Starting phenix.real_space_refine
on Thu Jul  2 23:48:34 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7zrm_14919/07_2026/7zrm_14919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zrm_14919/07_2026/7zrm_14919.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2026/7zrm_14919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2026/7zrm_14919.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2026/7zrm_14919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2026/7zrm_14919.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2026/7zrm_14919.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2026/7zrm_14919.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.007
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: 7
    Type Number    sf(0)   Gaussians
     K       5      8.98       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      62      5.16       5
     C    6971      2.51       5
     N    1826      2.21       5
     O    1971      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10839
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4155
          Classifications: {'peptide': 557}
          Link IDs: {'PTRANS': 25, 'TRANS': 531}
    Chain: "C"
      Number of atoms: 1431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1431
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 13, 'TRANS': 176}
    Chain: "D"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 200
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "B"
      Number of atoms: 5020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 676, 5020
          Classifications: {'peptide': 676}
          Link IDs: {'PTRANS': 26, 'TRANS': 649}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PHD:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {'  K': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.55, per 1000 atoms: 0.24
  Number of scatterers: 10839
  At special positions: 0
  Unit cell: (94.116, 110.308, 149.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     K       5     19.00
     S      62     16.00
     P       3     15.00
     Mg      1     11.99
     O    1971      8.00
     N    1826      7.00
     C    6971      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 425.0 milliseconds
  

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2638

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 11 sheets defined
      62.6% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 32
      Proline residue:  A  22  - end of helix
      removed outlier: 3.986A  pdb=" N   SER A  25 " --> pdb=" O   ARG A  21 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLY A  26 " --> pdb=" O   PRO A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 51
    Processing helix  chain 'A' and resid 58 through 83
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 125 through 132
    Processing helix  chain 'A' and resid 133 through 157
    Processing helix  chain 'A' and resid 165 through 177
    Processing helix  chain 'A' and resid 177 through 193
      removed outlier: 4.122A  pdb=" N   VAL A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 3.883A  pdb=" N   GLN A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 274
      removed outlier: 4.528A  pdb=" N   ILE A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
      Proline residue:  A 263  - end of helix
    Processing helix  chain 'A' and resid 277 through 305
      removed outlier: 4.067A  pdb=" N   LEU A 283 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ILE A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 312
      removed outlier: 3.965A  pdb=" N   LEU A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 342
    Processing helix  chain 'A' and resid 355 through 368
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 377 through 399
    Processing helix  chain 'A' and resid 410 through 437
      removed outlier: 4.588A  pdb=" N   THR A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      Proline residue:  A 425  - end of helix
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 449 through 465
      removed outlier: 4.059A  pdb=" N   PHE A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 509
      Proline residue:  A 499  - end of helix
      removed outlier: 3.795A  pdb=" N   SER A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 550
      removed outlier: 4.019A  pdb=" N   PHE A 527 " --> pdb=" O   HIS A 523 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR A 542 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   PHE A 543 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      Proline residue:  A 545  - end of helix
    Processing helix  chain 'A' and resid 550 through 557
    Processing helix  chain 'C' and resid 3 through 21
      removed outlier: 3.804A  pdb=" N   ALA C   7 " --> pdb=" O   GLY C   3 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   THR C  18 " --> pdb=" O   LEU C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 34
    Processing helix  chain 'C' and resid 34 through 39
    Processing helix  chain 'C' and resid 91 through 109
    Processing helix  chain 'C' and resid 133 through 140
    Processing helix  chain 'C' and resid 140 through 148
      removed outlier: 3.833A  pdb=" N   VAL C 144 " --> pdb=" O   GLN C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 162
    Processing helix  chain 'C' and resid 178 through 190
    Processing helix  chain 'D' and resid 2 through 25
    Processing helix  chain 'B' and resid 11 through 25
      removed outlier: 4.590A  pdb=" N   GLU B  20 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   ALA B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS B  23 " --> pdb=" O   LYS B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 32
