Starting phenix.real_space_refine
on Thu Feb 13 21:38:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ty4_26165/02_2025/7ty4_26165.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ty4_26165/02_2025/7ty4_26165.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ty4_26165/02_2025/7ty4_26165.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ty4_26165/02_2025/7ty4_26165.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ty4_26165/02_2025/7ty4_26165.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ty4_26165/02_2025/7ty4_26165.cif"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.043
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      36      5.16       5
     C    5798      2.51       5
     N    1310      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8636
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 4067
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 4067
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 29, 'TRANS': 485}
          Chain breaks: 1
    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: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 187
          Unusual residues: {'CLR': 1, 'PC1': 1, 'Y01': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 187
          Unusual residues: {'CLR': 1, 'PC1': 1, 'Y01': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 37
          Classifications: {'water': 37}
          Link IDs: {None: 36}
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 35
          Classifications: {'water': 35}
          Link IDs: {None: 34}
  Time building chain proxies: 6.28, per 1000 atoms: 0.73
  Number of scatterers: 8636
  At special positions: 0
  Unit cell: (112.98, 97.916, 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      36     16.00
     P       2     15.00
     O    1490      8.00
     N    1310      7.00
     C    5798      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  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 "
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 4 sheets defined
      74.6% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 379 through 390
    Processing helix  chain 'A' and resid 392 through 399
    Processing helix  chain 'A' and resid 402 through 432
      removed outlier: 3.501A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
      removed outlier: 3.626A  pdb=" N   GLY A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 455
    Processing helix  chain 'A' and resid 465 through 483
    Processing helix  chain 'A' and resid 485 through 507
      removed outlier: 3.859A  pdb=" N   VAL A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TRP A 492 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 515
    Processing helix  chain 'A' and resid 517 through 547
      removed outlier: 3.511A  pdb=" N   LEU A 540 " --> pdb=" O   THR A 536 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ILE A 543 " --> pdb=" O   LYS A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 593
    Processing helix  chain 'A' and resid 598 through 608
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.509A  pdb=" N   MET A 617 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 646
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 4.022A  pdb=" N   MET A 664 " --> pdb=" O   PRO A 660 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE A 665 " --> pdb=" O   ILE A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 690
    Processing helix  chain 'A' and resid 701 through 719
      removed outlier: 3.756A  pdb=" N   LEU A 718 " --> pdb=" O   GLY A 714 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   PHE A 719 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 738
    Processing helix  chain 'A' and resid 760 through 773
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 784 through 799
      removed outlier: 3.722A  pdb=" N   LEU A 788 " --> pdb=" O   PRO A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 812
      removed outlier: 3.535A  pdb=" N   LEU A 811 " --> pdb=" O   ASP A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 819
      removed outlier: 3.824A  pdb=" N   HIS A 819 " --> pdb=" O   PRO A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 827
    Processing helix  chain 'A' and resid 829 through 853
    Processing helix  chain 'A' and resid 858 through 865
      removed outlier: 3.605A  pdb=" N   LEU A 865 " --> pdb=" O   PHE A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 872
    Processing helix  chain 'A' and resid 873 through 878
      removed outlier: 3.606A  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 392 through 399
