Starting phenix.real_space_refine
on Wed Mar  4 04:09:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r88_24311/03_2026/7r88_24311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r88_24311/03_2026/7r88_24311.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r88_24311/03_2026/7r88_24311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r88_24311/03_2026/7r88_24311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r88_24311/03_2026/7r88_24311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r88_24311/03_2026/7r88_24311.cif"
  }
  resolution = 3.5
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    6964      2.51       5
     N    1826      2.21       5
     O    1931      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 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: 10787
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4620
          Classifications: {'peptide': 587}
          Link IDs: {'PTRANS': 21, 'TRANS': 565}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 562, 4463
          Classifications: {'peptide': 562}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 537}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 901
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "D"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 803
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100}
  Time building chain proxies: 2.36, per 1000 atoms: 0.22
  Number of scatterers: 10787
  At special positions: 0
  Unit cell: (113.288, 108.29, 120.785, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1931      8.00
     N    1826      7.00
     C    6964      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 587 " - pdb=" SG  CYS A 600 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  41 " - pdb=" SG  CYS C 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  43 " - pdb=" SG  CYS D 108 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 591.4 milliseconds
  

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2534

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      52.6% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 101
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 160 through 175
      removed outlier: 4.270A  pdb=" N   PHE A 164 " --> pdb=" O   ASN A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 181
    Processing helix  chain 'A' and resid 194 through 208
    Processing helix  chain 'A' and resid 224 through 241
    Processing helix  chain 'A' and resid 276 through 287
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 313 through 331
    Processing helix  chain 'A' and resid 332 through 347
      removed outlier: 3.908A  pdb=" N   HIS A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 381
    Processing helix  chain 'A' and resid 382 through 402
      removed outlier: 5.359A  pdb=" N   ASN A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   LEU A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 454
      Proline residue:  A 431  - end of helix
      Proline residue:  A 443  - end of helix
      removed outlier: 4.213A  pdb=" N   GLN A 454 " --> pdb=" O   ASP A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 491
      Proline residue:  A 473  - end of helix
      removed outlier: 4.676A  pdb=" N   TRP A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   THR A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY A 491 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 524
      Proline residue:  A 509  - end of helix
    Processing helix  chain 'A' and resid 526 through 545
    Processing helix  chain 'A' and resid 556 through 564
      removed outlier: 3.647A  pdb=" N   TYR A 564 " --> pdb=" O   LYS A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 580
      removed outlier: 4.270A  pdb=" N   TYR A 570 " --> pdb=" O   THR A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 613
    Processing helix  chain 'A' and resid 614 through 617
      removed outlier: 4.351A  pdb=" N   THR A 617 " --> pdb=" O   PRO A 614 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 614 through 617'
    Processing helix  chain 'A' and resid 619 through 649
      removed outlier: 4.258A  pdb=" N   ILE A 631 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      Proline residue:  A 632  - end of helix
      removed outlier: 4.430A  pdb=" N   HIS A 647 " --> pdb=" O   LYS A 643 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 120
    Processing helix  chain 'B' and resid 140 through 147
    Processing helix  chain 'B' and resid 162 through 175
    Processing helix  chain 'B' and resid 180 through 195
    Processing helix  chain 'B' and resid 214 through 227
    Processing helix  chain 'B' and resid 244 through 261
    Processing helix  chain 'B' and resid 273 through 279
      removed outlier: 3.674A  pdb=" N   LEU B 279 " --> pdb=" O   ASP B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 307
    Processing helix  chain 'B' and resid 316 through 325
      removed outlier: 4.050A  pdb=" N   THR B 325 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 353
      removed outlier: 3.512A  pdb=" N   GLU B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS B 341 " --> pdb=" O   ALA B 337 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LYS B 352 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 411
    Processing helix  chain 'B' and resid 413 through 435
    Processing helix  chain 'B' and resid 444 through 458
    Processing helix  chain 'B' and resid 458 through 473