      removed outlier: 4.497A  pdb=" N   ARG B  32 " --> pdb=" O   ALA B  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 29 through 32'
    Processing helix  chain 'B' and resid 33 through 55
      removed outlier: 3.522A  pdb=" N   VAL B  39 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 97
      removed outlier: 3.832A  pdb=" N   SER B  65 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 126
      removed outlier: 4.124A  pdb=" N   GLN B 125 " --> pdb=" O   PRO B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 207
      removed outlier: 4.099A  pdb=" N   VAL B 207 " --> pdb=" O   MET B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 247
      removed outlier: 3.844A  pdb=" N   TRP B 240 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      Proline residue:  B 241  - end of helix
    Processing helix  chain 'B' and resid 251 through 263
      removed outlier: 3.569A  pdb=" N   LEU B 255 " --> pdb=" O   SER B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 285
      removed outlier: 5.823A  pdb=" N   SER B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   ALA B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 298
      removed outlier: 3.980A  pdb=" N   VAL B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA B 297 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 341
      removed outlier: 3.843A  pdb=" N   ALA B 336 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU B 339 " --> pdb=" O   ASP B 335 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   SER B 341 " --> pdb=" O   ALA B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 361
    Processing helix  chain 'B' and resid 397 through 409
    Processing helix  chain 'B' and resid 413 through 427
    Processing helix  chain 'B' and resid 452 through 464
    Processing helix  chain 'B' and resid 474 through 484
      removed outlier: 3.801A  pdb=" N   GLU B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 509
      removed outlier: 4.141A  pdb=" N   LYS B 499 " --> pdb=" O   THR B 495 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   LEU B 500 " --> pdb=" O   PRO B 496 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ARG B 504 " --> pdb=" O   LEU B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 529
    Processing helix  chain 'B' and resid 539 through 546
    Processing helix  chain 'B' and resid 557 through 595
      removed outlier: 4.097A  pdb=" N   ASP B 583 " --> pdb=" O   SER B 579 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   VAL B 584 " --> pdb=" O   ILE B 580 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   ALA B 585 " --> pdb=" O   ALA B 581 " (cutoff:3.500A)
      Proline residue:  B 592  - end of helix
      removed outlier: 3.809A  pdb=" N   PHE B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 606
      removed outlier: 3.838A  pdb=" N   ASN B 603 " --> pdb=" O   PRO B 600 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ALA B 604 " --> pdb=" O   GLN B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 638
      removed outlier: 3.868A  pdb=" N   ILE B 628 " --> pdb=" O   ASN B 624 " (cutoff:3.500A)
      Proline residue:  B 633  - end of helix
    Processing helix  chain 'B' and resid 645 through 658
    Processing helix  chain 'B' and resid 658 through 680
      Proline residue:  B 665  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205
    Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45
      removed outlier: 3.915A  pdb=" N   GLY C  51 " --> pdb=" O   ILE C  43 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   GLU C  45 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   VAL C  49 " --> pdb=" O   GLU C  45 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132
      removed outlier: 3.718A  pdb=" N   ILE C 132 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 106 through 107
      removed outlier: 3.553A  pdb=" N   ALA B 106 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 134
      removed outlier: 3.542A  pdb=" N   VAL B 134 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 145
    Processing sheet with id=AA8, first strand: chain 'B' and resid 165 through 168
      removed outlier: 3.849A  pdb=" N   VAL B 165 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B 151 " --> pdb=" O   ARG B 167 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 287 through 289
      removed outlier: 6.199A  pdb=" N   ALA B 532 " --> pdb=" O   MET B 548 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   ASP B 550 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ALA B 534 " --> pdb=" O   ASP B 550 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL B 531 " --> pdb=" O   VAL B 513 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY B 517 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   LEU B 304 " --> pdb=" O   VAL B 468 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322
      removed outlier: 7.573A  pdb=" N   ALA B 444 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   PHE B 322 " --> pdb=" O   VAL B 442 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL B 442 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   GLY B 441 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL B 433 " --> pdb=" O   GLY B 441 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG B 394 " --> pdb=" O   VAL B 434 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 319 through 322
      removed outlier: 7.573A  pdb=" N   ALA B 444 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   PHE B 322 " --> pdb=" O   VAL B 442 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL B 442 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)

    654 hydrogen bonds defined for protein.
