 401 HIS
A 524 GLN
A 598 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.120550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.109439 restraints weight = 9548.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 1.90
r_work: 0.3462 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6522  Z= 0.280
  Angle     :  0.597   7.036   8856  Z= 0.309
  Chirality :  0.044   0.181    929
  Planarity :  0.005   0.046   1144
  Dihedral  :  7.976  68.216    877
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.12 %
    Favored  : 82.23 %
  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:  0.19 (0.31), residues: 776
  helix:  1.04 (0.28), residues: 376
  sheet:  2.22 (0.76), residues: 49
  loop : -1.23 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 353 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.027   0.002   PHE A 504 
 TYR   0.024   0.002   TYR A 183 
 ARG   0.006   0.000   ARG A 340 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 172
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  408 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8193 (ptm-80)
REVERT: A   30 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7385 (mp0)
REVERT: A   74 GLU cc_start: 0.7944 (tp30) cc_final: 0.7546 (tp30)
REVERT: A   75 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7640 (tm-30)
REVERT: A  160 GLU cc_start: 0.8063 (tp30) cc_final: 0.7858 (tt0)
REVERT: A  334 THR cc_start: 0.8593 (t) cc_final: 0.8334 (m)
REVERT: A  335 GLU cc_start: 0.7991 (tp30) cc_final: 0.7164 (mm-30)
REVERT: A  455 MET cc_start: 0.8079 (tmm) cc_final: 0.7850 (tmm)
REVERT: A  470 LYS cc_start: 0.8398 (tppp) cc_final: 0.8177 (tppp)
REVERT: A  509 ASP cc_start: 0.7132 (p0) cc_final: 0.6802 (p0)
REVERT: A  564 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7531 (mp0)
  outliers start: 18
  outliers final: 4
  residues processed: 177
  average time/residue: 1.1702
  time to fit residues: 217.2592
Evaluate side-chains
  169 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 162
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  564 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 10 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN
B 388 ASN
A 101 GLN
A 572 ASN
A 598 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.119353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.107975 restraints weight = 9568.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.89
r_work: 0.3445 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6522  Z= 0.332
  Angle     :  0.592   7.930   8856  Z= 0.309
  Chirality :  0.045   0.157    929
  Planarity :  0.005   0.043   1144
  Dihedral  :  6.434  53.735    875
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.21 %
    Favored  : 79.30 %
  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:  0.06 (0.30), residues: 776
  helix:  0.98 (0.28), residues: 378
  sheet:  2.03 (0.75), residues: 49
  loop : -1.33 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 353 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.020   0.002   PHE A 504 
 TYR   0.024   0.002   TYR A 183 
 ARG   0.006   0.000   ARG A 340 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 170
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 VAL cc_start: 0.7440 (OUTLIER) cc_final: 0.7220 (p)
REVERT: A   30 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7402 (mp0)
REVERT: A   74 GLU cc_start: 0.7937 (tp30) cc_final: 0.7686 (tp30)
REVERT: A   75 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7646 (tm-30)
REVERT: A  160 GLU cc_start: 0.8109 (tp30) cc_final: 0.7891 (tt0)
REVERT: A  335 GLU cc_start: 0.8022 (tp30) cc_final: 0.7327 (mm-30)
REVERT: A  455 MET cc_start: 0.8057 (tmm) cc_final: 0.7809 (tmm)
REVERT: A  470 LYS cc_start: 0.8390 (tppp) cc_final: 0.8119 (tppp)
REVERT: A  509 ASP cc_start: 0.7228 (p0) cc_final: 0.6917 (p0)
REVERT: A  564 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7626 (mp0)
REVERT: A  568 LEU cc_start: 0.8647 (tp) cc_final: 0.8427 (tt)
REVERT: A  596 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8301 (mtmm)
  outliers start: 17
  outliers final: 5
  residues processed: 177
  average time/residue: 1.1656
  time to fit residues: 216.4560
Evaluate side-chains
  173 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 165
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  611 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 53 optimal weight:    0.1980
   chunk 51 optimal weight:    0.2980
   chunk 72 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0970