      removed outlier: 4.488A  pdb=" N   ASN B 462 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 485
      removed outlier: 3.515A  pdb=" N   GLY B 485 " --> pdb=" O   GLU B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 517
      removed outlier: 4.005A  pdb=" N   PHE B 493 " --> pdb=" O   THR B 489 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   PHE B 494 " --> pdb=" O   GLY B 490 " (cutoff:3.500A)
      Proline residue:  B 502  - end of helix
      Proline residue:  B 514  - end of helix
      removed outlier: 4.352A  pdb=" N   TRP B 517 " --> pdb=" O   MET B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 525 through 553
    Processing helix  chain 'B' and resid 555 through 573
    Processing helix  chain 'B' and resid 585 through 593
      removed outlier: 3.603A  pdb=" N   TRP B 589 " --> pdb=" O   THR B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 608
    Processing helix  chain 'B' and resid 627 through 632
    Processing helix  chain 'B' and resid 639 through 665
    Processing helix  chain 'C' and resid 72 through 76
    Processing helix  chain 'D' and resid 99 through 103
      removed outlier: 3.971A  pdb=" N   LEU D 103 " --> pdb=" O   SER D 100 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77
      removed outlier: 6.876A  pdb=" N   LYS A  70 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   SER A  44 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   VAL A  72 " --> pdb=" O   HIS A  42 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ALA A  43 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU A 110 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132
      removed outlier: 6.441A  pdb=" N   ILE A 263 " --> pdb=" O   CYS A 274 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   CYS A 274 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE A 265 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 96
      removed outlier: 7.595A  pdb=" N   PHE B  93 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   ARG B  50 " --> pdb=" O   PHE B  93 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   VAL B  95 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   GLU B  48 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.730A  pdb=" N   GLY B 105 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   TYR B 293 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   THR B 287 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26
    Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 81
      removed outlier: 5.182A  pdb=" N   TRP C  66 " --> pdb=" O   ARG C  57 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   ARG C  57 " --> pdb=" O   TRP C  66 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27
    Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 32
      removed outlier: 6.479A  pdb=" N   LEU D  31 " --> pdb=" O   GLU D 125 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE D  68 " --> pdb=" O   TRP D  55 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   GLN D  57 " --> pdb=" O   ARG D  66 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   ARG D  66 " --> pdb=" O   GLN D  57 " (cutoff:3.500A)

    613 hydrogen bonds defined for protein.
    1776 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: 1.94

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3433
        1.34 -     1.46: 2498
        1.46 -     1.58: 4985
        1.58 -     1.69: 0
        1.69 -     1.81: 105
  Bond restraints: 11021
  Sorted by residual:
  bond pdb=" C   ILE B 459 "
       pdb=" N   PRO B 460 "
    ideal  model  delta    sigma   weight residual
    1.335  1.350 -0.016 1.28e-02 6.10e+03 1.50e+00
  bond pdb=" C   PHE A 442 "
       pdb=" N   PRO A 443 "
    ideal  model  delta    sigma   weight residual
    1.333  1.348 -0.015 1.44e-02 4.82e+03 1.07e+00
  bond pdb=" C   ASN A 296 "
       pdb=" N   PRO A 297 "
    ideal  model  delta    sigma   weight residual
    1.333  1.346 -0.013 1.44e-02 4.82e+03 8.22e-01
  bond pdb=" CA  VAL B 205 "
       pdb=" C   VAL B 205 "
    ideal  model  delta    sigma   weight residual
    1.523  1.534 -0.011 1.27e-02 6.20e+03 7.70e-01
  bond pdb=" CA  THR B 489 "
       pdb=" CB  THR B 489 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.013 1.69e-02 3.50e+03 6.21e-01
  ... (remaining 11016 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 14735
        1.55 -     3.10: 144
        3.10 -     4.65: 28
        4.65 -     6.20: 10
        6.20 -     7.75: 1
  Bond angle restraints: 14918
  Sorted by residual:
  angle pdb=" C   THR B 488 "
        pdb=" N   THR B 489 "
        pdb=" CA  THR B 489 "
      ideal   model   delta    sigma   weight residual
     121.54  129.29   -7.75 1.91e+00 2.74e-01 1.65e+01
  angle pdb=" N   SER B 581 "
        pdb=" CA  SER B 581 "
        pdb=" C   SER B 581 "
      ideal   model   delta    sigma   weight residual
     114.56  110.78    3.78 1.27e+00 6.20e-01 8.84e+00
  angle pdb=" N   VAL A 180 "
        pdb=" CA  VAL A 180 "
        pdb=" C   VAL A 180 "
      ideal   model   delta    sigma   weight residual
     111.88  109.23    2.65 1.06e+00 8.90e-01 6.27e+00
  angle pdb=" N   PHE A 442 "
        pdb=" CA  PHE A 442 "
        pdb=" C   PHE A 442 "
      ideal   model   delta    sigma   weight residual
     109.81  115.06   -5.25 2.21e+00 2.05e-01 5.64e+00
  angle pdb=" N   THR B 489 "
        pdb=" CA  THR B 489 "
        pdb=" CB  THR B 489 "
      ideal   model   delta    sigma   weight residual
