Starting phenix.real_space_refine
on Wed Mar  4 04:50:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zrm_14919/03_2026/7zrm_14919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zrm_14919/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zrm_14919/03_2026/7zrm_14919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zrm_14919/03_2026/7zrm_14919.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zrm_14919/03_2026/7zrm_14919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zrm_14919/03_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-5986/lib/python3.9/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: 2.41, per 1000 atoms: 0.22
  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: 0.96
  Conformation dependent library (CDL) restraints added in 420.3 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: 0.36
  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: 1.82

  Time building geometry restraints manager: 1.24 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:             1.080
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.660
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
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
  covalent geometry    : bond        0.00437 (11035)
  covalent geometry    : angle       0.80839 (15026)
  hydrogen bonds       : bond        0.10641 (  653)
  hydrogen bonds       : angle       5.32308 ( 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  : 0.374 
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: 0.0813
  time to fit residues: 22.5516
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  : 0.378 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3763 r_free = 0.3763 target = 0.143852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.115204 restraints weight = 17040.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.117307 restraints weight = 9248.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118396 restraints weight = 6254.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.119295 restraints weight = 5027.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.119919 restraints weight = 4317.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11035  Z= 0.150
  Angle     :  0.575   6.291  15026  Z= 0.288
  Chirality :  0.040   0.156   1811
  Planarity :  0.005   0.053   1902
  Dihedral  :  5.912 119.427   1537
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.47 %
    Favored  : 90.65 %
  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: -0.48 (0.22), residues: 1439
  helix:  0.83 (0.17), residues: 861
  sheet: -1.26 (0.75), 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   0.028   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
  covalent geometry    : bond        0.00340 (11035)
  covalent geometry    : angle       0.57523 (15026)
  hydrogen bonds       : bond        0.03935 (  653)
  hydrogen bonds       : angle       4.51969 ( 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  : 0.418 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7906 (m-90) cc_final: 0.7688 (m-90)
REVERT: A  360 MET cc_start: 0.7341 (tmm) cc_final: 0.7108 (tmm)
REVERT: A  366 MET cc_start: 0.8582 (ttm) cc_final: 0.8381 (ttm)
REVERT: C  170 TYR cc_start: 0.6979 (p90) cc_final: 0.6660 (p90)
REVERT: B  203 MET cc_start: 0.6375 (ptt) cc_final: 0.6153 (ptt)
REVERT: B  332 THR cc_start: 0.6830 (p) cc_final: 0.6465 (t)
REVERT: B  383 MET cc_start: 0.5963 (ppp) cc_final: 0.5507 (tpp)
  outliers start: 10
  outliers final: 8
  residues processed: 160
  average time/residue: 0.0893
  time to fit residues: 21.9580
Evaluate side-chains
  153 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 145
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 114 optimal weight:    6.9990
   chunk 104 optimal weight:   10.0000
   chunk 106 optimal weight:    0.0570
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 138 optimal weight:    0.5980
   chunk 135 optimal weight:    0.9980
   chunk 142 optimal weight:    4.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3779 r_free = 0.3779 target = 0.145140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.116725 restraints weight = 17159.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.118843 restraints weight = 9221.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120164 restraints weight = 6165.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.120825 restraints weight = 4849.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.121462 restraints weight = 4255.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1217

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= 0.109
  Angle     :  0.531   7.628  15026  Z= 0.264
  Chirality :  0.039   0.149   1811
  Planarity :  0.004   0.052   1902
  Dihedral  :  5.749 118.230   1537
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.55 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.07 (0.22), residues: 1439
  helix:  1.26 (0.18), residues: 851
  sheet: -1.37 (0.74), residues: 50
  loop : -2.14 (0.24), residues: 538

