Starting phenix.real_space_refine
on Wed Feb 12 06:16:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8m_36074/02_2025/8j8m_36074_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8m_36074/02_2025/8j8m_36074.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8m_36074/02_2025/8j8m_36074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8m_36074/02_2025/8j8m_36074.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8m_36074/02_2025/8j8m_36074_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8m_36074/02_2025/8j8m_36074_neut.cif"
  }
  resolution = 3.58
  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=   0.039
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      27      5.16       5
     C    4811      2.51       5
     N    1188      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7362
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3656
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3579
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 24, 'TRANS': 438}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 4.74, per 1000 atoms: 0.64
  Number of scatterers: 7362
  At special positions: 0
  Unit cell: (99.645, 83.22, 125.925, 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      27     16.00
     O    1336      8.00
     N    1188      7.00
     C    4811      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 382 "
      " NAG E   1 " - " ASN A 366 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 1.92
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1718

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      58.8% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
    Processing helix  chain 'A' and resid 178 through 207
      removed outlier: 3.672A  pdb=" N   ARG A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   TRP A 184 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
      removed outlier: 5.276A  pdb=" N   ASP A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   TYR A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A 252 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 324 through 340
      removed outlier: 4.371A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 354
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.747A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 3.552A  pdb=" N   ASP A 408 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A 409 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 428
    Processing helix  chain 'A' and resid 450 through 459
      removed outlier: 3.817A  pdb=" N   PHE A 459 " --> pdb=" O   GLN A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 516
      removed outlier: 4.218A  pdb=" N   GLU A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ASP A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 532
      removed outlier: 3.800A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'B' and resid 51 through 64
      removed outlier: 3.593A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 79
      removed outlier: 3.648A  pdb=" N   VAL B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 81 through 110
    Processing helix  chain 'B' and resid 115 through 123
      removed outlier: 3.732A  pdb=" N   LEU B 121 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.796A  pdb=" N   ALA B 129 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
      removed outlier: 3.702A  pdb=" N   GLN B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR B 146 " --> pdb=" O   PRO B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.581A  pdb=" N   SER B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 221
      removed outlier: 3.661A  pdb=" N   ALA B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 254
      removed outlier: 3.724A  pdb=" N   PHE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TYR B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 264
    Processing helix  chain 'B' and resid 269 through 300
      removed outlier: 3.596A  pdb=" N   LEU B 274 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
      removed outlier: 3.795A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B 300 " --> pdb=" O   TYR B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 308
    Processing helix  chain 'B' and resid 310 through 320
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.795A  pdb=" N   VAL B 329 " --> pdb=" O   TRP B 325 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLY B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU B 349 " --> pdb=" O   THR B 345 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU B 356 " --> pdb=" O   VAL B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
    Processing helix  chain 'B' and resid 387 through 390
      removed outlier: 3.566A  pdb=" N   SER B 390 " --> pdb=" O   TYR B 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 387 through 390'
    Processing helix  chain 'B' and resid 393 through 395
      No H-bonds generated for 'chain 'B' and resid 393 through 395'
    Processing helix  chain 'B' and resid 396 through 422
      removed outlier: 3.534A  pdb=" N   PHE B 400 " --> pdb=" O   VAL B 396 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA B 409 " --> pdb=" O   TRP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 454
    Processing helix  chain 'B' and resid 454 through 466
      removed outlier: 3.726A  pdb=" N   ILE B 465 " --> pdb=" O   GLY B 461 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 4.359A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 500
    Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227
      removed outlier: 6.320A  pdb=" N   LEU A 225 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   CYS A 432 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   VAL A 466 " --> pdb=" O   CYS A 432 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   SER A 468 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261
      removed outlier: 5.917A  pdb=" N   LEU A 260 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 8.496A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 8.712A  pdb=" N   ARG A 349 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.203A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   GLY A 622 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.997A  pdb=" N   SER A 599 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA A 594 " --> pdb=" O   LEU A 610 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576

    379 hydrogen bonds defined for protein.