     110.49  114.26   -3.77 1.69e+00 3.50e-01 4.99e+00
  ... (remaining 14913 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 6060
       17.97 -    35.95: 406
       35.95 -    53.92: 74
       53.92 -    71.90: 8
       71.90 -    89.87: 7
  Dihedral angle restraints: 6555
    sinusoidal: 2605
      harmonic: 3950
  Sorted by residual:
  dihedral pdb=" CB  CYS A 587 "
           pdb=" SG  CYS A 587 "
           pdb=" SG  CYS A 600 "
           pdb=" CB  CYS A 600 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -46.38  -39.62     1      1.00e+01 1.00e-02 2.21e+01
  dihedral pdb=" CA  CYS A 600 "
           pdb=" C   CYS A 600 "
           pdb=" N   ALA A 601 "
           pdb=" CA  ALA A 601 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.16   16.84     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CB  GLU B 189 "
           pdb=" CG  GLU B 189 "
           pdb=" CD  GLU B 189 "
           pdb=" OE1 GLU B 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.87  -89.87     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 6552 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1301
       0.038 -    0.076: 299
       0.076 -    0.114: 84
       0.114 -    0.152: 11
       0.152 -    0.190: 2
  Chirality restraints: 1697
  Sorted by residual:
  chirality pdb=" CB  VAL B 205 "
            pdb=" CA  VAL B 205 "
            pdb=" CG1 VAL B 205 "
            pdb=" CG2 VAL B 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.04e-01
  chirality pdb=" CA  THR B 489 "
            pdb=" N   THR B 489 "
            pdb=" C   THR B 489 "
            pdb=" CB  THR B 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.16 2.00e-01 2.50e+01 6.74e-01
  chirality pdb=" CA  VAL B 210 "
            pdb=" N   VAL B 210 "
            pdb=" C   VAL B 210 "
            pdb=" CB  VAL B 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 1694 not shown)

  Planarity restraints: 1878
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 276 "    0.022 5.00e-02 4.00e+02   3.27e-02 1.71e+00
        pdb=" N   PRO A 277 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 488 "    0.006 2.00e-02 2.50e+03   1.15e-02 1.33e+00
        pdb=" C   THR B 488 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   THR B 488 "    0.007 2.00e-02 2.50e+03
        pdb=" N   THR B 489 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 555 "    0.017 5.00e-02 4.00e+02   2.61e-02 1.09e+00
        pdb=" N   PRO A 556 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 556 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 556 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1875 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2777
        2.80 -     3.32: 9800
        3.32 -     3.85: 17768
        3.85 -     4.37: 19939
        4.37 -     4.90: 36069
  Nonbonded interactions: 86353
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  54 "
            pdb=" O   GLY B 125 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG  SER D  83 "
            pdb=" OG1 THR D  94 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" ND2 ASN A 551 "
            pdb=" OE1 GLU A 554 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   ARG B 198 "
            pdb=" OG  SER D  50 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OG1 THR C  43 "
            pdb=" O   ASN C  98 "
     model   vdw
     2.313 3.040
  ... (remaining 86348 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:             1.730
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     11.800
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
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      :  0.002   0.037  11024  Z= 0.094
  Angle     :  0.454   7.753  14924  Z= 0.268
  Chirality :  0.036   0.190   1697
  Planarity :  0.003   0.033   1878
  Dihedral  : 12.488  89.872   4012
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  5.76 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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: -1.50 (0.21), residues: 1348
  helix:  0.30 (0.18), residues: 701
  sheet: -1.30 (0.34), residues: 185
  loop : -2.89 (0.24), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 611 
 TYR   0.006   0.001   TYR C 115 
 PHE   0.006   0.001   PHE C  48 
 TRP   0.004   0.001   TRP B 229 
 HIS   0.002   0.000   HIS B 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00167 (11021)
  covalent geometry    : angle       0.45419 (14918)
  SS BOND              : bond        0.00047 (    3)
  SS BOND              : angle       0.27830 (    6)
  hydrogen bonds       : bond        0.14566 (  613)
  hydrogen bonds       : angle       4.81094 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 229
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7407 (mtt180)
REVERT: A  368 LEU cc_start: 0.8453 (tp) cc_final: 0.8240 (tp)
REVERT: A  564 TYR cc_start: 0.8546 (m-80) cc_final: 0.8336 (m-80)
REVERT: B  185 ASP cc_start: 0.7818 (m-30) cc_final: 0.7548 (m-30)
REVERT: C   81 TYR cc_start: 0.8545 (m-80) cc_final: 0.8330 (m-80)
REVERT: C  104 MET cc_start: 0.7995 (mtm) cc_final: 0.7689 (mtm)
REVERT: D   99 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8083 (mp0)
  outliers start: 12
  outliers final: 8
  residues processed: 240
  average time/residue: 0.1072
  time to fit residues: 35.8678
Evaluate side-chains
  180 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 172
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  224 ASP
