Starting phenix.real_space_refine
on Tue Mar  3 23:26:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ty6_26167/03_2026/7ty6_26167.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ty6_26167/03_2026/7ty6_26167.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ty6_26167/03_2026/7ty6_26167.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ty6_26167/03_2026/7ty6_26167.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ty6_26167/03_2026/7ty6_26167.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ty6_26167/03_2026/7ty6_26167.map"
  }
  resolution = 2.98
  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=  -0.002 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      44      5.16       5
     C    5824      2.51       5
     N    1320      2.21       5
     O    1482      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 8672
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4082
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 516, 4075
          Classifications: {'peptide': 516}
          Link IDs: {'PTRANS': 29, 'TRANS': 486}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 516, 4075
          Classifications: {'peptide': 516}
          Link IDs: {'PTRANS': 29, 'TRANS': 486}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4169
    Chain: "B"
      Number of atoms: 4082
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 516, 4075
          Classifications: {'peptide': 516}
          Link IDs: {'PTRANS': 29, 'TRANS': 486}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 516, 4075
          Classifications: {'peptide': 516}
          Link IDs: {'PTRANS': 29, 'TRANS': 486}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4169
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 194
          Unusual residues: {'4DS': 1, 'CLR': 4, 'PC1': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 194
          Unusual residues: {'4DS': 1, 'CLR': 4, 'PC1': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 30
          Classifications: {'water': 30}
          Link IDs: {None: 29}
    Chain: "B"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 34
          Classifications: {'water': 34}
          Link IDs: {None: 33}
  Time building chain proxies: 3.87, per 1000 atoms: 0.45
  Number of scatterers: 8672
  At special positions: 0
  Unit cell: (112.98, 95.764, 83.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P       2     15.00
     O    1482      8.00
     N    1320      7.00
     C    5824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 642 "
      " NAG D   1 " - " ASN B 642 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 723.8 milliseconds
  

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1924

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 4 sheets defined
      73.1% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 379 through 390
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 394 through 399
    Processing helix  chain 'A' and resid 402 through 431
      removed outlier: 3.734A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 436 through 455
    Processing helix  chain 'A' and resid 465 through 482
    Processing helix  chain 'A' and resid 485 through 507
      removed outlier: 3.586A  pdb=" N   VAL A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TRP A 492 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 516
    Processing helix  chain 'A' and resid 517 through 547
      removed outlier: 3.559A  pdb=" N   ILE A 543 " --> pdb=" O   LYS A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 594
    Processing helix  chain 'A' and resid 598 through 608
    Processing helix  chain 'A' and resid 608 through 624
      removed outlier: 3.648A  pdb=" N   ILE A 624 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 667
    Processing helix  chain 'A' and resid 667 through 690
    Processing helix  chain 'A' and resid 701 through 718
      removed outlier: 3.650A  pdb=" N   LEU A 706 " --> pdb=" O   PHE A 702 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU A 718 " --> pdb=" O   GLY A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 738
    Processing helix  chain 'A' and resid 760 through 772
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 784 through 799
      removed outlier: 3.665A  pdb=" N   LEU A 788 " --> pdb=" O   PRO A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 811
    Processing helix  chain 'A' and resid 822 through 827
      removed outlier: 3.825A  pdb=" N   ARG A 827 " --> pdb=" O   PRO A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 829 through 853