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   0.012   0.001   PHE A 494 
 TRP   0.012   0.001   TRP B 186 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (11035)
  covalent geometry    : angle       0.53104 (15026)
  hydrogen bonds       : bond        0.03594 (  653)
  hydrogen bonds       : angle       4.30901 ( 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
  170 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 156
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7858 (m-90) cc_final: 0.7538 (m-90)
REVERT: A  366 MET cc_start: 0.8544 (ttm) cc_final: 0.8328 (ttm)
REVERT: B  101 LYS cc_start: 0.6623 (mtmm) cc_final: 0.6068 (pptt)
REVERT: B  131 ILE cc_start: 0.6798 (tp) cc_final: 0.6533 (tt)
REVERT: B  203 MET cc_start: 0.6625 (ptt) cc_final: 0.6420 (ptt)
REVERT: B  383 MET cc_start: 0.6206 (ppp) cc_final: 0.5851 (tpp)
  outliers start: 14
  outliers final: 10
  residues processed: 162
  average time/residue: 0.0900
  time to fit residues: 22.2276
Evaluate side-chains
  153 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
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  348 ILE
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  200 LEU
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  629 VAL
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:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:   20.0000
   chunk 52 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0050
   chunk 40 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 68 optimal weight:    9.9990
   overall best weight:    0.9598

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3767 r_free = 0.3767 target = 0.144117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.115515 restraints weight = 17216.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.117590 restraints weight = 9312.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.118751 restraints weight = 6287.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.119739 restraints weight = 5014.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.119999 restraints weight = 4307.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11035  Z= 0.118
  Angle     :  0.529   6.449  15026  Z= 0.263
  Chirality :  0.039   0.149   1811
  Planarity :  0.004   0.049   1902
  Dihedral  :  5.675 116.463   1537
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.11 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.09 (0.22), residues: 1439
  helix:  1.38 (0.18), residues: 857
  sheet: -1.39 (0.73), residues: 50
  loop : -2.08 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 293 
 TYR   0.025   0.001   TYR A 381 
 PHE   0.014   0.001   PHE A 327 
 TRP   0.014   0.001   TRP B 186 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (11035)
  covalent geometry    : angle       0.52912 (15026)
  hydrogen bonds       : bond        0.03548 (  653)
  hydrogen bonds       : angle       4.24827 ( 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
  173 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7843 (m-90) cc_final: 0.7495 (m-90)
REVERT: A  347 VAL cc_start: 0.7631 (m) cc_final: 0.7426 (m)
REVERT: A  366 MET cc_start: 0.8665 (ttm) cc_final: 0.8450 (ttm)
REVERT: C  169 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7896 (mtmt)
REVERT: C  170 TYR cc_start: 0.6924 (p90) cc_final: 0.6264 (p90)
REVERT: B   36 MET cc_start: 0.7313 (mmt) cc_final: 0.7072 (mmt)
REVERT: B  131 ILE cc_start: 0.6862 (tp) cc_final: 0.6568 (tt)
REVERT: B  186 TRP cc_start: 0.2544 (p-90) cc_final: 0.2309 (p-90)
REVERT: B  383 MET cc_start: 0.6182 (ppp) cc_final: 0.5860 (tpp)
  outliers start: 19
  outliers final: 14
  residues processed: 165
  average time/residue: 0.0867
  time to fit residues: 21.6686
Evaluate side-chains
  160 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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  414 MET
Chi-restraints excluded: chain C residue  167 LEU
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  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:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 118 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 91 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 67 optimal weight:   10.0000
   chunk 116 optimal weight:    6.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
** 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 = 0.3735 r_free = 0.3735 target = 0.141592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.113756 restraints weight = 17209.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.114230 restraints weight = 10549.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.114964 restraints weight = 7824.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.115869 restraints weight = 6318.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.115870 restraints weight = 5658.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1592