    1113 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: 2.16

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2229
        1.34 -     1.45: 1114
        1.45 -     1.57: 4161
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7544
  Sorted by residual:
  bond pdb=" CD2 TRP B 601 "
       pdb=" CE3 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.398  1.555 -0.157 1.60e-02 3.91e+03 9.64e+01
  bond pdb=" CE2 TRP B 601 "
       pdb=" CZ2 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.394  1.549 -0.155 2.10e-02 2.27e+03 5.47e+01
  bond pdb=" CZ2 TRP B 601 "
       pdb=" CH2 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.368  1.491 -0.123 1.90e-02 2.77e+03 4.17e+01
  bond pdb=" CG  TRP B 601 "
       pdb=" CD2 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.433  1.341  0.092 1.80e-02 3.09e+03 2.61e+01
  bond pdb=" CE3 TRP B 601 "
       pdb=" CZ3 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.382  1.493 -0.111 3.00e-02 1.11e+03 1.36e+01
  ... (remaining 7539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 9945
        1.61 -     3.22: 249
        3.22 -     4.83: 53
        4.83 -     6.43: 19
        6.43 -     8.04: 8
  Bond angle restraints: 10274
  Sorted by residual:
  angle pdb=" C   PHE B 231 "
        pdb=" CA  PHE B 231 "
        pdb=" CB  PHE B 231 "
      ideal   model   delta    sigma   weight residual
     116.54  110.91    5.63 1.15e+00 7.56e-01 2.40e+01
  angle pdb=" CA  ILE B 327 "
        pdb=" C   ILE B 327 "
        pdb=" N   PRO B 328 "
      ideal   model   delta    sigma   weight residual
     120.83  118.02    2.81 5.90e-01 2.87e+00 2.27e+01
  angle pdb=" N   TRP B 325 "
        pdb=" CA  TRP B 325 "
        pdb=" C   TRP B 325 "
      ideal   model   delta    sigma   weight residual
     114.31  109.78    4.53 1.29e+00 6.01e-01 1.23e+01
  angle pdb=" CG  TRP B 601 "
        pdb=" CD2 TRP B 601 "
        pdb=" CE3 TRP B 601 "
      ideal   model   delta    sigma   weight residual
     133.90  130.50    3.40 1.00e+00 1.00e+00 1.16e+01
  angle pdb=" N   GLY B 321 "
        pdb=" CA  GLY B 321 "
        pdb=" C   GLY B 321 "
      ideal   model   delta    sigma   weight residual
     115.59  111.10    4.49 1.32e+00 5.74e-01 1.16e+01
  ... (remaining 10269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.12: 4096
       23.12 -    46.23: 306
       46.23 -    69.35: 56
       69.35 -    92.47: 30
       92.47 -   115.58: 32
  Dihedral angle restraints: 4520
    sinusoidal: 1847
      harmonic: 2673
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 164 "
           pdb=" CB  CYS B 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.18  -89.82     1      1.00e+01 1.00e-02 9.57e+01
  dihedral pdb=" O3  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.45  179.87  115.58     1      3.00e+01 1.11e-03 1.53e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   60.03  115.08     1      3.00e+01 1.11e-03 1.52e+01
  ... (remaining 4517 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.194: 1207
       0.194 -    0.389: 3
       0.389 -    0.583: 1
       0.583 -    0.778: 0
       0.778 -    0.972: 1
  Chirality restraints: 1212
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.43   -0.97 2.00e-02 2.50e+03 2.36e+03
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-02 2.50e+03 1.37e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.28   -0.12 2.00e-02 2.50e+03 3.89e+01
  ... (remaining 1209 not shown)

  Planarity restraints: 1275
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 366 "    0.160 2.00e-02 2.50e+03   3.78e-01 1.78e+03
        pdb=" CG  ASN A 366 "   -0.111 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 366 "    0.177 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 366 "   -0.669 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "    0.443 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 425 "   -0.217 2.00e-02 2.50e+03   2.84e-01 1.01e+03
        pdb=" CG  ASN A 425 "    0.094 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 425 "   -0.016 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 425 "    0.481 2.00e-02 2.50e+03
        pdb=" C1  NAG F   1 "   -0.341 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.332 2.00e-02 2.50e+03   2.82e-01 9.96e+02
        pdb=" C7  NAG D   2 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.178 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.495 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.068 2.00e-02 2.50e+03
  ... (remaining 1272 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 717
        2.74 -     3.28: 7868
        3.28 -     3.82: 12483