    1929 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: 1.79

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1767
        1.32 -     1.44: 2731
        1.44 -     1.57: 6421
        1.57 -     1.70: 4
        1.70 -     1.82: 112
  Bond restraints: 11035
  Sorted by residual:
  bond pdb=" OD1 PHD B 307 "
       pdb=" P   PHD B 307 "
    ideal  model  delta    sigma   weight residual
    1.816  1.593  0.223 2.00e-02 2.50e+03 1.24e+02
  bond pdb=" C   ASN B  26 "
       pdb=" N   PRO B  27 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.57e+00
  bond pdb=" CG  PHD B 307 "
       pdb=" OD1 PHD B 307 "
    ideal  model  delta    sigma   weight residual
    1.300  1.330 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" SD  MET A 489 "
       pdb=" CE  MET A 489 "
    ideal  model  delta    sigma   weight residual
    1.791  1.754  0.037 2.50e-02 1.60e+03 2.17e+00
  bond pdb=" CB  PRO B 164 "
       pdb=" CG  PRO B 164 "
    ideal  model  delta    sigma   weight residual
    1.492  1.561 -0.069 5.00e-02 4.00e+02 1.93e+00
  ... (remaining 11030 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 14697
        2.33 -     4.66: 246
        4.66 -     6.99: 66
        6.99 -     9.32: 14
        9.32 -    11.65: 3
  Bond angle restraints: 15026
  Sorted by residual:
  angle pdb=" C   GLY A 374 "
        pdb=" N   GLY A 375 "
        pdb=" CA  GLY A 375 "
      ideal   model   delta    sigma   weight residual
     121.41  130.73   -9.32 1.96e+00 2.60e-01 2.26e+01
  angle pdb=" CB  MET A 501 "
        pdb=" CG  MET A 501 "
        pdb=" SD  MET A 501 "
      ideal   model   delta    sigma   weight residual
     112.70  124.35  -11.65 3.00e+00 1.11e-01 1.51e+01
  angle pdb=" C   PHE A 471 "
        pdb=" N   ALA A 472 "
        pdb=" CA  ALA A 472 "
      ideal   model   delta    sigma   weight residual
     121.54  128.79   -7.25 1.91e+00 2.74e-01 1.44e+01
  angle pdb=" CA  TYR A 381 "
        pdb=" CB  TYR A 381 "
        pdb=" CG  TYR A 381 "
      ideal   model   delta    sigma   weight residual
     113.90  120.47   -6.57 1.80e+00 3.09e-01 1.33e+01
  angle pdb=" C   PRO B  27 "
        pdb=" N   GLN B  28 "
        pdb=" CA  GLN B  28 "
      ideal   model   delta    sigma   weight residual
     122.08  127.12   -5.04 1.47e+00 4.63e-01 1.17e+01
  ... (remaining 15021 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.60: 6172
       24.60 -    49.19: 345
       49.19 -    73.79: 29
       73.79 -    98.38: 8
       98.38 -   122.98: 1
  Dihedral angle restraints: 6555
    sinusoidal: 2449
      harmonic: 4106
  Sorted by residual:
  dihedral pdb=" O1B ADP B 701 "
           pdb=" O3A ADP B 701 "
           pdb=" PB  ADP B 701 "
           pdb=" PA  ADP B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   62.97 -122.98     1      2.00e+01 2.50e-03 3.71e+01
  dihedral pdb=" CA  THR A 542 "
           pdb=" C   THR A 542 "
           pdb=" N   PHE A 543 "
           pdb=" CA  PHE A 543 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.34  -20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  GLY A 495 "
           pdb=" C   GLY A 495 "
           pdb=" N   VAL A 496 "
           pdb=" CA  VAL A 496 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.52   20.48     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 6552 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1361
       0.051 -    0.101: 365
       0.101 -    0.152: 75
       0.152 -    0.203: 8
       0.203 -    0.253: 2
  Chirality restraints: 1811
  Sorted by residual:
  chirality pdb=" CB  ILE A 348 "
            pdb=" CA  ILE A 348 "
            pdb=" CG1 ILE A 348 "
            pdb=" CG2 ILE A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  THR A 424 "
            pdb=" N   THR A 424 "
            pdb=" C   THR A 424 "
            pdb=" CB  THR A 424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CG  LEU A  77 "
            pdb=" CB  LEU A  77 "
            pdb=" CD1 LEU A  77 "
            pdb=" CD2 LEU A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1808 not shown)

  Planarity restraints: 1902
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 163 "   -0.067 5.00e-02 4.00e+02   1.01e-01 1.63e+01
        pdb=" N   PRO B 164 "    0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO B 164 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 164 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 100 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.69e+00
        pdb=" C   VAL B 100 "    0.045 2.00e-02 2.50e+03
        pdb=" O   VAL B 100 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS B 101 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 495 "   -0.042 5.00e-02 4.00e+02   6.33e-02 6.40e+00
        pdb=" N   PRO B 496 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 496 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 496 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1899 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.84: 3415
        2.84 -     3.41: 12354
        3.41 -     3.99: 20829
        3.99 -     4.56: 29249
        4.56 -     5.14: 42180
  Nonbonded interactions: 108027