    Processing helix  chain 'A' and resid 855 through 857
      No H-bonds generated for 'chain 'A' and resid 855 through 857'
    Processing helix  chain 'A' and resid 858 through 865
    Processing helix  chain 'A' and resid 865 through 872
    Processing helix  chain 'A' and resid 873 through 878
      removed outlier: 3.686A  pdb=" N   ILE A 877 " --> pdb=" O   LEU A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 887
    Processing helix  chain 'B' and resid 379 through 390
    Processing helix  chain 'B' and resid 391 through 393
      No H-bonds generated for 'chain 'B' and resid 391 through 393'
    Processing helix  chain 'B' and resid 394 through 399
    Processing helix  chain 'B' and resid 402 through 431
      removed outlier: 3.734A  pdb=" N   LEU B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE B 414 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
    Processing helix  chain 'B' and resid 436 through 455
    Processing helix  chain 'B' and resid 465 through 482
    Processing helix  chain 'B' and resid 485 through 507
      removed outlier: 3.585A  pdb=" N   VAL B 491 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TRP B 492 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 516
    Processing helix  chain 'B' and resid 517 through 547
      removed outlier: 3.548A  pdb=" N   ILE B 543 " --> pdb=" O   LYS B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 594
    Processing helix  chain 'B' and resid 598 through 608
    Processing helix  chain 'B' and resid 608 through 624
      removed outlier: 3.650A  pdb=" N   ILE B 624 " --> pdb=" O   VAL B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 667
    Processing helix  chain 'B' and resid 667 through 690
    Processing helix  chain 'B' and resid 701 through 718
      removed outlier: 3.648A  pdb=" N   LEU B 706 " --> pdb=" O   PHE B 702 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU B 718 " --> pdb=" O   GLY B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 727 through 738
    Processing helix  chain 'B' and resid 760 through 772
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 784 through 799
      removed outlier: 3.663A  pdb=" N   LEU B 788 " --> pdb=" O   PRO B 784 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 811
    Processing helix  chain 'B' and resid 822 through 827
      removed outlier: 3.825A  pdb=" N   ARG B 827 " --> pdb=" O   PRO B 823 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 829 through 853
    Processing helix  chain 'B' and resid 855 through 857
      No H-bonds generated for 'chain 'B' and resid 855 through 857'
    Processing helix  chain 'B' and resid 858 through 865
    Processing helix  chain 'B' and resid 865 through 872
    Processing helix  chain 'B' and resid 873 through 878
      removed outlier: 3.688A  pdb=" N   ILE B 877 " --> pdb=" O   LEU B 873 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 879 through 887
    Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463
    Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 741
      removed outlier: 3.877A  pdb=" N   GLU A 755 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463
    Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 741
      removed outlier: 3.863A  pdb=" N   GLU B 755 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)

    522 hydrogen bonds defined for protein.
    1524 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: 1.44

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1396
        1.33 -     1.45: 2166
        1.45 -     1.57: 5202
        1.57 -     1.70: 8
        1.70 -     1.82: 70
  Bond restraints: 8842
  Sorted by residual:
  bond pdb=" CAK 4DS B2204 "
       pdb=" CAL 4DS B2204 "
    ideal  model  delta    sigma   weight residual
    1.336  1.541 -0.205 2.00e-02 2.50e+03 1.05e+02
  bond pdb=" CAK 4DS A2204 "
       pdb=" CAL 4DS A2204 "
    ideal  model  delta    sigma   weight residual
    1.336  1.533 -0.197 2.00e-02 2.50e+03 9.71e+01
  bond pdb=" CAT 4DS B2204 "
       pdb=" NAS 4DS B2204 "
    ideal  model  delta    sigma   weight residual
    1.170  1.322 -0.152 2.00e-02 2.50e+03 5.80e+01
  bond pdb=" CBA 4DS A2204 "
       pdb=" NAZ 4DS A2204 "
    ideal  model  delta    sigma   weight residual
    1.170  1.318 -0.148 2.00e-02 2.50e+03 5.51e+01
  bond pdb=" CBA 4DS B2204 "
       pdb=" NAZ 4DS B2204 "
    ideal  model  delta    sigma   weight residual
    1.170  1.318 -0.148 2.00e-02 2.50e+03 5.50e+01
  ... (remaining 8837 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.13: 12047
       11.13 -    22.27: 1
       22.27 -    33.40: 0