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  624 PHE
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain C residue   95 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0170
   chunk 66 optimal weight:    0.3980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.9820

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
A 206 GLN
A 378 ASN
A 392 GLN
A 462 GLN
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 HIS
A 578 ASN
A 604 GLN
A 607 GLN
B  99 GLN
B 135 ASN
B 153 GLN
B 183 GLN
B 199 GLN
B 302 GLN
B 409 ASN
B 438 HIS
B 526 GLN
B 568 ASN
B 607 GLN
C  75 ASN
D  26 GLN
D  58 GLN
D  65 GLN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.115096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.093212 restraints weight = 16274.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.096552 restraints weight = 8392.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.098861 restraints weight = 5515.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.100359 restraints weight = 4148.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.101358 restraints weight = 3404.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11024  Z= 0.135
  Angle     :  0.538   9.889  14924  Z= 0.265
  Chirality :  0.040   0.196   1697
  Planarity :  0.003   0.043   1878
  Dihedral  :  3.923  50.467   1510
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 11.19 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.23), residues: 1348
  helix:  1.52 (0.20), residues: 708
  sheet: -0.87 (0.34), residues: 182
  loop : -2.25 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  88 
 TYR   0.014   0.001   TYR B 507 
 PHE   0.022   0.001   PHE A 109 
 TRP   0.006   0.001   TRP B 229 
 HIS   0.004   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (11021)
  covalent geometry    : angle       0.53816 (14918)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       0.22344 (    6)
  hydrogen bonds       : bond        0.03557 (  613)
  hydrogen bonds       : angle       3.71463 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A  564 TYR cc_start: 0.8679 (m-80) cc_final: 0.8403 (m-80)
REVERT: B  286 MET cc_start: 0.8936 (mmm) cc_final: 0.8136 (mtm)
REVERT: B  477 MET cc_start: 0.8469 (tmm) cc_final: 0.7947 (ttp)
REVERT: B  513 MET cc_start: 0.5846 (ttp) cc_final: 0.4644 (tpp)
REVERT: B  571 TYR cc_start: 0.9007 (t80) cc_final: 0.8679 (t80)
REVERT: C   75 ASN cc_start: 0.9264 (m-40) cc_final: 0.8671 (m110)
REVERT: C  104 MET cc_start: 0.7807 (mtm) cc_final: 0.7478 (mtm)
  outliers start: 26
  outliers final: 16
  residues processed: 204
  average time/residue: 0.0946
  time to fit residues: 28.6738
Evaluate side-chains
  173 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  560 SER
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain D residue  117 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 123 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0970
   chunk 46 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   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 116 ASN
A 160 ASN
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 HIS
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  26 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.108618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.086039 restraints weight = 16516.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.089279 restraints weight = 8558.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.091460 restraints weight = 5667.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.092930 restraints weight = 4314.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.093902 restraints weight = 3580.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11024  Z= 0.149
  Angle     :  0.549   8.431  14924  Z= 0.272
  Chirality :  0.041   0.208   1697
  Planarity :  0.003   0.045   1878
  Dihedral  :  3.820  57.281   1501
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 13.56 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  0.51 (0.24), residues: 1348
  helix:  1.85 (0.20), residues: 707
  sheet: -0.47 (0.35), residues: 183
  loop : -1.80 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  38 
 TYR   0.020   0.001   TYR B 507 
 PHE   0.015   0.001   PHE A 109 
 TRP   0.008   0.001   TRP C 128 
 HIS   0.005   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (11021)
  covalent geometry    : angle       0.54904 (14918)
  SS BOND              : bond        0.00953 (    3)
  SS BOND              : angle       0.88364 (    6)
  hydrogen bonds       : bond        0.03909 (  613)
  hydrogen bonds       : angle       3.76904 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A  324 MET cc_start: 0.8402 (tmm) cc_final: 0.8175 (tmm)
REVERT: B  286 MET cc_start: 0.8915 (mmm) cc_final: 0.8212 (mtm)
REVERT: B  406 GLN cc_start: 0.8579 (tt0) cc_final: 0.8365 (tt0)
REVERT: B  484 ASP cc_start: 0.8393 (m-30) cc_final: 0.8128 (m-30)
REVERT: B  513 MET cc_start: 0.5963 (ttp) cc_final: 0.5620 (mmt)
REVERT: B  584 TRP cc_start: 0.8873 (OUTLIER) cc_final: 0.8585 (p-90)
REVERT: C   38 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8049 (mtp85)
REVERT: C   75 ASN cc_start: 0.9283 (m-40) cc_final: 0.8614 (m110)
REVERT: D   97 SER cc_start: 0.8195 (t) cc_final: 0.7932 (p)
  outliers start: 35
  outliers final: 17
  residues processed: 181
  average time/residue: 0.0850
  time to fit residues: 23.1052
Evaluate side-chains
  167 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  493 HIS