        3.82 -     4.36: 13722
        4.36 -     4.90: 23686
  Nonbonded interactions: 58476
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 145 "
            pdb=" OG  SER B 342 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OG1 THR A 460 "
            pdb=" OH  TYR A 554 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OH  TYR A 469 "
            pdb=" O   PRO A 488 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OD1 ASP A 493 "
            pdb=" OG  SER A 496 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   TYR A 251 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.246 3.040
  ... (remaining 58471 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.400
  Find NCS groups from input model:        0.120
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
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   0.157   7544  Z= 0.312
  Angle     :  0.677   8.043  10274  Z= 0.347
  Chirality :  0.053   0.972   1212
  Planarity :  0.016   0.282   1271
  Dihedral  : 20.770 115.585   2799
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  0.63 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.29), residues: 928
  helix:  1.64 (0.25), residues: 498
  sheet: -0.59 (0.58), residues: 63
  loop : -1.04 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 478 
 HIS   0.004   0.001   HIS A 221 
 PHE   0.022   0.001   PHE A 320 
 TYR   0.013   0.001   TYR B 318 
 ARG   0.003   0.000   ARG B 421 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A  508 MET cc_start: 0.7810 (mpp) cc_final: 0.7484 (mpp)
REVERT: B  120 MET cc_start: 0.8447 (ttp) cc_final: 0.7933 (tmm)
REVERT: B  132 LYS cc_start: 0.8921 (tptp) cc_final: 0.8695 (tptp)
REVERT: B  305 MET cc_start: 0.9077 (mtt) cc_final: 0.8713 (mtt)
REVERT: B  365 MET cc_start: 0.8216 (mpp) cc_final: 0.7951 (mpp)
  outliers start: 7
  outliers final: 2
  residues processed: 93
  average time/residue: 0.1453
  time to fit residues: 20.2905
Evaluate side-chains
  59 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  327 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 438 GLN
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 ASN
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 367 HIS
B 505 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.074009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.052503 restraints weight = 31380.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.054478 restraints weight = 15494.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.055648 restraints weight = 10878.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7544  Z= 0.227
  Angle     :  0.750  11.350  10274  Z= 0.337
  Chirality :  0.046   0.300   1212
  Planarity :  0.004   0.046   1271
  Dihedral  : 20.355 116.388   1160
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.99 %
    Favored  : 90.74 %
  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:  0.88 (0.29), residues: 928
  helix:  1.80 (0.24), residues: 505
  sheet: -0.64 (0.59), residues: 63
  loop : -0.95 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 478 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.021   0.002   PHE B 439 
 TYR   0.014   0.001   TYR B 117 
 ARG   0.003   0.000   ARG B 348 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A  271 ASP cc_start: 0.8742 (m-30) cc_final: 0.8440 (t0)
REVERT: A  508 MET cc_start: 0.8292 (mpp) cc_final: 0.7790 (mpp)
REVERT: B  120 MET cc_start: 0.9219 (ttp) cc_final: 0.8621 (tmm)
REVERT: B  365 MET cc_start: 0.8454 (mpp) cc_final: 0.8003 (mpp)
REVERT: B  500 MET cc_start: 0.8670 (mtm) cc_final: 0.8023 (mmt)
  outliers start: 10
  outliers final: 5
  residues processed: 64
  average time/residue: 0.1388
  time to fit residues: 13.8698
Evaluate side-chains
  54 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 273 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.074662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.053567 restraints weight = 31415.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.055609 restraints weight = 15172.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.056803 restraints weight = 10521.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7544  Z= 0.164
  Angle     :  0.693   9.201  10274  Z= 0.306
  Chirality :  0.045   0.290   1212
  Planarity :  0.004   0.041   1271
  Dihedral  : 16.767 110.745   1156
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.42 %
    Favored  : 87.31 %
  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:  1.06 (0.29), residues: 928
  helix:  2.03 (0.24), residues: 499
  sheet: -0.73 (0.60), residues: 65
  loop : -0.91 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.014   0.001   PHE B 439 