       33.40 -    44.54: 0
       44.54 -    55.67: 6
  Bond angle restraints: 12054
  Sorted by residual:
  angle pdb=" CAP 4DS A2204 "
        pdb=" NAS 4DS A2204 "
        pdb=" CAT 4DS A2204 "
      ideal   model   delta    sigma   weight residual
     180.00  124.33   55.67 3.00e+00 1.11e-01 3.44e+02
  angle pdb=" CAP 4DS B2204 "
        pdb=" NAS 4DS B2204 "
        pdb=" CAT 4DS B2204 "
      ideal   model   delta    sigma   weight residual
     180.00  124.43   55.57 3.00e+00 1.11e-01 3.43e+02
  angle pdb=" NAS 4DS A2204 "
        pdb=" CAT 4DS A2204 "
        pdb=" SAU 4DS A2204 "
      ideal   model   delta    sigma   weight residual
     180.00  125.79   54.21 3.00e+00 1.11e-01 3.27e+02
  angle pdb=" NAS 4DS B2204 "
        pdb=" CAT 4DS B2204 "
        pdb=" SAU 4DS B2204 "
      ideal   model   delta    sigma   weight residual
     180.00  126.11   53.89 3.00e+00 1.11e-01 3.23e+02
  angle pdb=" CAG 4DS A2204 "
        pdb=" NAZ 4DS A2204 "
        pdb=" CBA 4DS A2204 "
      ideal   model   delta    sigma   weight residual
     177.62  125.11   52.51 3.00e+00 1.11e-01 3.06e+02
  ... (remaining 12049 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.93: 5258
       21.93 -    43.86: 279
       43.86 -    65.79: 89
       65.79 -    87.72: 14
       87.72 -   109.65: 16
  Dihedral angle restraints: 5656
    sinusoidal: 2672
      harmonic: 2984
  Sorted by residual:
  dihedral pdb=" C   ASN B 554 "
           pdb=" N   ASN B 554 "
           pdb=" CA  ASN B 554 "
           pdb=" CB  ASN B 554 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.27   10.67     0      2.50e+00 1.60e-01 1.82e+01
  dihedral pdb=" C   ASN A 554 "
           pdb=" N   ASN A 554 "
           pdb=" CA  ASN A 554 "
           pdb=" CB  ASN A 554 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.22   10.62     0      2.50e+00 1.60e-01 1.80e+01
  dihedral pdb=" C2  NAG D   2 "
           pdb=" C3  NAG D   2 "
           pdb=" C4  NAG D   2 "
           pdb=" O4  NAG D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   65.46  109.65     1      3.00e+01 1.11e-03 1.43e+01
  ... (remaining 5653 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 722
       0.067 -    0.135: 573
       0.135 -    0.202: 135
       0.202 -    0.269: 5
       0.269 -    0.337: 3
  Chirality restraints: 1438
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-02 2.50e+03 2.83e+02
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-02 2.50e+03 9.31e+01
  chirality pdb=" CA  ASN B 554 "
            pdb=" N   ASN B 554 "
            pdb=" C   ASN B 554 "
            pdb=" CB  ASN B 554 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.65e+00
  ... (remaining 1435 not shown)

  Planarity restraints: 1416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "    0.339 2.00e-02 2.50e+03   2.91e-01 1.06e+03
        pdb=" C7  NAG C   2 "   -0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "    0.152 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "   -0.518 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "    0.108 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.327 2.00e-02 2.50e+03   2.78e-01 9.68e+02
        pdb=" C7  NAG D   2 "    0.081 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.178 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.488 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.064 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAP 4DS A2204 "    0.111 2.00e-02 2.50e+03   2.22e-01 4.92e+02
        pdb=" CAT 4DS A2204 "    0.285 2.00e-02 2.50e+03
        pdb=" NAS 4DS A2204 "   -0.309 2.00e-02 2.50e+03
        pdb=" SAU 4DS A2204 "   -0.087 2.00e-02 2.50e+03
  ... (remaining 1413 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 1992
        2.87 -     3.38: 9513
        3.38 -     3.89: 14846
        3.89 -     4.39: 17699
        4.39 -     4.90: 29025
  Nonbonded interactions: 73075
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 863 "
            pdb=" OG1 THR B 866 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   LEU A 863 "
            pdb=" OG1 THR A 866 "
     model   vdw
     2.381 3.040
  nonbonded pdb=" O   THR A 686 "
            pdb=" OG  SER A 690 "
     model   vdw
     2.396 3.040
  nonbonded pdb=" O   THR B 686 "
            pdb=" OG  SER B 690 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" O   THR A 727 "
            pdb=" OG  SER A 731 "
     model   vdw
     2.448 3.040
  ... (remaining 73070 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 369 through 650 or resid 652 through 2206))