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  560 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  126 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.108173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.085499 restraints weight = 16646.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.088765 restraints weight = 8659.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.090952 restraints weight = 5739.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.092340 restraints weight = 4385.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.093333 restraints weight = 3670.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11024  Z= 0.134
  Angle     :  0.524   8.550  14924  Z= 0.259
  Chirality :  0.040   0.185   1697
  Planarity :  0.003   0.045   1878
  Dihedral  :  3.651  50.378   1498
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.25 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  0.84 (0.24), residues: 1348
  helix:  2.05 (0.20), residues: 706
  sheet: -0.19 (0.36), residues: 183
  loop : -1.57 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 108 
 TYR   0.014   0.001   TYR B 507 
 PHE   0.019   0.001   PHE B 556 
 TRP   0.008   0.001   TRP A 461 
 HIS   0.017   0.001   HIS A 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (11021)
  covalent geometry    : angle       0.52432 (14918)
  SS BOND              : bond        0.00195 (    3)
  SS BOND              : angle       0.55884 (    6)
  hydrogen bonds       : bond        0.03651 (  613)
  hydrogen bonds       : angle       3.71537 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  324 MET cc_start: 0.8395 (tmm) cc_final: 0.8022 (tmm)
REVERT: A  552 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8972 (pt)
REVERT: B  286 MET cc_start: 0.8874 (mmm) cc_final: 0.8233 (mtm)
REVERT: B  406 GLN cc_start: 0.8567 (tt0) cc_final: 0.8362 (tt0)
REVERT: B  484 ASP cc_start: 0.8536 (m-30) cc_final: 0.8315 (m-30)
REVERT: B  545 MET cc_start: 0.9047 (tmm) cc_final: 0.8586 (ttp)
REVERT: B  584 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.8530 (p-90)
REVERT: C   38 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7619 (mtp85)
REVERT: C   75 ASN cc_start: 0.9264 (m-40) cc_final: 0.8609 (m110)
REVERT: C  103 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8146 (tp40)
REVERT: D   90 ASP cc_start: 0.7908 (m-30) cc_final: 0.7678 (m-30)
REVERT: D   97 SER cc_start: 0.8224 (t) cc_final: 0.7956 (p)
  outliers start: 30
  outliers final: 17
  residues processed: 170
  average time/residue: 0.0938
  time to fit residues: 24.3855
Evaluate side-chains
  164 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  560 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 91 optimal weight:    0.5980
   chunk 133 optimal weight:    2.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.105615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.082979 restraints weight = 16529.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.086215 restraints weight = 8537.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.088401 restraints weight = 5629.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.089821 restraints weight = 4279.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.090773 restraints weight = 3563.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11024  Z= 0.152
  Angle     :  0.537   8.706  14924  Z= 0.267
  Chirality :  0.041   0.176   1697
  Planarity :  0.003   0.045   1878
  Dihedral  :  3.526  16.175   1497
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 15.08 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  0.97 (0.24), residues: 1348
  helix:  2.12 (0.20), residues: 702
  sheet: -0.16 (0.36), residues: 190
  loop : -1.41 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 198 
 TYR   0.016   0.001   TYR B 507 
 PHE   0.014   0.001   PHE B 445 
 TRP   0.009   0.001   TRP A 461 
 HIS   0.005   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (11021)
  covalent geometry    : angle       0.53749 (14918)
  SS BOND              : bond        0.00150 (    3)
  SS BOND              : angle       0.49873 (    6)
  hydrogen bonds       : bond        0.03846 (  613)
  hydrogen bonds       : angle       3.75796 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 142
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  324 MET cc_start: 0.8399 (tmm) cc_final: 0.8054 (tmm)
REVERT: A  552 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8855 (pt)
REVERT: A  637 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7714 (tp)
REVERT: B  286 MET cc_start: 0.8869 (mmm) cc_final: 0.8244 (mtm)
REVERT: B  406 GLN cc_start: 0.8642 (tt0) cc_final: 0.8433 (tt0)
REVERT: B  484 ASP cc_start: 0.8766 (m-30) cc_final: 0.8541 (m-30)
REVERT: B  545 MET cc_start: 0.9027 (tmm) cc_final: 0.8363 (ttp)
REVERT: B  584 TRP cc_start: 0.8926 (OUTLIER) cc_final: 0.8643 (p-90)
REVERT: B  628 LYS cc_start: 0.6551 (pmtt) cc_final: 0.6225 (pttp)
REVERT: C   38 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8173 (mtp85)
REVERT: C   75 ASN cc_start: 0.9231 (m-40) cc_final: 0.8668 (m-40)
REVERT: D   97 SER cc_start: 0.8320 (t) cc_final: 0.8038 (p)
  outliers start: 39
  outliers final: 23
  residues processed: 169
  average time/residue: 0.0919
  time to fit residues: 23.2668
Evaluate side-chains
  165 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  359 LYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  552 ILE