 TYR   0.012   0.001   TYR B 117 
 ARG   0.001   0.000   ARG B 348 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 ASP cc_start: 0.8790 (m-30) cc_final: 0.8469 (t0)
REVERT: A  508 MET cc_start: 0.8418 (mpp) cc_final: 0.7884 (mpp)
REVERT: B  120 MET cc_start: 0.9172 (ttp) cc_final: 0.8518 (tmm)
REVERT: B  365 MET cc_start: 0.8340 (mpp) cc_final: 0.8030 (mpp)
REVERT: B  383 MET cc_start: 0.8752 (mtp) cc_final: 0.8185 (ttm)
REVERT: B  500 MET cc_start: 0.8650 (mtm) cc_final: 0.7983 (mmt)
  outliers start: 10
  outliers final: 8
  residues processed: 64
  average time/residue: 0.1370
  time to fit residues: 13.7509
Evaluate side-chains
  60 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  382 ASN
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0050
   chunk 78 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    2.0000

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

Flipped N/Q/H residues before XYZ refinement:
A 347 GLN
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.072788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.052104 restraints weight = 31497.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.054049 restraints weight = 15366.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.055239 restraints weight = 10638.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7544  Z= 0.236
  Angle     :  0.702  13.038  10274  Z= 0.316
  Chirality :  0.045   0.322   1212
  Planarity :  0.004   0.041   1271
  Dihedral  : 15.073 111.677   1156
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.34 %
    Favored  : 83.63 %
  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:  1.08 (0.29), residues: 928
  helix:  2.00 (0.24), residues: 505
  sheet: -0.79 (0.61), residues: 65
  loop : -0.88 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 405 
 HIS   0.002   0.001   HIS A 266 
 PHE   0.013   0.001   PHE B 130 
 TYR   0.011   0.001   TYR B 117 
 ARG   0.003   0.000   ARG B 348 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A  271 ASP cc_start: 0.8765 (m-30) cc_final: 0.8401 (t0)
REVERT: A  508 MET cc_start: 0.8508 (mpp) cc_final: 0.7941 (mpp)
REVERT: B  120 MET cc_start: 0.9173 (ttp) cc_final: 0.7970 (tmm)
REVERT: B  365 MET cc_start: 0.8365 (mpp) cc_final: 0.8083 (mpp)
REVERT: B  383 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8456 (ttm)
REVERT: B  500 MET cc_start: 0.8682 (mtm) cc_final: 0.8029 (mmt)
  outliers start: 16
  outliers final: 11
  residues processed: 63
  average time/residue: 0.1455
  time to fit residues: 14.3200
Evaluate side-chains
  62 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 4 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0770
   chunk 56 optimal weight:    0.6980
   chunk 67 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** A 539 HIS ** 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 = 0.3502 r_free = 0.3502 target = 0.073767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.052706 restraints weight = 31000.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.054714 restraints weight = 14967.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.055897 restraints weight = 10382.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7544  Z= 0.154
  Angle     :  0.659  11.633  10274  Z= 0.294
  Chirality :  0.044   0.291   1212
  Planarity :  0.003   0.039   1271
  Dihedral  : 14.382 111.580   1156
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.62 %
    Favored  : 81.85 %
  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:  1.16 (0.29), residues: 928
  helix:  2.07 (0.24), residues: 506
  sheet: -0.72 (0.60), residues: 65
  loop : -0.86 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 367 
 PHE   0.010   0.001   PHE B 402 
 TYR   0.011   0.001   TYR B 472 
 ARG   0.001   0.000   ARG B 348 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A  271 ASP cc_start: 0.8768 (m-30) cc_final: 0.8357 (t0)
REVERT: A  508 MET cc_start: 0.8523 (mpp) cc_final: 0.7941 (mpp)
REVERT: B  120 MET cc_start: 0.9138 (ttp) cc_final: 0.8001 (tmm)
REVERT: B  365 MET cc_start: 0.8310 (mpp) cc_final: 0.8018 (mpp)
REVERT: B  500 MET cc_start: 0.8599 (mtm) cc_final: 0.7999 (mmt)
  outliers start: 12
  outliers final: 9
  residues processed: 62
  average time/residue: 0.1378
  time to fit residues: 13.4006
Evaluate side-chains
  59 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 47 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    2.3388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.079833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.060052 restraints weight = 30306.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.061764 restraints weight = 17223.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.062805 restraints weight = 12768.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7544  Z= 0.268