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= 0.149
  Angle     :  0.548   7.545  15026  Z= 0.274
  Chirality :  0.040   0.153   1811
  Planarity :  0.004   0.050   1902
  Dihedral  :  5.643 115.790   1537
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.52 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.40 (0.18), residues: 850
  sheet: -1.38 (0.74), residues: 50
  loop : -2.01 (0.24), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  44 
 TYR   0.023   0.001   TYR A 381 
 PHE   0.014   0.001   PHE A 494 
 TRP   0.010   0.001   TRP B 186 
 HIS   0.003   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (11035)
  covalent geometry    : angle       0.54775 (15026)
  hydrogen bonds       : bond        0.03697 (  653)
  hydrogen bonds       : angle       4.30788 ( 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
  171 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7879 (m-90) cc_final: 0.7539 (m-90)
REVERT: A  366 MET cc_start: 0.8722 (ttm) cc_final: 0.8506 (ttm)
REVERT: B   36 MET cc_start: 0.7431 (mmt) cc_final: 0.7149 (mmt)
REVERT: B  131 ILE cc_start: 0.6880 (tp) cc_final: 0.6610 (tt)
REVERT: B  383 MET cc_start: 0.6467 (ppp) cc_final: 0.5960 (tpp)
  outliers start: 24
  outliers final: 20
  residues processed: 158
  average time/residue: 0.0818
  time to fit residues: 19.8499
Evaluate side-chains
  163 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
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  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  140 ILE
Chi-restraints excluded: chain B residue  200 LEU
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  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:    9.9990
   chunk 80 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
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 521 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.141001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.112761 restraints weight = 17237.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.113585 restraints weight = 10227.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.114272 restraints weight = 6828.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.115857 restraints weight = 5983.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.115860 restraints weight = 4957.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1737

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= 0.142
  Angle     :  0.548   8.771  15026  Z= 0.273
  Chirality :  0.040   0.151   1811
  Planarity :  0.004   0.050   1902
  Dihedral  :  5.569 115.209   1537
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.49 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.10 (0.22), residues: 1439
  helix:  1.41 (0.18), residues: 856
  sheet: -1.80 (0.66), residues: 60
  loop : -2.05 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 400 
 TYR   0.023   0.001   TYR A 381 
 PHE   0.014   0.001   PHE A 494 
 TRP   0.016   0.001   TRP B 186 
 HIS   0.002   0.001   HIS A 351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (11035)
  covalent geometry    : angle       0.54768 (15026)
  hydrogen bonds       : bond        0.03695 (  653)
  hydrogen bonds       : angle       4.29894 ( 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
  175 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7890 (m-90) cc_final: 0.7518 (m-90)
REVERT: A  366 MET cc_start: 0.8809 (ttm) cc_final: 0.8419 (ttm)
REVERT: A  389 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7838 (mp)
REVERT: B   36 MET cc_start: 0.7605 (mmt) cc_final: 0.7329 (mmt)
REVERT: B  131 ILE cc_start: 0.6834 (tp) cc_final: 0.6554 (tt)
REVERT: B  383 MET cc_start: 0.6374 (ppp) cc_final: 0.5881 (tpp)
  outliers start: 29
  outliers final: 19
  residues processed: 163
  average time/residue: 0.0802
  time to fit residues: 20.1614
Evaluate side-chains
  161 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
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  389 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  140 ILE
Chi-restraints excluded: chain B residue  200 LEU
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 90 optimal weight:    0.3980
   chunk 92 optimal weight:    7.9990
   chunk 119 optimal weight:    5.9990
   chunk 123 optimal weight:    0.0980
   chunk 127 optimal weight:    0.1980
   chunk 132 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 141 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    0.5182