  selection = (chain 'B' and (resid 369 through 650 or resid 652 through 2206))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.790
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
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      :  0.014   0.205   8848  Z= 1.036
  Angle     :  2.159  55.672  12066  Z= 1.418
  Chirality :  0.086   0.337   1438
  Planarity :  0.016   0.291   1414
  Dihedral  : 15.989 109.651   3732
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  4.89 %
    Favored  : 94.22 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.21), residues: 1026
  helix: -1.62 (0.16), residues: 692
  sheet:  None (None), residues: 0
  loop : -2.17 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 760 
 TYR   0.013   0.003   TYR B 824 
 PHE   0.018   0.003   PHE B 675 
 TRP   0.026   0.004   TRP A 492 
 HIS   0.005   0.002   HIS B 819 

Details of bonding type rmsd
  covalent geometry    : bond        0.01377 ( 8842)
  covalent geometry    : angle       2.15611 (12054)
  hydrogen bonds       : bond        0.23216 (  522)
  hydrogen bonds       : angle       8.08905 ( 1524)
  Misc. bond           : bond        0.14713 (    2)
  link_BETA1-4         : bond        0.00949 (    2)
  link_BETA1-4         : angle       2.46546 (    6)
  link_NAG-ASN         : bond        0.00262 (    2)
  link_NAG-ASN         : angle       5.58940 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  880 ASN cc_start: 0.9403 (t0) cc_final: 0.9154 (t0)
REVERT: B  473 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8841 (tp30)
REVERT: B  880 ASN cc_start: 0.9396 (t0) cc_final: 0.9152 (t0)
  outliers start: 8
  outliers final: 2
  residues processed: 75
  average time/residue: 0.7123
  time to fit residues: 56.5348
Evaluate side-chains
  51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  603 ARG
Chi-restraints excluded: chain B residue  603 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 554 ASN
A 564 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.056964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.045926 restraints weight = 58192.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.2654 rms_B_bonded: 4.38
r_work: 0.2480 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2480
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2486 r_free = 0.2486    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2486 r_free = 0.2486    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8848  Z= 0.161
  Angle     :  0.730  12.854  12066  Z= 0.338
  Chirality :  0.041   0.230   1438
  Planarity :  0.005   0.047   1414
  Dihedral  : 12.534  83.210   1830
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  9.11 %
    Favored  : 90.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.26), residues: 1026
  helix:  1.01 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop : -1.48 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 387 
 TYR   0.010   0.001   TYR B 555 
 PHE   0.017   0.001   PHE B 411 
 TRP   0.018   0.002   TRP B 492 
 HIS   0.004   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8842)
  covalent geometry    : angle       0.72810 (12054)
  hydrogen bonds       : bond        0.05431 (  522)
  hydrogen bonds       : angle       4.60430 ( 1524)
  Misc. bond           : bond        0.00234 (    2)
  link_BETA1-4         : bond        0.00368 (    2)
  link_BETA1-4         : angle       1.85383 (    6)
  link_NAG-ASN         : bond        0.00507 (    2)
  link_NAG-ASN         : angle       1.38006 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8728 (mp0)
REVERT: A  721 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9101 (mmm)
REVERT: B  473 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8562 (tm-30)
REVERT: B  559 MET cc_start: 0.8658 (mmm) cc_final: 0.8313 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 50
  average time/residue: 0.6844
  time to fit residues: 36.3957
Evaluate side-chains
  46 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  555 TYR
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain B residue  672 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0970
   chunk 48 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 433 ASN
A 554 ASN
B 433 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.056784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.046139 restraints weight = 52178.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.2662 rms_B_bonded: 4.14
r_work: 0.2497 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.2497
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2500 r_free = 0.2500    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2500 r_free = 0.2500    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8848  Z= 0.139