    Processing helix  chain 'B' and resid 402 through 432
      removed outlier: 3.501A  pdb=" N   LEU B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE B 414 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
      removed outlier: 3.626A  pdb=" N   GLY B 424 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 455
    Processing helix  chain 'B' and resid 465 through 483
    Processing helix  chain 'B' and resid 485 through 507
      removed outlier: 3.859A  pdb=" N   VAL B 491 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TRP B 492 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE B 493 " --> pdb=" O   GLY B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 515
    Processing helix  chain 'B' and resid 517 through 547
      removed outlier: 3.509A  pdb=" N   LEU B 540 " --> pdb=" O   THR B 536 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ILE B 543 " --> pdb=" O   LYS B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 593
    Processing helix  chain 'B' and resid 598 through 608
    Processing helix  chain 'B' and resid 608 through 623
      removed outlier: 3.509A  pdb=" N   MET B 617 " --> pdb=" O   SER B 613 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 646
    Processing helix  chain 'B' and resid 660 through 667
      removed outlier: 4.023A  pdb=" N   MET B 664 " --> pdb=" O   PRO B 660 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE B 665 " --> pdb=" O   ILE B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 690
    Processing helix  chain 'B' and resid 701 through 719
      removed outlier: 3.757A  pdb=" N   LEU B 718 " --> pdb=" O   GLY B 714 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   PHE B 719 " --> pdb=" O   VAL B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 738
    Processing helix  chain 'B' and resid 760 through 773
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 784 through 799
      removed outlier: 3.724A  pdb=" N   LEU B 788 " --> pdb=" O   PRO B 784 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 812
      removed outlier: 3.534A  pdb=" N   LEU B 811 " --> pdb=" O   ASP B 807 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 815 through 819
      removed outlier: 3.824A  pdb=" N   HIS B 819 " --> pdb=" O   PRO B 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 822 through 827
    Processing helix  chain 'B' and resid 829 through 853
    Processing helix  chain 'B' and resid 858 through 865
      removed outlier: 3.605A  pdb=" N   LEU B 865 " --> pdb=" O   PHE B 861 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 865 through 872
    Processing helix  chain 'B' and resid 873 through 878
      removed outlier: 3.607A  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 461 through 463
      removed outlier: 4.792A  pdb=" N   VAL A 461 " --> pdb=" O   THR A 727 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742
      removed outlier: 7.659A  pdb=" N   VAL A 740 " --> pdb=" O   GLN A 754 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLN A 754 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN A 752 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 461 through 463
      removed outlier: 4.792A  pdb=" N   VAL B 461 " --> pdb=" O   THR B 727 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742
      removed outlier: 7.661A  pdb=" N   VAL B 740 " --> pdb=" O   GLN B 754 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLN B 754 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN B 752 " --> pdb=" O   GLY B 742 " (cutoff:3.500A)

    524 hydrogen bonds defined for protein.
    1518 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.30

  Time building geometry restraints manager: 2.54 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1254
        1.32 -     1.45: 2267
        1.45 -     1.57: 5201
        1.57 -     1.69: 4
        1.69 -     1.82: 66
  Bond restraints: 8792
  Sorted by residual:
  bond pdb=" N   LEU B 669 "
       pdb=" CA  LEU B 669 "
    ideal  model  delta    sigma   weight residual
    1.463  1.491 -0.027 6.90e-03 2.10e+04 1.58e+01
  bond pdb=" N   LEU A 669 "
       pdb=" CA  LEU A 669 "
    ideal  model  delta    sigma   weight residual
    1.463  1.491 -0.027 6.90e-03 2.10e+04 1.57e+01
  bond pdb=" N   LEU B 874 "
       pdb=" CA  LEU B 874 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.033 8.50e-03 1.38e+04 1.53e+01
  bond pdb=" N   THR A 431 "
       pdb=" CA  THR A 431 "
    ideal  model  delta    sigma   weight residual
    1.457  1.502 -0.045 1.16e-02 7.43e+03 1.49e+01
  bond pdb=" N   THR B 431 "
       pdb=" CA  THR B 431 "