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.143369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.114303 restraints weight = 16932.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116517 restraints weight = 9134.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117655 restraints weight = 6075.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.118591 restraints weight = 4870.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.119180 restraints weight = 4217.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  11035  Z= 0.109
  Angle     :  0.531   7.917  15026  Z= 0.263
  Chirality :  0.039   0.143   1811
  Planarity :  0.004   0.050   1902
  Dihedral  :  5.396 113.916   1537
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.81 %
    Favored  : 80.25 %
  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:  0.25 (0.22), residues: 1439
  helix:  1.54 (0.18), residues: 856
  sheet: -1.66 (0.67), residues: 60
  loop : -2.04 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 400 
 TYR   0.025   0.001   TYR A 381 
 PHE   0.013   0.001   PHE A 494 
 TRP   0.015   0.001   TRP B 186 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (11035)
  covalent geometry    : angle       0.53107 (15026)
  hydrogen bonds       : bond        0.03499 (  653)
  hydrogen bonds       : angle       4.20922 ( 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
  170 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7857 (m-90) cc_final: 0.7454 (m-90)
REVERT: A  225 ILE cc_start: 0.9200 (tp) cc_final: 0.8940 (tp)
REVERT: A  366 MET cc_start: 0.8609 (ttm) cc_final: 0.8346 (ttm)
REVERT: B  131 ILE cc_start: 0.6852 (tp) cc_final: 0.6505 (tt)
REVERT: B  383 MET cc_start: 0.6219 (ppp) cc_final: 0.5876 (tpp)
  outliers start: 22
  outliers final: 14
  residues processed: 161
  average time/residue: 0.0863
  time to fit residues: 21.3006
Evaluate side-chains
  152 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
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  422 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain C residue  171 ILE
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  629 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 71 optimal weight:    0.0370
   chunk 108 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 94 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 135 optimal weight:    6.9990
   chunk 42 optimal weight:    0.7980
   chunk 139 optimal weight:    7.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3763 r_free = 0.3763 target = 0.143869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.114891 restraints weight = 17089.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116812 restraints weight = 9070.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118347 restraints weight = 6186.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.119063 restraints weight = 4800.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.119637 restraints weight = 4192.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11035  Z= 0.106
  Angle     :  0.525   7.566  15026  Z= 0.261
  Chirality :  0.039   0.141   1811
  Planarity :  0.004   0.049   1902
  Dihedral  :  5.303 112.321   1537
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.46 %
    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:  0.29 (0.22), residues: 1439
  helix:  1.58 (0.18), residues: 856
  sheet: -1.56 (0.68), residues: 60
  loop : -2.03 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  44 
 TYR   0.029   0.001   TYR A 381 
 PHE   0.012   0.001   PHE A 494 
 TRP   0.013   0.001   TRP B 186 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (11035)
  covalent geometry    : angle       0.52550 (15026)
  hydrogen bonds       : bond        0.03460 (  653)
  hydrogen bonds       : angle       4.17668 ( 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
  170 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  225 ILE cc_start: 0.9178 (tp) cc_final: 0.8916 (tp)
REVERT: A  357 LEU cc_start: 0.7934 (tt) cc_final: 0.7480 (tt)
REVERT: A  366 MET cc_start: 0.8605 (ttm) cc_final: 0.8359 (ttm)
REVERT: B  131 ILE cc_start: 0.6862 (tp) cc_final: 0.6553 (tt)
REVERT: B  383 MET cc_start: 0.6298 (ppp) cc_final: 0.5924 (tpp)
  outliers start: 22
  outliers final: 17
  residues processed: 160
  average time/residue: 0.0854
  time to fit residues: 20.9606
Evaluate side-chains
  156 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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  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  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  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:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 121 optimal weight:    0.6980
   chunk 127 optimal weight:    9.9990
   chunk 97 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 132 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
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**
B  30 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.143908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.116370 restraints weight = 16925.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116728 restraints weight = 9390.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.117362 restraints weight = 7613.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.117637 restraints weight = 6095.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.117830 restraints weight = 5976.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1824