  Angle     :  0.642  11.528  12066  Z= 0.293
  Chirality :  0.039   0.154   1438
  Planarity :  0.005   0.051   1414
  Dihedral  : 10.168  75.059   1822
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  8.44 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.15 (0.26), residues: 1026
  helix:  1.63 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.21 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 603 
 TYR   0.010   0.001   TYR A 519 
 PHE   0.014   0.001   PHE B 411 
 TRP   0.013   0.001   TRP A 492 
 HIS   0.004   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8842)
  covalent geometry    : angle       0.64057 (12054)
  hydrogen bonds       : bond        0.04410 (  522)
  hydrogen bonds       : angle       4.21991 ( 1524)
  Misc. bond           : bond        0.00201 (    2)
  link_BETA1-4         : bond        0.00628 (    2)
  link_BETA1-4         : angle       1.90919 (    6)
  link_NAG-ASN         : bond        0.00073 (    2)
  link_NAG-ASN         : angle       0.80291 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  482 ASN cc_start: 0.9151 (m110) cc_final: 0.8942 (m110)
REVERT: A  721 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8632 (mpp)
REVERT: B  473 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8479 (tm-30)
REVERT: B  559 MET cc_start: 0.8710 (mmm) cc_final: 0.8316 (mmm)
REVERT: B  664 MET cc_start: 0.9144 (ttm) cc_final: 0.8888 (ttp)
  outliers start: 11
  outliers final: 4
  residues processed: 55
  average time/residue: 0.5971
  time to fit residues: 35.2707
Evaluate side-chains
  47 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  555 TYR
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain B residue  672 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0170
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 554 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.056839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.045757 restraints weight = 78046.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.2658 rms_B_bonded: 4.87
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8848  Z= 0.126
  Angle     :  0.625  11.445  12066  Z= 0.283
  Chirality :  0.039   0.121   1438
  Planarity :  0.005   0.051   1414
  Dihedral  :  9.323  76.451   1822
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  8.33 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.27), residues: 1026
  helix:  1.79 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.97 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 603 
 TYR   0.010   0.001   TYR B 519 
 PHE   0.015   0.001   PHE B 411 
 TRP   0.012   0.001   TRP B 492 
 HIS   0.003   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8842)
  covalent geometry    : angle       0.62290 (12054)
  hydrogen bonds       : bond        0.04102 (  522)
  hydrogen bonds       : angle       4.09469 ( 1524)
  Misc. bond           : bond        0.00139 (    2)
  link_BETA1-4         : bond        0.00476 (    2)
  link_BETA1-4         : angle       2.40229 (    6)
  link_NAG-ASN         : bond        0.00110 (    2)
  link_NAG-ASN         : angle       1.00376 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  586 MET cc_start: 0.9333 (mmm) cc_final: 0.9080 (mmt)
REVERT: A  663 MET cc_start: 0.9210 (tpp) cc_final: 0.8934 (tpt)
REVERT: A  721 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8299 (mpp)
REVERT: B  559 MET cc_start: 0.8682 (mmm) cc_final: 0.8306 (mmm)
REVERT: B  721 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8787 (mmm)
  outliers start: 11
  outliers final: 3
  residues processed: 53
  average time/residue: 0.5766
  time to fit residues: 32.9157
Evaluate side-chains
  44 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  555 TYR
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain B residue  721 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 80 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 554 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.056361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.045340 restraints weight = 75248.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.2647 rms_B_bonded: 4.81
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8848  Z= 0.136
  Angle     :  0.618  10.354  12066  Z= 0.280
  Chirality :  0.039   0.142   1438
  Planarity :  0.005   0.050   1414
  Dihedral  :  9.057  77.339   1822
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  8.89 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.27), residues: 1026