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  560 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 130 optimal weight:    0.0170
   chunk 37 optimal weight:    0.5980
   chunk 96 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.6620

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.108759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.086131 restraints weight = 16444.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.089414 restraints weight = 8539.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.091591 restraints weight = 5650.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.093060 restraints weight = 4303.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.094046 restraints weight = 3575.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11024  Z= 0.106
  Angle     :  0.514   8.105  14924  Z= 0.253
  Chirality :  0.039   0.181   1697
  Planarity :  0.003   0.044   1878
  Dihedral  :  3.421  15.720   1497
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.78 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.24 (0.24), residues: 1348
  helix:  2.31 (0.20), residues: 703
  sheet:  0.07 (0.37), residues: 189
  loop : -1.27 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.014   0.001   TYR D 111 
 PHE   0.014   0.001   PHE B 556 
 TRP   0.009   0.001   TRP A 461 
 HIS   0.006   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (11021)
  covalent geometry    : angle       0.51363 (14918)
  SS BOND              : bond        0.00160 (    3)
  SS BOND              : angle       0.42099 (    6)
  hydrogen bonds       : bond        0.03346 (  613)
  hydrogen bonds       : angle       3.63321 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 MET cc_start: 0.8362 (tmm) cc_final: 0.8026 (tmm)
REVERT: A  451 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7884 (tm-30)
REVERT: A  506 LEU cc_start: 0.8916 (mt) cc_final: 0.8688 (mt)
REVERT: A  630 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8336 (t80)
REVERT: A  637 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7565 (tt)
REVERT: B  286 MET cc_start: 0.8773 (mmm) cc_final: 0.8209 (mtm)
REVERT: B  484 ASP cc_start: 0.8793 (m-30) cc_final: 0.8543 (m-30)
REVERT: B  545 MET cc_start: 0.9079 (tmm) cc_final: 0.8403 (ttp)
REVERT: B  584 TRP cc_start: 0.8825 (OUTLIER) cc_final: 0.8450 (p-90)
REVERT: B  628 LYS cc_start: 0.6501 (pmtt) cc_final: 0.6244 (pttp)
REVERT: C   75 ASN cc_start: 0.9239 (m-40) cc_final: 0.8685 (m-40)
REVERT: D   97 SER cc_start: 0.8272 (t) cc_final: 0.8030 (p)
  outliers start: 29
  outliers final: 21
  residues processed: 168
  average time/residue: 0.0933
  time to fit residues: 23.3946
Evaluate side-chains
  166 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  359 LYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  630 PHE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  560 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 94 optimal weight:    0.2980
   chunk 83 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0030
   chunk 31 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.6596

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

Flipped N/Q/H residues before XYZ refinement:
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 HIS
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.104031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.081317 restraints weight = 16494.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.084516 restraints weight = 8605.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.086636 restraints weight = 5706.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.088037 restraints weight = 4363.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.088970 restraints weight = 3645.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11024  Z= 0.185
  Angle     :  0.573   9.610  14924  Z= 0.284
  Chirality :  0.042   0.172   1697
  Planarity :  0.003   0.043   1878
  Dihedral  :  3.671  15.566   1497
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.78 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.16 (0.24), residues: 1348
  helix:  2.18 (0.20), residues: 703
  sheet:  0.06 (0.37), residues: 190
  loop : -1.22 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 263 
 TYR   0.022   0.001   TYR D 111 
 PHE   0.015   0.001   PHE B 445 
 TRP   0.009   0.001   TRP B 584 
 HIS   0.006   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (11021)
  covalent geometry    : angle       0.57282 (14918)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       0.53899 (    6)
  hydrogen bonds       : bond        0.04121 (  613)
  hydrogen bonds       : angle       3.84807 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 139
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7748 (mtm-85)
REVERT: A  324 MET cc_start: 0.8446 (tmm) cc_final: 0.8108 (tmm)
REVERT: A  435 MET cc_start: 0.8482 (tmm) cc_final: 0.8206 (tmm)
REVERT: A  637 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7808 (tp)
REVERT: B  286 MET cc_start: 0.8850 (mmm) cc_final: 0.8284 (mtm)
REVERT: B  484 ASP cc_start: 0.8827 (m-30) cc_final: 0.8602 (m-30)
REVERT: B  584 TRP cc_start: 0.8971 (OUTLIER) cc_final: 0.8765 (p-90)
REVERT: B  628 LYS cc_start: 0.6715 (pmtt) cc_final: 0.6416 (pttp)
REVERT: C   75 ASN cc_start: 0.9248 (m-40) cc_final: 0.8700 (m-40)
REVERT: D   97 SER cc_start: 0.8418 (t) cc_final: 0.8140 (p)
  outliers start: 39
  outliers final: 29
  residues processed: 164
  average time/residue: 0.0945
  time to fit residues: 23.0928