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= 0.110
  Angle     :  0.529   7.086  15026  Z= 0.263
  Chirality :  0.039   0.141   1811
  Planarity :  0.004   0.049   1902
  Dihedral  :  5.277 111.258   1537
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.52 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.34 (0.22), residues: 1439
  helix:  1.60 (0.18), residues: 858
  sheet: -1.54 (0.68), residues: 60
  loop : -1.99 (0.25), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 400 
 TYR   0.027   0.001   TYR A 381 
 PHE   0.020   0.001   PHE A 327 
 TRP   0.013   0.001   TRP B 186 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (11035)
  covalent geometry    : angle       0.52894 (15026)
  hydrogen bonds       : bond        0.03451 (  653)
  hydrogen bonds       : angle       4.17456 ( 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
  163 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7834 (m-90) cc_final: 0.7355 (m-90)
REVERT: A  225 ILE cc_start: 0.9145 (tp) cc_final: 0.8890 (tp)
REVERT: A  357 LEU cc_start: 0.7927 (tt) cc_final: 0.7483 (tt)
REVERT: A  366 MET cc_start: 0.8606 (ttm) cc_final: 0.8357 (ttm)
REVERT: B  131 ILE cc_start: 0.6859 (tp) cc_final: 0.6558 (tt)
REVERT: B  383 MET cc_start: 0.6386 (ppp) cc_final: 0.5957 (tpp)
  outliers start: 20
  outliers final: 18
  residues processed: 154
  average time/residue: 0.0817
  time to fit residues: 19.3965
Evaluate side-chains
  157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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  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  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  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:    0.0980
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 140 optimal weight:    0.9980
   chunk 123 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 138 optimal weight:    7.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3731 r_free = 0.3731 target = 0.141371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.111871 restraints weight = 17049.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.114063 restraints weight = 9162.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.115221 restraints weight = 6111.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.116211 restraints weight = 4869.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.116379 restraints weight = 4189.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  11035  Z= 0.134
  Angle     :  0.558  12.189  15026  Z= 0.280
  Chirality :  0.040   0.167   1811
  Planarity :  0.004   0.050   1902
  Dihedral  :  5.327 111.129   1537
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.34 %
    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:  0.31 (0.22), residues: 1439
  helix:  1.58 (0.18), residues: 857
  sheet: -1.50 (0.68), residues: 60
  loop : -2.02 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  44 
 TYR   0.025   0.001   TYR A 381 
 PHE   0.024   0.001   PHE A 327 
 TRP   0.012   0.001   TRP B 186 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11035)
  covalent geometry    : angle       0.55817 (15026)
  hydrogen bonds       : bond        0.03565 (  653)
  hydrogen bonds       : angle       4.23219 ( 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
  162 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7864 (m-90) cc_final: 0.7404 (m-90)
REVERT: A  225 ILE cc_start: 0.9164 (tp) cc_final: 0.8905 (tp)
REVERT: A  366 MET cc_start: 0.8688 (ttm) cc_final: 0.8443 (ttm)
REVERT: B  131 ILE cc_start: 0.6871 (tp) cc_final: 0.6548 (tt)
REVERT: B  383 MET cc_start: 0.6174 (ppp) cc_final: 0.5864 (tpp)
  outliers start: 20
  outliers final: 18
  residues processed: 153
  average time/residue: 0.0791
  time to fit residues: 18.7209
Evaluate side-chains
  158 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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  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  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  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:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 115 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 91 optimal weight:    0.5980
   chunk 130 optimal weight:    0.0070
   chunk 30 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3762 r_free = 0.3762 target = 0.143960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.116598 restraints weight = 17062.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.116968 restraints weight = 10836.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.117274 restraints weight = 8016.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117809 restraints weight = 7452.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117855 restraints weight = 6164.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1893

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= 0.110
  Angle     :  0.533   7.275  15026  Z= 0.265
  Chirality :  0.039   0.181   1811
  Planarity :  0.004   0.049   1902
  Dihedral  :  5.277 110.759   1537
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.61 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.39 (0.22), residues: 1439
  helix:  1.68 (0.18), residues: 852
  sheet: -1.50 (0.69), residues: 60
  loop : -2.01 (0.25), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  44 
 TYR   0.026   0.001   TYR A 381 
 PHE   0.024   0.001   PHE A 327 
 TRP   0.020   0.001   TRP B 186 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (11035)
  covalent geometry    : angle       0.53273 (15026)
  hydrogen bonds       : bond        0.03449 (  653)
  hydrogen bonds       : angle       4.19661 ( 1929)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1690.62 seconds
wall clock time: 29 minutes 59.37 seconds (1799.37 seconds total)