   chunk 58 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN
A 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.120956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.109518 restraints weight = 9719.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.91
r_work: 0.3465 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6522  Z= 0.229
  Angle     :  0.571   9.231   8856  Z= 0.288
  Chirality :  0.042   0.129    929
  Planarity :  0.004   0.044   1144
  Dihedral  :  5.553  55.850    875
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.41 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.31), residues: 776
  helix:  1.21 (0.28), residues: 369
  sheet:  1.97 (0.75), residues: 49
  loop : -1.25 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 349 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.018   0.001   PHE A  28 
 TYR   0.023   0.001   TYR A 183 
 ARG   0.006   0.000   ARG A 340 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7284 (mp0)
REVERT: A   74 GLU cc_start: 0.7928 (tp30) cc_final: 0.7489 (tp30)
REVERT: A   75 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: A  160 GLU cc_start: 0.8062 (tp30) cc_final: 0.7841 (tt0)
REVERT: A  190 MET cc_start: 0.8187 (tmm) cc_final: 0.7723 (ttt)
REVERT: A  238 GLU cc_start: 0.7983 (tt0) cc_final: 0.7762 (tt0)
REVERT: A  335 GLU cc_start: 0.8093 (tp30) cc_final: 0.7446 (mm-30)
REVERT: A  455 MET cc_start: 0.8051 (tmm) cc_final: 0.7825 (tmm)
REVERT: A  509 ASP cc_start: 0.7108 (p0) cc_final: 0.6796 (p0)
REVERT: A  564 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7589 (mp0)
REVERT: A  596 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8310 (mtmm)
  outliers start: 18
  outliers final: 8
  residues processed: 168
  average time/residue: 1.2796
  time to fit residues: 226.9294
Evaluate side-chains
  173 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 163
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  611 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    0.0370
   chunk 54 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0060
   chunk 23 optimal weight:    0.5980
   chunk 40 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.3074

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN
B 388 ASN
A 175 GLN
A 572 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.121253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.109880 restraints weight = 9579.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 1.91
r_work: 0.3469 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6522  Z= 0.210
  Angle     :  0.556   7.924   8856  Z= 0.282
  Chirality :  0.041   0.134    929
  Planarity :  0.004   0.044   1144
  Dihedral  :  5.305  58.005    875
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.53 %
    Favored  : 77.09 %
  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:  0.35 (0.31), residues: 776
  helix:  1.35 (0.28), residues: 368
  sheet:  1.98 (0.75), residues: 49
  loop : -1.26 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 353 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.020   0.001   PHE A  28 
 TYR   0.021   0.001   TYR A 183 
 ARG   0.006   0.000   ARG A 340 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 168
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: B  408 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8175 (ptm-80)
REVERT: A   30 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7236 (mp0)
REVERT: A   74 GLU cc_start: 0.7906 (tp30) cc_final: 0.7487 (tp30)
REVERT: A   75 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7735 (tm-30)
REVERT: A  160 GLU cc_start: 0.8008 (tp30) cc_final: 0.7796 (tt0)
REVERT: A  190 MET cc_start: 0.8154 (tmm) cc_final: 0.7683 (ttt)
REVERT: A  238 GLU cc_start: 0.8000 (tt0) cc_final: 0.7788 (tt0)
REVERT: A  335 GLU cc_start: 0.8082 (tp30) cc_final: 0.7448 (mm-30)
REVERT: A  509 ASP cc_start: 0.7097 (p0) cc_final: 0.6780 (p0)
REVERT: A  564 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7567 (mp0)
REVERT: A  568 LEU cc_start: 0.8628 (tp) cc_final: 0.8409 (tt)
REVERT: A  597 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8177 (mm-30)
REVERT: A  600 ARG cc_start: 0.8144 (ptp90) cc_final: 0.7858 (ptp-170)
  outliers start: 23
  outliers final: 11
  residues processed: 175
  average time/residue: 1.0969
  time to fit residues: 202.0639
Evaluate side-chains
  178 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  611 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0970