  Angle     :  0.701  12.434  10274  Z= 0.321
  Chirality :  0.044   0.298   1212
  Planarity :  0.004   0.039   1271
  Dihedral  : 13.935 112.822   1156
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.50 %
    Favored  : 82.11 %
  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:  1.18 (0.29), residues: 928
  helix:  2.11 (0.24), residues: 505
  sheet: -0.76 (0.61), residues: 65
  loop : -0.86 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 405 
 HIS   0.003   0.001   HIS A 620 
 PHE   0.013   0.001   PHE B 130 
 TYR   0.010   0.001   TYR B 117 
 ARG   0.004   0.000   ARG B 348 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.844 
Fit side-chains
REVERT: A  271 ASP cc_start: 0.8134 (m-30) cc_final: 0.7930 (t0)
REVERT: A  508 MET cc_start: 0.8624 (mpp) cc_final: 0.7953 (mpp)
REVERT: B  120 MET cc_start: 0.8845 (ttp) cc_final: 0.8072 (tmm)
REVERT: B  365 MET cc_start: 0.8505 (mpp) cc_final: 0.8199 (mpp)
  outliers start: 11
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1299
  time to fit residues: 12.0064
Evaluate side-chains
  56 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 73 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 539 HIS ** 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 = 0.3679 r_free = 0.3679 target = 0.079179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.059409 restraints weight = 30232.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.061248 restraints weight = 16969.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.062368 restraints weight = 12473.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7544  Z= 0.206
  Angle     :  0.666  11.562  10274  Z= 0.303
  Chirality :  0.043   0.288   1212
  Planarity :  0.003   0.039   1271
  Dihedral  : 13.624 113.287   1156
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.50 %
    Favored  : 81.73 %
  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:  1.24 (0.29), residues: 928
  helix:  2.10 (0.24), residues: 510
  sheet: -0.58 (0.63), residues: 65
  loop : -0.82 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 405 
 HIS   0.002   0.001   HIS A 620 
 PHE   0.014   0.001   PHE B 130 
 TYR   0.010   0.001   TYR B 117 
 ARG   0.002   0.000   ARG B 348 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A  170 LEU cc_start: 0.9180 (tp) cc_final: 0.8979 (tt)
REVERT: A  271 ASP cc_start: 0.8070 (m-30) cc_final: 0.7816 (t0)
REVERT: A  508 MET cc_start: 0.8653 (mpp) cc_final: 0.7956 (mpp)
REVERT: B  120 MET cc_start: 0.8863 (ttp) cc_final: 0.8182 (tmm)
REVERT: B  289 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8422 (m-10)
REVERT: B  365 MET cc_start: 0.8502 (mpp) cc_final: 0.8177 (mpp)
REVERT: B  500 MET cc_start: 0.8342 (mtm) cc_final: 0.8043 (mmt)
  outliers start: 14
  outliers final: 10
  residues processed: 60
  average time/residue: 0.1536
  time to fit residues: 14.2941
Evaluate side-chains
  60 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 86 optimal weight:    9.9990
   chunk 67 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 30 optimal weight:    0.4980
   chunk 9 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 539 HIS ** 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 = 0.3627 r_free = 0.3627 target = 0.076109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.056277 restraints weight = 31911.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.058260 restraints weight = 16441.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059462 restraints weight = 11807.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7544  Z= 0.176
  Angle     :  0.661  13.189  10274  Z= 0.302
  Chirality :  0.043   0.286   1212
  Planarity :  0.003   0.038   1271
  Dihedral  : 13.400 113.386   1156
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 17.39 %
    Favored  : 81.22 %
  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:  1.31 (0.29), residues: 928
  helix:  2.17 (0.24), residues: 509
  sheet: -0.50 (0.63), residues: 65
  loop : -0.82 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 405 
 HIS   0.002   0.001   HIS A 620 
 PHE   0.027   0.001   PHE B 439 
 TYR   0.009   0.001   TYR B 117 
 ARG   0.002   0.000   ARG B 348 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A  508 MET cc_start: 0.8660 (mpp) cc_final: 0.7957 (mpp)
REVERT: B  120 MET cc_start: 0.8969 (ttp) cc_final: 0.8426 (tmm)
REVERT: B  289 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8397 (m-10)