Evaluate side-chains
  165 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  359 LYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  560 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  123 MET
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 123 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 105 optimal weight:    0.7980
   chunk 124 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 107 optimal weight:    0.0670
   chunk 106 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.108038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.085464 restraints weight = 16534.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.088734 restraints weight = 8626.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.090898 restraints weight = 5709.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.092199 restraints weight = 4355.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.093184 restraints weight = 3665.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.3745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11024  Z= 0.106
  Angle     :  0.521   9.164  14924  Z= 0.256
  Chirality :  0.040   0.233   1697
  Planarity :  0.003   0.044   1878
  Dihedral  :  3.490  14.210   1497
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.63 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.36 (0.24), residues: 1348
  helix:  2.37 (0.20), residues: 698
  sheet:  0.09 (0.37), residues: 194
  loop : -1.10 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 198 
 TYR   0.011   0.001   TYR D 111 
 PHE   0.013   0.001   PHE B 445 
 TRP   0.009   0.001   TRP A 461 
 HIS   0.006   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (11021)
  covalent geometry    : angle       0.52089 (14918)
  SS BOND              : bond        0.00098 (    3)
  SS BOND              : angle       0.65245 (    6)
  hydrogen bonds       : bond        0.03341 (  613)
  hydrogen bonds       : angle       3.63982 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 144
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ARG cc_start: 0.8089 (mtp180) cc_final: 0.7747 (mtm-85)
REVERT: A  324 MET cc_start: 0.8378 (tmm) cc_final: 0.8071 (tmm)
REVERT: A  451 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: A  630 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8328 (t80)
REVERT: A  637 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7654 (tt)
REVERT: B  286 MET cc_start: 0.8753 (mmm) cc_final: 0.8194 (mtm)
REVERT: B  484 ASP cc_start: 0.8819 (m-30) cc_final: 0.8569 (m-30)
REVERT: B  545 MET cc_start: 0.9101 (tmm) cc_final: 0.8355 (ttp)
REVERT: B  584 TRP cc_start: 0.8808 (OUTLIER) cc_final: 0.8460 (p-90)
REVERT: B  628 LYS cc_start: 0.6714 (pmtt) cc_final: 0.6379 (pttm)
REVERT: C   75 ASN cc_start: 0.9247 (m-40) cc_final: 0.8710 (m-40)
REVERT: D   97 SER cc_start: 0.8324 (t) cc_final: 0.8093 (p)
  outliers start: 32
  outliers final: 28
  residues processed: 165
  average time/residue: 0.0936
  time to fit residues: 23.2370
Evaluate side-chains
  170 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  359 LYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  630 PHE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  560 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  123 MET
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 63 optimal weight:    0.0270
   chunk 56 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    1.2842

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

Flipped N/Q/H residues before XYZ refinement:
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.105102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.082510 restraints weight = 16492.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.085666 restraints weight = 8547.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.087820 restraints weight = 5657.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.089230 restraints weight = 4314.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.090091 restraints weight = 3599.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11024  Z= 0.152
  Angle     :  0.557   9.473  14924  Z= 0.274
  Chirality :  0.041   0.232   1697
  Planarity :  0.003   0.044   1878
  Dihedral  :  3.604  14.808   1497
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.54 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.33 (0.24), residues: 1348
  helix:  2.31 (0.20), residues: 701
  sheet:  0.14 (0.37), residues: 195
  loop : -1.11 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 263 
 TYR   0.018   0.001   TYR D 111 
 PHE   0.015   0.001   PHE B 445 
 TRP   0.009   0.001   TRP A 461 
 HIS   0.006   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (11021)
  covalent geometry    : angle       0.55719 (14918)
  SS BOND              : bond        0.00165 (    3)
  SS BOND              : angle       0.66609 (    6)
  hydrogen bonds       : bond        0.03811 (  613)
  hydrogen bonds       : angle       3.73609 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7655 (mtm-85)
REVERT: A  324 MET cc_start: 0.8418 (tmm) cc_final: 0.8106 (tmm)
REVERT: A  435 MET cc_start: 0.8456 (tmm) cc_final: 0.8178 (tmm)
REVERT: A  637 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7725 (tt)
REVERT: B  286 MET cc_start: 0.8835 (mmm) cc_final: 0.8280 (mtm)
REVERT: B  545 MET cc_start: 0.9111 (tmm) cc_final: 0.8447 (ttp)
REVERT: B  584 TRP cc_start: 0.8897 (OUTLIER) cc_final: 0.8620 (p-90)
REVERT: B  628 LYS cc_start: 0.6847 (pmtt) cc_final: 0.6496 (pttp)