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
B 450 ASN
A 394 ASN
A 572 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.118368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.107210 restraints weight = 9476.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.91
r_work: 0.3429 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   6522  Z= 0.391
  Angle     :  0.635   7.148   8856  Z= 0.327
  Chirality :  0.046   0.144    929
  Planarity :  0.005   0.045   1144
  Dihedral  :  5.340  58.197    875
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.29 %
    Favored  : 76.21 %
  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:  0.10 (0.31), residues: 776
  helix:  1.16 (0.28), residues: 372
  sheet:  1.59 (0.74), residues: 51
  loop : -1.42 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 477 
 HIS   0.006   0.002   HIS A 241 
 PHE   0.027   0.002   PHE A  28 
 TYR   0.027   0.002   TYR A 587 
 ARG   0.008   0.001   ARG A 340 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 172
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
REVERT: B  408 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8170 (ptm-80)
REVERT: A   30 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7406 (mp0)
REVERT: A   74 GLU cc_start: 0.7941 (tp30) cc_final: 0.7731 (tp30)
REVERT: A   75 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7657 (tm-30)
REVERT: A  190 MET cc_start: 0.8211 (tmm) cc_final: 0.7762 (ttt)
REVERT: A  238 GLU cc_start: 0.8009 (tt0) cc_final: 0.7797 (tt0)
REVERT: A  335 GLU cc_start: 0.7919 (tp30) cc_final: 0.7344 (mm-30)
REVERT: A  435 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7275 (mt-10)
REVERT: A  509 ASP cc_start: 0.7314 (p0) cc_final: 0.7011 (p0)
REVERT: A  525 PHE cc_start: 0.8520 (m-10) cc_final: 0.8310 (m-10)
REVERT: A  564 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7565 (mp0)
REVERT: A  568 LEU cc_start: 0.8656 (tp) cc_final: 0.8441 (tt)
REVERT: A  597 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8226 (mm-30)
REVERT: A  600 ARG cc_start: 0.8186 (ptp90) cc_final: 0.7905 (ptp-170)
  outliers start: 17
  outliers final: 10
  residues processed: 177
  average time/residue: 1.1286
  time to fit residues: 210.0109
Evaluate side-chains
  180 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 166
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  611 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0980
   chunk 12 optimal weight:    0.5980
   chunk 20 optimal weight:    0.1980
   chunk 25 optimal weight:    0.4980
   chunk 47 optimal weight:    0.0980
   chunk 29 optimal weight:    0.1980
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.2180

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

Flipped N/Q/H residues before XYZ refinement:
A 572 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.122103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.110724 restraints weight = 9586.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.91
r_work: 0.3483 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6522  Z= 0.190
  Angle     :  0.590   9.346   8856  Z= 0.296
  Chirality :  0.040   0.131    929
  Planarity :  0.004   0.044   1144
  Dihedral  :  4.711  45.747    875
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.15 %
    Favored  : 75.33 %
  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:  0.42 (0.31), residues: 776
  helix:  1.38 (0.28), residues: 371
  sheet:  1.64 (0.75), residues: 51
  loop : -1.17 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 353 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.020   0.001   PHE A  28 
 TYR   0.022   0.001   TYR A 183 
 ARG   0.007   0.000   ARG A 340 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  365 TYR cc_start: 0.8532 (m-10) cc_final: 0.8158 (m-10)
REVERT: B  524 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.7203 (p)
REVERT: A   30 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7141 (mp0)
REVERT: A   66 GLU cc_start: 0.7925 (tp30) cc_final: 0.7721 (tp30)
REVERT: A   74 GLU cc_start: 0.7894 (tp30) cc_final: 0.7481 (tp30)
REVERT: A   75 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7751 (tm-30)
REVERT: A   78 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7998 (tmmm)
REVERT: A  190 MET cc_start: 0.8197 (tmm) cc_final: 0.7696 (ttt)
REVERT: A  238 GLU cc_start: 0.7999 (tt0) cc_final: 0.7786 (tt0)
REVERT: A  335 GLU cc_start: 0.7937 (tp30) cc_final: 0.7388 (mm-30)
REVERT: A  509 ASP cc_start: 0.7081 (p0) cc_final: 0.6764 (p0)