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 413 "
            pdb=" OG1 THR A 417 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG  SER A 343 "
            pdb=" O   ASN A 466 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   SER A 119 "
            pdb=" OG1 THR A 123 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   VAL A 107 "
            pdb=" OG1 THR A 111 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OG1 THR A 113 "
            pdb=" OD1 ASN A 466 "
     model   vdw
     2.305 3.040
  ... (remaining 108022 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 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:             0.900
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.930
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
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      :  0.004   0.223  11035  Z= 0.209
  Angle     :  0.808  11.653  15026  Z= 0.402
  Chirality :  0.048   0.253   1811
  Planarity :  0.006   0.101   1902
  Dihedral  : 14.868 122.976   3917
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.20), residues: 1439
  helix:  0.02 (0.16), residues: 864
  sheet: -1.95 (0.59), residues: 74
  loop : -2.29 (0.24), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A  44 
 TYR   0.034   0.002   TYR A 381 
 PHE   0.023   0.002   PHE A 109 
 TRP   0.041   0.002   TRP A 176 
 HIS   0.005   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.21 (11035)
  covalent geometry    : angle       0.80839 /  0.40 (15026)
  hydrogen bonds       : bond        0.10641 /  7.27 (  653)
  hydrogen bonds       : angle       5.32308 /  3.83 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A  360 MET cc_start: 0.7207 (tmm) cc_final: 0.6960 (tmm)
REVERT: C  170 TYR cc_start: 0.6769 (p90) cc_final: 0.6355 (p90)
REVERT: D   21 TYR cc_start: 0.7067 (t80) cc_final: 0.6453 (t80)
REVERT: B   36 MET cc_start: 0.7431 (mmt) cc_final: 0.7136 (mmt)
REVERT: B   74 ILE cc_start: 0.7513 (pt) cc_final: 0.7143 (mt)
REVERT: B  101 LYS cc_start: 0.6504 (mtmm) cc_final: 0.6014 (pptt)
REVERT: B  332 THR cc_start: 0.6743 (p) cc_final: 0.6405 (t)
REVERT: B  383 MET cc_start: 0.5847 (ppp) cc_final: 0.5314 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0796
  time to fit residues: 22.2083
Evaluate side-chains
  150 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.5384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
A 129 GLN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 231 ASN
** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 GLN
B 521 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.143815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.115171 restraints weight = 17046.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.117227 restraints weight = 9261.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118573 restraints weight = 6280.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.119195 restraints weight = 4931.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.119732 restraints weight = 4349.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11035  Z= 0.152
  Angle     :  0.578   6.302  15026  Z= 0.290
  Chirality :  0.040   0.155   1811
  Planarity :  0.005   0.053   1902
  Dihedral  :  5.914 119.548   1537
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.82 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.22), residues: 1439
  helix:  0.83 (0.17), residues: 861
  sheet: -1.26 (0.74), residues: 50
  loop : -2.19 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  44 
 TYR   0.027   0.001   TYR A 381 
 PHE   0.014   0.001   PHE A 373 
 TRP   0.012   0.001   TRP A 176 
 HIS   0.003   0.001   HIS A 351 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 (11035)
  covalent geometry    : angle       0.57771 /  0.29 (15026)
  hydrogen bonds       : bond        0.03919 /  2.65 (  653)
  hydrogen bonds       : angle       4.52305 /  3.28 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 157
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A  360 MET cc_start: 0.7369 (tmm) cc_final: 0.7135 (tmm)
REVERT: A  366 MET cc_start: 0.8584 (ttm) cc_final: 0.8375 (ttm)
REVERT: C  170 TYR cc_start: 0.7000 (p90) cc_final: 0.6641 (p90)
REVERT: B  203 MET cc_start: 0.6322 (ptt) cc_final: 0.6115 (ptt)
REVERT: B  332 THR cc_start: 0.6803 (p) cc_final: 0.6450 (t)
REVERT: B  383 MET cc_start: 0.6066 (ppp) cc_final: 0.5543 (tpp)
  outliers start: 10
  outliers final: 8
  residues processed: 160
  average time/residue: 0.0832
  time to fit residues: 20.4564
Evaluate side-chains
  152 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  629 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 109 optimal weight:    8.9990
   chunk 114 optimal weight:    7.9990
   chunk 104 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 138 optimal weight:    0.3980
   chunk 135 optimal weight:    0.8980
   chunk 142 optimal weight:    5.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 231 ASN
A 319 ASN
A 367 GLN
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 ASN