  helix:  1.86 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.82 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 603 
 TYR   0.010   0.001   TYR B 519 
 PHE   0.013   0.001   PHE B 411 
 TRP   0.015   0.001   TRP B 492 
 HIS   0.002   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8842)
  covalent geometry    : angle       0.61623 (12054)
  hydrogen bonds       : bond        0.04093 (  522)
  hydrogen bonds       : angle       4.06385 ( 1524)
  Misc. bond           : bond        0.00114 (    2)
  link_BETA1-4         : bond        0.00279 (    2)
  link_BETA1-4         : angle       2.24139 (    6)
  link_NAG-ASN         : bond        0.00062 (    2)
  link_NAG-ASN         : angle       1.03574 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  586 MET cc_start: 0.9352 (mmm) cc_final: 0.9100 (mmt)
REVERT: A  663 MET cc_start: 0.9208 (tpp) cc_final: 0.8828 (tpt)
REVERT: A  721 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.7909 (mmm)
REVERT: B  482 ASN cc_start: 0.9092 (m110) cc_final: 0.8805 (m110)
REVERT: B  559 MET cc_start: 0.8678 (mmm) cc_final: 0.8282 (mmm)
REVERT: B  663 MET cc_start: 0.9196 (tpt) cc_final: 0.8797 (tpt)
REVERT: B  721 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.7789 (mmm)
  outliers start: 11
  outliers final: 4
  residues processed: 46
  average time/residue: 0.5619
  time to fit residues: 28.0109
Evaluate side-chains
  47 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  555 TYR
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  833 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.056230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.045664 restraints weight = 56663.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.2662 rms_B_bonded: 4.29
r_work: 0.2493 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.2493
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2500 r_free = 0.2500    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2500 r_free = 0.2500    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8848  Z= 0.130
  Angle     :  0.609  10.913  12066  Z= 0.274
  Chirality :  0.038   0.123   1438
  Planarity :  0.005   0.049   1414
  Dihedral  :  8.700  78.335   1822
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.00 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.27), residues: 1026
  helix:  1.96 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.73 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 603 
 TYR   0.010   0.001   TYR B 519 
 PHE   0.013   0.001   PHE B 471 
 TRP   0.013   0.001   TRP B 492 
 HIS   0.002   0.001   HIS A 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8842)
  covalent geometry    : angle       0.60710 (12054)
  hydrogen bonds       : bond        0.04003 (  522)
  hydrogen bonds       : angle       3.98768 ( 1524)
  Misc. bond           : bond        0.00106 (    2)
  link_BETA1-4         : bond        0.00286 (    2)
  link_BETA1-4         : angle       1.88782 (    6)
  link_NAG-ASN         : bond        0.00037 (    2)
  link_NAG-ASN         : angle       1.02667 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  586 MET cc_start: 0.9520 (mmm) cc_final: 0.9310 (mmt)
REVERT: A  663 MET cc_start: 0.9290 (tpp) cc_final: 0.8921 (tpt)
REVERT: A  721 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8285 (mmm)
REVERT: B  482 ASN cc_start: 0.9161 (m110) cc_final: 0.8888 (m110)
REVERT: B  559 MET cc_start: 0.8625 (mmm) cc_final: 0.8174 (mmm)
REVERT: B  721 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8107 (mmm)
  outliers start: 10
  outliers final: 4
  residues processed: 45
  average time/residue: 0.6099
  time to fit residues: 29.4843
Evaluate side-chains
  47 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  555 TYR
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  833 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0970
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0870
   chunk 7 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.5156

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.056707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.045705 restraints weight = 79543.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2667 rms_B_bonded: 4.95
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2667
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2667 r_free = 0.2667    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2667 r_free = 0.2667    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2667
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8848  Z= 0.115
  Angle     :  0.613  11.899  12066  Z= 0.274