REVERT: B  365 MET cc_start: 0.8507 (mpp) cc_final: 0.8146 (mpp)
REVERT: B  500 MET cc_start: 0.8510 (mtm) cc_final: 0.8073 (mmt)
  outliers start: 11
  outliers final: 9
  residues processed: 57
  average time/residue: 0.1417
  time to fit residues: 12.9333
Evaluate side-chains
  59 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.076542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.056335 restraints weight = 31576.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.058254 restraints weight = 16691.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059408 restraints weight = 12170.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7544  Z= 0.195
  Angle     :  0.666  13.197  10274  Z= 0.304
  Chirality :  0.043   0.282   1212
  Planarity :  0.003   0.038   1271
  Dihedral  : 13.224 113.351   1156
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.64 %
    Favored  : 80.84 %
  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:  1.33 (0.29), residues: 928
  helix:  2.17 (0.24), residues: 508
  sheet: -0.40 (0.64), residues: 65
  loop : -0.80 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 405 
 HIS   0.003   0.001   HIS A 620 
 PHE   0.019   0.001   PHE B 439 
 TYR   0.008   0.001   TYR B 117 
 ARG   0.003   0.000   ARG B 348 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A  508 MET cc_start: 0.8670 (mpp) cc_final: 0.7984 (mpp)
REVERT: B  120 MET cc_start: 0.8903 (ttp) cc_final: 0.8160 (tmm)
REVERT: B  289 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8360 (m-10)
REVERT: B  365 MET cc_start: 0.8496 (mpp) cc_final: 0.8153 (mpp)
  outliers start: 12
  outliers final: 9
  residues processed: 58
  average time/residue: 0.1325
  time to fit residues: 12.2248
Evaluate side-chains
  58 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 539 HIS ** 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 = 0.3624 r_free = 0.3624 target = 0.076023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.055559 restraints weight = 32449.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.057477 restraints weight = 17404.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.058622 restraints weight = 12797.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7544  Z= 0.208
  Angle     :  0.689  13.253  10274  Z= 0.313
  Chirality :  0.044   0.279   1212
  Planarity :  0.003   0.038   1271
  Dihedral  : 13.106 113.346   1156
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 18.02 %
    Favored  : 80.58 %
  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:  1.34 (0.29), residues: 928
  helix:  2.16 (0.24), residues: 509
  sheet: -0.46 (0.64), residues: 65
  loop : -0.75 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 405 
 HIS   0.002   0.001   HIS A 221 
 PHE   0.019   0.001   PHE B 439 
 TYR   0.009   0.001   TYR B 117 
 ARG   0.003   0.000   ARG B 348 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.868 
Fit side-chains
REVERT: A  508 MET cc_start: 0.8671 (mpp) cc_final: 0.7997 (mpp)
REVERT: A  615 LEU cc_start: 0.8967 (mt) cc_final: 0.8552 (mt)
REVERT: B  120 MET cc_start: 0.8955 (ttp) cc_final: 0.8054 (tmm)
REVERT: B  289 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8377 (m-10)
REVERT: B  365 MET cc_start: 0.8501 (mpp) cc_final: 0.8151 (mpp)
  outliers start: 11
  outliers final: 9
  residues processed: 54
  average time/residue: 0.1383
  time to fit residues: 12.0424
Evaluate side-chains
  59 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 218 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 = 0.3660 r_free = 0.3660 target = 0.078316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.058151 restraints weight = 30433.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.059903 restraints weight = 17121.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.060983 restraints weight = 12709.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7544  Z= 0.284
  Angle     :  0.712  13.370  10274  Z= 0.329
  Chirality :  0.045   0.272   1212
  Planarity :  0.004   0.037   1271
  Dihedral  : 13.080 112.948   1156
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 18.40 %
    Favored  : 80.20 %
  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:  1.29 (0.29), residues: 928
  helix:  2.10 (0.24), residues: 510
  sheet: -0.54 (0.64), residues: 65
  loop : -0.73 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 405 
 HIS   0.004   0.001   HIS A 620 
 PHE   0.019   0.001   PHE B 439 
 TYR   0.009   0.001   TYR B 117 
 ARG   0.003   0.000   ARG B 348 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2262.02 seconds
wall clock time: 41 minutes 26.32 seconds (2486.32 seconds total)