B 563 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.144622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.116047 restraints weight = 17188.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.118176 restraints weight = 9247.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.119268 restraints weight = 6198.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120283 restraints weight = 4969.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.120709 restraints weight = 4263.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11035  Z= 0.114
  Angle     :  0.536   7.665  15026  Z= 0.267
  Chirality :  0.039   0.151   1811
  Planarity :  0.004   0.051   1902
  Dihedral  :  5.762 118.341   1537
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.73 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.22), residues: 1439
  helix:  1.25 (0.18), residues: 852
  sheet: -1.36 (0.74), residues: 50
  loop : -2.15 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 293 
 TYR   0.028   0.001   TYR A 381 
 PHE   0.013   0.001   PHE A 494 
 TRP   0.016   0.001   TRP A 176 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.11 (11035)
  covalent geometry    : angle       0.53626 /  0.27 (15026)
  hydrogen bonds       : bond        0.03632 /  2.45 (  653)
  hydrogen bonds       : angle       4.31687 /  3.13 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  366 MET cc_start: 0.8556 (ttm) cc_final: 0.8343 (ttm)
REVERT: B  131 ILE cc_start: 0.6775 (tp) cc_final: 0.6486 (tt)
REVERT: B  203 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6426 (ptt)
REVERT: B  383 MET cc_start: 0.6175 (ppp) cc_final: 0.5842 (tpp)
  outliers start: 16
  outliers final: 10
  residues processed: 164
  average time/residue: 0.0797
  time to fit residues: 19.8130
Evaluate side-chains
  154 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   24 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  679 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 140 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 97 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 68 optimal weight:   10.0000
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 231 ASN
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.143294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.114605 restraints weight = 17197.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116666 restraints weight = 9313.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.118015 restraints weight = 6286.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.118673 restraints weight = 4924.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.119109 restraints weight = 4325.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11035  Z= 0.126
  Angle     :  0.533   6.277  15026  Z= 0.266
  Chirality :  0.039   0.152   1811
  Planarity :  0.004   0.049   1902
  Dihedral  :  5.696 116.854   1537
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.55 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.22), residues: 1439
  helix:  1.38 (0.18), residues: 851
  sheet: -1.37 (0.73), residues: 50
  loop : -2.09 (0.24), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 400 
 TYR   0.025   0.001   TYR A 381 
 PHE   0.013   0.001   PHE A 327 
 TRP   0.016   0.001   TRP A 176 
 HIS   0.002   0.001   HIS A 351 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 (11035)
  covalent geometry    : angle       0.53267 /  0.27 (15026)
  hydrogen bonds       : bond        0.03609 /  2.43 (  653)
  hydrogen bonds       : angle       4.30096 /  3.12 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A  366 MET cc_start: 0.8668 (ttm) cc_final: 0.8443 (ttm)
REVERT: C  169 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7863 (mtmt)
REVERT: B   36 MET cc_start: 0.7328 (mmt) cc_final: 0.7087 (mmt)
REVERT: B  131 ILE cc_start: 0.6868 (tp) cc_final: 0.6585 (tt)
REVERT: B  186 TRP cc_start: 0.2571 (p-90) cc_final: 0.2328 (p-90)
REVERT: B  203 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.6347 (ptt)
REVERT: B  383 MET cc_start: 0.6259 (ppp) cc_final: 0.5849 (tpp)
  outliers start: 22
  outliers final: 16
  residues processed: 165
  average time/residue: 0.0746
  time to fit residues: 18.6473
Evaluate side-chains
  160 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  414 MET
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   24 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  679 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 129 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 118 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 101 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 116 optimal weight:    0.9980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
A 129 GLN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 231 ASN
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.142265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.113206 restraints weight = 17187.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.115132 restraints weight = 9125.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.116702 restraints weight = 6224.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.117460 restraints weight = 4811.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.118115 restraints weight = 4181.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11035  Z= 0.134