  Chirality :  0.038   0.127   1438
  Planarity :  0.005   0.048   1414
  Dihedral  :  8.380  79.271   1822
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.56 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.27), residues: 1026
  helix:  2.02 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.66 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 603 
 TYR   0.010   0.001   TYR B 519 
 PHE   0.012   0.001   PHE B 471 
 TRP   0.014   0.001   TRP A 492 
 HIS   0.002   0.001   HIS B 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8842)
  covalent geometry    : angle       0.61198 (12054)
  hydrogen bonds       : bond        0.03847 (  522)
  hydrogen bonds       : angle       3.94551 ( 1524)
  Misc. bond           : bond        0.00113 (    2)
  link_BETA1-4         : bond        0.00285 (    2)
  link_BETA1-4         : angle       1.71943 (    6)
  link_NAG-ASN         : bond        0.00038 (    2)
  link_NAG-ASN         : angle       0.95210 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  586 MET cc_start: 0.9362 (mmm) cc_final: 0.9104 (mmt)
REVERT: A  663 MET cc_start: 0.9179 (tpp) cc_final: 0.8903 (tpp)
REVERT: A  721 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8242 (mpp)
REVERT: B  482 ASN cc_start: 0.9098 (m110) cc_final: 0.8840 (m110)
REVERT: B  559 MET cc_start: 0.8632 (mmm) cc_final: 0.8223 (mmm)
REVERT: B  721 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.7695 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 46
  average time/residue: 0.5608
  time to fit residues: 27.9484
Evaluate side-chains
  50 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  555 TYR
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  833 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.055828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.045201 restraints weight = 59841.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.2657 rms_B_bonded: 4.40
r_work: 0.2484 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8848  Z= 0.138
  Angle     :  0.610  11.804  12066  Z= 0.275
  Chirality :  0.038   0.122   1438
  Planarity :  0.005   0.048   1414
  Dihedral  :  8.214  79.902   1822
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.78 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.84 (0.27), residues: 1026
  helix:  2.03 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -0.66 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 603 
 TYR   0.009   0.001   TYR B 519 
 PHE   0.013   0.001   PHE A 471 
 TRP   0.012   0.001   TRP A 492 
 HIS   0.001   0.001   HIS A 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8842)
  covalent geometry    : angle       0.60897 (12054)
  hydrogen bonds       : bond        0.03956 (  522)
  hydrogen bonds       : angle       3.95379 ( 1524)
  Misc. bond           : bond        0.00099 (    2)
  link_BETA1-4         : bond        0.00229 (    2)
  link_BETA1-4         : angle       1.58096 (    6)
  link_NAG-ASN         : bond        0.00055 (    2)
  link_NAG-ASN         : angle       1.04420 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  586 MET cc_start: 0.9526 (mmm) cc_final: 0.9315 (mmt)
REVERT: B  482 ASN cc_start: 0.9164 (m110) cc_final: 0.8909 (m110)
REVERT: B  559 MET cc_start: 0.8587 (mmm) cc_final: 0.8119 (mmm)
REVERT: B  721 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8033 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 47
  average time/residue: 0.5350
  time to fit residues: 27.1222
Evaluate side-chains
  49 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  555 TYR
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  833 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 819 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.055951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.045118 restraints weight = 73943.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.2650 rms_B_bonded: 4.82
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8848  Z= 0.136
  Angle     :  0.628  13.101  12066  Z= 0.280
  Chirality :  0.039   0.125   1438
  Planarity :  0.005   0.048   1414
  Dihedral  :  8.111  80.469   1822
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.33 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.81 (0.27), residues: 1026
  helix:  2.01 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -0.66 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 603 
 TYR   0.010   0.001   TYR B 519 
 PHE   0.013   0.001   PHE A 471 
 TRP   0.015   0.001   TRP B 492 
 HIS   0.002   0.001   HIS A 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8842)