REVERT: A  564 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7528 (mp0)
REVERT: A  568 LEU cc_start: 0.8626 (tp) cc_final: 0.8391 (tt)
REVERT: A  597 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8164 (mm-30)
REVERT: A  600 ARG cc_start: 0.8133 (ptp90) cc_final: 0.7871 (ptp-170)
  outliers start: 24
  outliers final: 12
  residues processed: 176
  average time/residue: 1.1040
  time to fit residues: 204.6292
Evaluate side-chains
  178 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  611 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0570
   chunk 66 optimal weight:    0.9980
   chunk 10 optimal weight:    0.1980
   chunk 46 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.3098

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
A 493 HIS
A 572 ASN
A 598 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.121550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.110148 restraints weight = 9523.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.94
r_work: 0.3472 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6522  Z= 0.218
  Angle     :  0.585   9.325   8856  Z= 0.295
  Chirality :  0.041   0.129    929
  Planarity :  0.004   0.044   1144
  Dihedral  :  4.642  45.561    875
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 22.17 %
    Favored  : 75.18 %
  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:  0.45 (0.31), residues: 776
  helix:  1.44 (0.28), residues: 371
  sheet:  1.56 (0.74), residues: 51
  loop : -1.17 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.024   0.001   PHE A  28 
 TYR   0.022   0.001   TYR A 183 
 ARG   0.007   0.000   ARG A 340 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
REVERT: B  365 TYR cc_start: 0.8521 (m-10) cc_final: 0.8189 (m-10)
REVERT: B  408 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8223 (ptm-80)
REVERT: B  524 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7253 (p)
REVERT: A   30 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7151 (mp0)
REVERT: A   66 GLU cc_start: 0.7921 (tp30) cc_final: 0.7673 (tp30)
REVERT: A   74 GLU cc_start: 0.7937 (tp30) cc_final: 0.7511 (tp30)
REVERT: A   75 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: A   78 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8020 (tmmm)
REVERT: A  190 MET cc_start: 0.8222 (tmm) cc_final: 0.7732 (ttt)
REVERT: A  238 GLU cc_start: 0.8010 (tt0) cc_final: 0.7799 (tt0)
REVERT: A  335 GLU cc_start: 0.7928 (tp30) cc_final: 0.7359 (mm-30)
REVERT: A  509 ASP cc_start: 0.7140 (p0) cc_final: 0.6819 (p0)
REVERT: A  564 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7562 (mp0)
  outliers start: 18
  outliers final: 10
  residues processed: 168
  average time/residue: 1.1247
  time to fit residues: 198.9827
Evaluate side-chains
  174 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 159
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  611 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 74 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0970
   chunk 1 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
A 572 ASN
A 598 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.119855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.108509 restraints weight = 9536.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.93
r_work: 0.3447 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6522  Z= 0.296
  Angle     :  0.625   9.558   8856  Z= 0.317
  Chirality :  0.044   0.177    929
  Planarity :  0.004   0.044   1144
  Dihedral  :  4.816  47.396    875
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 23.64 %
    Favored  : 74.01 %
  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:  0.33 (0.31), residues: 776
  helix:  1.36 (0.28), residues: 372
  sheet:  1.59 (0.74), residues: 51
  loop : -1.29 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 165 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.029   0.002   PHE A  28 
 TYR   0.025   0.002   TYR A 183 
 ARG   0.004   0.000   ARG A 559 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: B  350 VAL cc_start: 0.8055 (t) cc_final: 0.7846 (p)
REVERT: B  408 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8207 (ptm-80)
REVERT: B  524 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7325 (p)
REVERT: A   30 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7296 (mp0)
REVERT: A   66 GLU cc_start: 0.7958 (tp30) cc_final: 0.7693 (tp30)
REVERT: A   74 GLU cc_start: 0.7947 (tp30) cc_final: 0.7491 (tp30)