  Angle     :  0.539   6.198  15026  Z= 0.270
  Chirality :  0.039   0.152   1811
  Planarity :  0.004   0.050   1902
  Dihedral  :  5.633 115.758   1537
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.34 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.22), residues: 1439
  helix:  1.39 (0.18), residues: 857
  sheet: -1.36 (0.74), residues: 50
  loop : -2.05 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  44 
 TYR   0.024   0.001   TYR A 381 
 PHE   0.015   0.001   PHE A 494 
 TRP   0.023   0.001   TRP A 176 
 HIS   0.002   0.001   HIS A 351 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 (11035)
  covalent geometry    : angle       0.53862 /  0.27 (15026)
  hydrogen bonds       : bond        0.03634 /  2.44 (  653)
  hydrogen bonds       : angle       4.30040 /  3.13 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  366 MET cc_start: 0.8717 (ttm) cc_final: 0.8505 (ttm)
REVERT: C  169 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7898 (mtmt)
REVERT: B   36 MET cc_start: 0.7491 (mmt) cc_final: 0.7215 (mmt)
REVERT: B  131 ILE cc_start: 0.6869 (tp) cc_final: 0.6563 (tt)
REVERT: B  203 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6328 (ptt)
REVERT: B  383 MET cc_start: 0.6274 (ppp) cc_final: 0.5860 (tpp)
  outliers start: 28
  outliers final: 21
  residues processed: 161
  average time/residue: 0.0854
  time to fit residues: 20.9576
Evaluate side-chains
  166 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  414 MET
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   24 ILE
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  679 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 111 optimal weight:    7.9990
   chunk 80 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
A 129 GLN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN
B 521 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.142313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.113294 restraints weight = 17192.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.115444 restraints weight = 9443.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116514 restraints weight = 6337.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.117536 restraints weight = 5092.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.117941 restraints weight = 4363.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11035  Z= 0.124
  Angle     :  0.536   8.668  15026  Z= 0.266
  Chirality :  0.039   0.148   1811
  Planarity :  0.004   0.050   1902
  Dihedral  :  5.498 114.677   1537
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.84 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.22), residues: 1439
  helix:  1.46 (0.18), residues: 858
  sheet: -1.79 (0.67), residues: 60
  loop : -2.06 (0.25), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  44 
 TYR   0.024   0.001   TYR A 381 
 PHE   0.014   0.001   PHE A 494 
 TRP   0.017   0.001   TRP B 186 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 (11035)
  covalent geometry    : angle       0.53638 /  0.27 (15026)
  hydrogen bonds       : bond        0.03593 /  2.41 (  653)
  hydrogen bonds       : angle       4.26296 /  3.10 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  366 MET cc_start: 0.8752 (ttm) cc_final: 0.8362 (ttm)
REVERT: A  389 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7813 (mp)
REVERT: B   36 MET cc_start: 0.7550 (mmt) cc_final: 0.7275 (mmt)
REVERT: B  131 ILE cc_start: 0.6816 (tp) cc_final: 0.6511 (tt)
REVERT: B  383 MET cc_start: 0.6224 (ppp) cc_final: 0.5865 (tpp)
  outliers start: 29
  outliers final: 21
  residues processed: 164
  average time/residue: 0.0818
  time to fit residues: 20.5425
Evaluate side-chains
  162 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   24 ILE
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  679 CYS
Chi-restraints excluded: chain B residue  681 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 90 optimal weight:    0.5980
   chunk 92 optimal weight:   10.0000
   chunk 119 optimal weight:   30.0000
   chunk 123 optimal weight:    7.9990
   chunk 127 optimal weight:    5.9990
   chunk 132 optimal weight:    6.9990
   chunk 11 optimal weight:    0.5980
   chunk 141 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
A 129 GLN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.143130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.115685 restraints weight = 16891.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.116250 restraints weight = 9922.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.116478 restraints weight = 7212.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.116903 restraints weight = 6458.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.116972 restraints weight = 5855.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11035  Z= 0.113
  Angle     :  0.531   8.038  15026  Z= 0.263
  Chirality :  0.039   0.143   1811
  Planarity :  0.004   0.050   1902
  Dihedral  :  5.376 113.450   1537
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.81 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.22), residues: 1439