REVERT: C   75 ASN cc_start: 0.9242 (m-40) cc_final: 0.8675 (m-40)
REVERT: D   97 SER cc_start: 0.8438 (t) cc_final: 0.8188 (p)
  outliers start: 34
  outliers final: 28
  residues processed: 161
  average time/residue: 0.1003
  time to fit residues: 23.8101
Evaluate side-chains
  165 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  359 LYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  462 ASN
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  560 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  123 MET
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 131 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 133 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   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 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.105077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.082534 restraints weight = 16471.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.085694 restraints weight = 8541.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.087835 restraints weight = 5656.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.089241 restraints weight = 4314.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.090203 restraints weight = 3604.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11024  Z= 0.147
  Angle     :  0.565  10.638  14924  Z= 0.275
  Chirality :  0.041   0.227   1697
  Planarity :  0.003   0.044   1878
  Dihedral  :  3.622  14.553   1497
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.71 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.36 (0.24), residues: 1348
  helix:  2.27 (0.20), residues: 704
  sheet:  0.20 (0.38), residues: 193
  loop : -1.03 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 263 
 TYR   0.016   0.001   TYR D 111 
 PHE   0.015   0.001   PHE B 445 
 TRP   0.009   0.001   TRP A 461 
 HIS   0.006   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (11021)
  covalent geometry    : angle       0.56517 (14918)
  SS BOND              : bond        0.00142 (    3)
  SS BOND              : angle       0.75276 (    6)
  hydrogen bonds       : bond        0.03752 (  613)
  hydrogen bonds       : angle       3.74803 ( 1776)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 137
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ARG cc_start: 0.8065 (mtp180) cc_final: 0.7643 (mtm-85)
REVERT: A  302 MET cc_start: 0.7904 (mmm) cc_final: 0.7325 (mtp)
REVERT: A  324 MET cc_start: 0.8430 (tmm) cc_final: 0.8119 (tmm)
REVERT: A  435 MET cc_start: 0.8459 (tmm) cc_final: 0.8183 (tmm)
REVERT: A  637 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7692 (tt)
REVERT: B  286 MET cc_start: 0.8831 (mmm) cc_final: 0.8301 (mtm)
REVERT: B  545 MET cc_start: 0.9104 (tmm) cc_final: 0.8426 (ttp)
REVERT: B  584 TRP cc_start: 0.8877 (OUTLIER) cc_final: 0.8600 (p-90)
REVERT: B  628 LYS cc_start: 0.6873 (pmtt) cc_final: 0.6530 (pttp)
REVERT: C   75 ASN cc_start: 0.9240 (m-40) cc_final: 0.8695 (m-40)
REVERT: D   97 SER cc_start: 0.8424 (t) cc_final: 0.8179 (p)
  outliers start: 32
  outliers final: 28
  residues processed: 159
  average time/residue: 0.1009
  time to fit residues: 23.4854
Evaluate side-chains
  165 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  146 GLU
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  359 LYS
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  648 LEU
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  462 ASN
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  560 SER
Chi-restraints excluded: chain B residue  584 TRP
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  123 MET
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   83 SER
Chi-restraints excluded: chain D residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 124 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 131 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 117 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.106711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.084106 restraints weight = 16558.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.087370 restraints weight = 8566.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.089530 restraints weight = 5650.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.091017 restraints weight = 4294.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.091985 restraints weight = 3556.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11024  Z= 0.115
  Angle     :  0.542  11.390  14924  Z= 0.263
  Chirality :  0.040   0.218   1697
  Planarity :  0.003   0.044   1878
  Dihedral  :  3.514  13.908   1497
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.63 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.42 (0.24), residues: 1348
  helix:  2.36 (0.20), residues: 700
  sheet:  0.18 (0.38), residues: 195
  loop : -1.03 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 121 
 TYR   0.013   0.001   TYR D 111 
 PHE   0.014   0.001   PHE B 445 
 TRP   0.010   0.001   TRP A 461 
 HIS   0.006   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (11021)
  covalent geometry    : angle       0.54159 (14918)
  SS BOND              : bond        0.00125 (    3)
  SS BOND              : angle       0.34042 (    6)
  hydrogen bonds       : bond        0.03418 (  613)
  hydrogen bonds       : angle       3.66122 ( 1776)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1656.33 seconds
wall clock time: 29 minutes 20.10 seconds (1760.10 seconds total)