REVERT: A   75 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7675 (tm-30)
REVERT: A  190 MET cc_start: 0.8202 (tmm) cc_final: 0.7758 (ttt)
REVERT: A  238 GLU cc_start: 0.7995 (tt0) cc_final: 0.7783 (tt0)
REVERT: A  333 LEU cc_start: 0.8694 (mm) cc_final: 0.8469 (mt)
REVERT: A  335 GLU cc_start: 0.7931 (tp30) cc_final: 0.7380 (mm-30)
REVERT: A  338 ASP cc_start: 0.7777 (p0) cc_final: 0.7523 (p0)
REVERT: A  509 ASP cc_start: 0.7184 (p0) cc_final: 0.6870 (p0)
REVERT: A  525 PHE cc_start: 0.8510 (m-10) cc_final: 0.8304 (m-10)
REVERT: A  564 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7596 (mp0)
  outliers start: 16
  outliers final: 11
  residues processed: 168
  average time/residue: 1.1226
  time to fit residues: 198.5498
Evaluate side-chains
  178 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  408 ARG
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  611 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 64 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0370
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
A 572 ASN
A 598 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.119709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.108410 restraints weight = 9639.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.94
r_work: 0.3442 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6522  Z= 0.300
  Angle     :  0.627   9.242   8856  Z= 0.320
  Chirality :  0.044   0.173    929
  Planarity :  0.004   0.045   1144
  Dihedral  :  4.840  46.548    875
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 23.79 %
    Favored  : 74.01 %
  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:  0.28 (0.30), residues: 776
  helix:  1.32 (0.28), residues: 372
  sheet:  1.62 (0.73), residues: 51
  loop : -1.34 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 165 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.030   0.002   PHE A  28 
 TYR   0.024   0.002   TYR A 183 
 ARG   0.007   0.000   ARG A 340 

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
REVERT: B  350 VAL cc_start: 0.8070 (t) cc_final: 0.7739 (p)
REVERT: B  365 TYR cc_start: 0.8501 (m-10) cc_final: 0.8163 (m-10)
REVERT: B  524 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7371 (p)
REVERT: A   30 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7320 (mp0)
REVERT: A   66 GLU cc_start: 0.7969 (tp30) cc_final: 0.7701 (tp30)
REVERT: A   74 GLU cc_start: 0.7942 (tp30) cc_final: 0.7499 (tp30)
REVERT: A   75 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7673 (tm-30)
REVERT: A  190 MET cc_start: 0.8232 (tmm) cc_final: 0.7784 (ttt)
REVERT: A  238 GLU cc_start: 0.8002 (tt0) cc_final: 0.7791 (tt0)
REVERT: A  333 LEU cc_start: 0.8698 (mm) cc_final: 0.8471 (mt)
REVERT: A  335 GLU cc_start: 0.7934 (tp30) cc_final: 0.7388 (mm-30)
REVERT: A  509 ASP cc_start: 0.7201 (p0) cc_final: 0.6892 (p0)
REVERT: A  564 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7612 (mp0)
REVERT: A  568 LEU cc_start: 0.8651 (tm) cc_final: 0.8439 (tt)
  outliers start: 15
  outliers final: 11
  residues processed: 169
  average time/residue: 1.1375
  time to fit residues: 202.4312
Evaluate side-chains
  179 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain A residue  611 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 36 optimal weight:    0.0570
   chunk 34 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0970
   chunk 16 optimal weight:    0.9990
   chunk 40 optimal weight:    0.2980
   overall best weight:    0.1496

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
A 572 ASN
A 598 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.123797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.112180 restraints weight = 9807.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.99
r_work: 0.3501 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6522  Z= 0.173
  Angle     :  0.588   9.446   8856  Z= 0.295
  Chirality :  0.040   0.160    929
  Planarity :  0.004   0.045   1144
  Dihedral  :  4.395  39.931    875
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 24.23 %
    Favored  : 73.72 %
  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:  0.59 (0.31), residues: 776
  helix:  1.57 (0.28), residues: 368
  sheet:  1.54 (0.74), residues: 51
  loop : -1.08 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.025   0.001   PHE A  28 
 TYR   0.022   0.001   TYR A 183 
 ARG   0.008   0.000   ARG A 340 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5978.07 seconds
wall clock time: 106 minutes 3.92 seconds (6363.92 seconds total)