  helix:  1.53 (0.18), residues: 856
  sheet: -1.65 (0.67), residues: 60
  loop : -2.06 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  44 
 TYR   0.027   0.001   TYR A 381 
 PHE   0.013   0.001   PHE A 494 
 TRP   0.015   0.001   TRP B 186 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 (11035)
  covalent geometry    : angle       0.53128 /  0.26 (15026)
  hydrogen bonds       : bond        0.03525 /  2.36 (  653)
  hydrogen bonds       : angle       4.23145 /  3.09 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  225 ILE cc_start: 0.9197 (tp) cc_final: 0.8953 (tp)
REVERT: A  316 SER cc_start: 0.8683 (t) cc_final: 0.8433 (p)
REVERT: A  366 MET cc_start: 0.8600 (ttm) cc_final: 0.8328 (ttm)
REVERT: A  389 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7821 (mp)
REVERT: B  131 ILE cc_start: 0.6806 (tp) cc_final: 0.6526 (tt)
REVERT: B  383 MET cc_start: 0.6329 (ppp) cc_final: 0.5915 (tpp)
  outliers start: 20
  outliers final: 16
  residues processed: 159
  average time/residue: 0.0755
  time to fit residues: 18.6815
Evaluate side-chains
  157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  679 CYS
Chi-restraints excluded: chain B residue  681 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 71 optimal weight:    0.3980
   chunk 108 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 94 optimal weight:    8.9990
   chunk 8 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 135 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 139 optimal weight:    6.9990
   overall best weight:    0.8520

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.142946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.113770 restraints weight = 17114.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.115987 restraints weight = 9133.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.117224 restraints weight = 6101.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.118180 restraints weight = 4827.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.118581 restraints weight = 4181.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11035  Z= 0.115
  Angle     :  0.530   7.545  15026  Z= 0.262
  Chirality :  0.039   0.145   1811
  Planarity :  0.004   0.049   1902
  Dihedral  :  5.324 112.122   1537
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.28 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.22), residues: 1439
  helix:  1.52 (0.18), residues: 860
  sheet: -1.55 (0.68), residues: 60
  loop : -2.11 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 400 
 TYR   0.026   0.001   TYR A 381 
 PHE   0.010   0.001   PHE A 373 
 TRP   0.014   0.001   TRP B 186 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.12 (11035)
  covalent geometry    : angle       0.52993 /  0.26 (15026)
  hydrogen bonds       : bond        0.03504 /  2.34 (  653)
  hydrogen bonds       : angle       4.22056 /  3.09 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A  225 ILE cc_start: 0.9193 (tp) cc_final: 0.8931 (tp)
REVERT: A  316 SER cc_start: 0.8678 (t) cc_final: 0.8476 (p)
REVERT: A  366 MET cc_start: 0.8640 (ttm) cc_final: 0.8374 (ttm)
REVERT: A  389 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7781 (mp)
REVERT: B  131 ILE cc_start: 0.6848 (tp) cc_final: 0.6520 (tt)
REVERT: B  383 MET cc_start: 0.6292 (ppp) cc_final: 0.5912 (tpp)
  outliers start: 27
  outliers final: 20
  residues processed: 162
  average time/residue: 0.0728
  time to fit residues: 18.1404
Evaluate side-chains
  160 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  414 MET
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  679 CYS
Chi-restraints excluded: chain B residue  681 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 123 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 121 optimal weight:    6.9990
   chunk 127 optimal weight:    8.9990
   chunk 97 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 132 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
A 129 GLN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.143367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.115810 restraints weight = 16930.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.116172 restraints weight = 10366.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.116661 restraints weight = 7233.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117195 restraints weight = 6496.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.117310 restraints weight = 5918.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11035  Z= 0.114
  Angle     :  0.537   7.195  15026  Z= 0.266
  Chirality :  0.039   0.146   1811
  Planarity :  0.004   0.049   1902
  Dihedral  :  5.314 111.377   1537
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.90 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.22), residues: 1439
  helix:  1.56 (0.18), residues: 859
  sheet: -1.49 (0.68), residues: 60
  loop : -2.07 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 400 
 TYR   0.025   0.001   TYR A 381 
 PHE   0.013   0.001   PHE A 494 
 TRP   0.026   0.001   TRP A 176 
 HIS   0.003   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 (11035)
  covalent geometry    : angle       0.53656 /  0.27 (15026)