  covalent geometry    : angle       0.62640 (12054)
  hydrogen bonds       : bond        0.03940 (  522)
  hydrogen bonds       : angle       3.98024 ( 1524)
  Misc. bond           : bond        0.00094 (    2)
  link_BETA1-4         : bond        0.00185 (    2)
  link_BETA1-4         : angle       1.51874 (    6)
  link_NAG-ASN         : bond        0.00027 (    2)
  link_NAG-ASN         : angle       1.12561 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  586 MET cc_start: 0.9366 (mmm) cc_final: 0.9110 (mmt)
REVERT: A  663 MET cc_start: 0.9291 (tpp) cc_final: 0.9019 (tpp)
REVERT: B  482 ASN cc_start: 0.9115 (m110) cc_final: 0.8872 (m110)
REVERT: B  559 MET cc_start: 0.8638 (mmm) cc_final: 0.8237 (mmm)
REVERT: B  721 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.7806 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 48
  average time/residue: 0.5761
  time to fit residues: 30.0009
Evaluate side-chains
  50 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  555 TYR
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  833 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0980
   chunk 65 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.056491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.045732 restraints weight = 73415.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.2664 rms_B_bonded: 4.78
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8848  Z= 0.118
  Angle     :  0.623  12.477  12066  Z= 0.277
  Chirality :  0.038   0.130   1438
  Planarity :  0.005   0.048   1414
  Dihedral  :  7.958  81.428   1822
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.44 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.27), residues: 1026
  helix:  2.04 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -0.67 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 603 
 TYR   0.010   0.001   TYR B 519 
 PHE   0.012   0.001   PHE A 471 
 TRP   0.013   0.001   TRP A 492 
 HIS   0.002   0.001   HIS A 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8842)
  covalent geometry    : angle       0.62171 (12054)
  hydrogen bonds       : bond        0.03844 (  522)
  hydrogen bonds       : angle       3.94276 ( 1524)
  Misc. bond           : bond        0.00106 (    2)
  link_BETA1-4         : bond        0.00229 (    2)
  link_BETA1-4         : angle       1.40361 (    6)
  link_NAG-ASN         : bond        0.00043 (    2)
  link_NAG-ASN         : angle       1.02422 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  586 MET cc_start: 0.9372 (mmm) cc_final: 0.9115 (mmt)
REVERT: A  663 MET cc_start: 0.9274 (tpp) cc_final: 0.8943 (tpp)
REVERT: B  482 ASN cc_start: 0.9098 (m110) cc_final: 0.8861 (m110)
REVERT: B  559 MET cc_start: 0.8621 (mmm) cc_final: 0.8213 (mmm)
REVERT: B  721 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.7717 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 48
  average time/residue: 0.5324
  time to fit residues: 27.8125
Evaluate side-chains
  50 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  555 TYR
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  833 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 93 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.055979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.045296 restraints weight = 69690.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.2655 rms_B_bonded: 4.68
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8848  Z= 0.135
  Angle     :  0.627  12.486  12066  Z= 0.280
  Chirality :  0.038   0.126   1438
  Planarity :  0.005   0.048   1414
  Dihedral  :  7.920  82.034   1822
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.11 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.84 (0.27), residues: 1026
  helix:  2.04 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -0.66 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 603 
 TYR   0.010   0.001   TYR B 519 
 PHE   0.012   0.001   PHE A 471 
 TRP   0.015   0.001   TRP A 492 
 HIS   0.001   0.001   HIS B 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8842)
  covalent geometry    : angle       0.62568 (12054)
  hydrogen bonds       : bond        0.03908 (  522)
  hydrogen bonds       : angle       3.97783 ( 1524)
  Misc. bond           : bond        0.00100 (    2)
  link_BETA1-4         : bond        0.00189 (    2)
  link_BETA1-4         : angle       1.35596 (    6)
  link_NAG-ASN         : bond        0.00060 (    2)
  link_NAG-ASN         : angle       1.11429 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2077.83 seconds
wall clock time: 36 minutes 16.35 seconds (2176.35 seconds total)