  hydrogen bonds       : bond        0.03498 /  2.34 (  653)
  hydrogen bonds       : angle       4.21349 /  3.08 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  225 ILE cc_start: 0.9171 (tp) cc_final: 0.8919 (tp)
REVERT: A  357 LEU cc_start: 0.8047 (tt) cc_final: 0.7634 (tt)
REVERT: A  366 MET cc_start: 0.8605 (ttm) cc_final: 0.8347 (ttm)
REVERT: A  389 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7771 (mp)
REVERT: B  131 ILE cc_start: 0.6870 (tp) cc_final: 0.6577 (tt)
REVERT: B  383 MET cc_start: 0.6283 (ppp) cc_final: 0.5908 (tpp)
  outliers start: 25
  outliers final: 20
  residues processed: 157
  average time/residue: 0.0784
  time to fit residues: 19.0401
Evaluate side-chains
  161 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  679 CYS
Chi-restraints excluded: chain B residue  681 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0570
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 140 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 109 optimal weight:    9.9990
   chunk 67 optimal weight:    0.3980
   chunk 138 optimal weight:    3.9990
   overall best weight:    0.8902

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.143345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.114151 restraints weight = 16968.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.116270 restraints weight = 9089.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117687 restraints weight = 6129.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.118390 restraints weight = 4788.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118792 restraints weight = 4199.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  11035  Z= 0.121
  Angle     :  0.552  12.366  15026  Z= 0.277
  Chirality :  0.039   0.163   1811
  Planarity :  0.004   0.049   1902
  Dihedral  :  5.312 110.916   1537
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.81 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.22), residues: 1439
  helix:  1.62 (0.18), residues: 854
  sheet: -1.43 (0.69), residues: 60
  loop : -2.05 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 400 
 TYR   0.025   0.001   TYR A 381 
 PHE   0.024   0.001   PHE A 327 
 TRP   0.025   0.001   TRP A 176 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 (11035)
  covalent geometry    : angle       0.55237 /  0.28 (15026)
  hydrogen bonds       : bond        0.03508 /  2.34 (  653)
  hydrogen bonds       : angle       4.22558 /  3.09 ( 1929)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  225 ILE cc_start: 0.9166 (tp) cc_final: 0.8916 (tp)
REVERT: A  357 LEU cc_start: 0.7967 (tt) cc_final: 0.7573 (tt)
REVERT: A  366 MET cc_start: 0.8648 (ttm) cc_final: 0.8386 (ttm)
REVERT: A  389 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7769 (mp)
REVERT: B  131 ILE cc_start: 0.6840 (tp) cc_final: 0.6524 (tt)
REVERT: B  383 MET cc_start: 0.6207 (ppp) cc_final: 0.5877 (tpp)
  outliers start: 23
  outliers final: 20
  residues processed: 156
  average time/residue: 0.0746
  time to fit residues: 18.1633
Evaluate side-chains
  161 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  114 ASN
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  679 CYS
Chi-restraints excluded: chain B residue  681 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 115 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 93 optimal weight:   20.0000
   chunk 91 optimal weight:    0.0070
   chunk 130 optimal weight:    0.0870
   chunk 30 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.5776

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
A 129 GLN
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 ASN
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.144233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.115189 restraints weight = 17077.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.117121 restraints weight = 9097.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118708 restraints weight = 6221.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.119438 restraints weight = 4806.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.120038 restraints weight = 4182.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11035  Z= 0.108
  Angle     :  0.532   7.312  15026  Z= 0.265
  Chirality :  0.039   0.178   1811
  Planarity :  0.004   0.049   1902
  Dihedral  :  5.263 110.330   1537
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.17 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.22), residues: 1439
  helix:  1.67 (0.18), residues: 855
  sheet: -1.40 (0.70), residues: 60
  loop : -2.06 (0.25), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 400 
 TYR   0.026   0.001   TYR A 381 
 PHE   0.012   0.001   PHE A 494 
 TRP   0.025   0.001   TRP A 176 
 HIS   0.003   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 (11035)
  covalent geometry    : angle       0.53188 /  0.27 (15026)
  hydrogen bonds       : bond        0.03436 /  2.29 (  653)
  hydrogen bonds       : angle       4.20157 /  3.08 ( 1929)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1620.78 seconds
wall clock time: 28 minutes 46.71 seconds (1726.71 seconds total)