    ideal  model  delta    sigma   weight residual
    1.457  1.502 -0.045 1.16e-02 7.43e+03 1.49e+01
  ... (remaining 8787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 9035
        2.13 -     4.26: 2548
        4.26 -     6.39: 383
        6.39 -     8.53: 6
        8.53 -    10.66: 2
  Bond angle restraints: 11974
  Sorted by residual:
  angle pdb=" N   VAL A 825 "
        pdb=" CA  VAL A 825 "
        pdb=" C   VAL A 825 "
      ideal   model   delta    sigma   weight residual
     111.00  105.19    5.81 1.09e+00 8.42e-01 2.84e+01
  angle pdb=" C   PRO B 598 "
        pdb=" N   GLY B 599 "
        pdb=" CA  GLY B 599 "
      ideal   model   delta    sigma   weight residual
     120.03  125.79   -5.76 1.12e+00 7.97e-01 2.65e+01
  angle pdb=" C   PRO A 598 "
        pdb=" N   GLY A 599 "
        pdb=" CA  GLY A 599 "
      ideal   model   delta    sigma   weight residual
     120.03  125.76   -5.73 1.12e+00 7.97e-01 2.62e+01
  angle pdb=" N   TYR B 596 "
        pdb=" CA  TYR B 596 "
        pdb=" C   TYR B 596 "
      ideal   model   delta    sigma   weight residual
     108.41  116.71   -8.30 1.63e+00 3.76e-01 2.59e+01
  angle pdb=" N   GLU A 429 "
        pdb=" CA  GLU A 429 "
        pdb=" C   GLU A 429 "
      ideal   model   delta    sigma   weight residual
     111.82  106.03    5.79 1.16e+00 7.43e-01 2.49e+01
  ... (remaining 11969 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.46: 5185
       19.46 -    38.93: 348
       38.93 -    58.39: 94
       58.39 -    77.85: 22
       77.85 -    97.32: 5
  Dihedral angle restraints: 5654
    sinusoidal: 2684
      harmonic: 2970
  Sorted by residual:
  dihedral pdb=" CA  TYR A 596 "
           pdb=" C   TYR A 596 "
           pdb=" N   PHE A 597 "
           pdb=" CA  PHE A 597 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.14   20.86     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  TYR B 555 "
           pdb=" C   TYR B 555 "
           pdb=" N   ASN B 556 "
           pdb=" CA  ASN B 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.45   19.55     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  TYR A 555 "
           pdb=" C   TYR A 555 "
           pdb=" N   ASN A 556 "
           pdb=" CA  ASN A 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.86   19.14     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 5651 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 775
       0.077 -    0.154: 596
       0.154 -    0.232: 61
       0.232 -    0.309: 0
       0.309 -    0.386: 2
  Chirality restraints: 1434
  Sorted by residual:
  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   -2.24   -0.16 2.00e-02 2.50e+03 6.67e+01
  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   -2.33   -0.07 2.00e-02 2.50e+03 1.29e+01
  chirality pdb=" CA  VAL A 825 "
            pdb=" N   VAL A 825 "
            pdb=" C   VAL A 825 "
            pdb=" CB  VAL A 825 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.83   -0.39 2.00e-01 2.50e+01 3.72e+00
  ... (remaining 1431 not shown)

  Planarity restraints: 1410
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.326 2.00e-02 2.50e+03   2.77e-01 9.58e+02
        pdb=" C7  NAG C   1 "   -0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.182 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.483 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.291 2.00e-02 2.50e+03   2.44e-01 7.44e+02
        pdb=" C7  NAG D   1 "    0.077 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.187 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.415 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "   -0.221 2.00e-02 2.50e+03   1.83e-01 4.17e+02
        pdb=" C7  NAG C   2 "    0.059 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "   -0.157 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "    0.299 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1407 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 401
        2.75 -     3.29: 9297
        3.29 -     3.83: 13893
        3.83 -     4.36: 18726
        4.36 -     4.90: 30644
  Nonbonded interactions: 72961
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 555 "
            pdb=" OH  TYR B 555 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   ASP B 607 "
            pdb=" O   HOH B2301 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OE1 GLN A 447 "
            pdb=" O   HOH A2301 "
     model   vdw
     2.422 3.040
  nonbonded pdb=" OE1 GLN B 447 "
            pdb=" O   HOH B2302 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" NH2 ARG A 490 "
            pdb=" O   MET A 721 "
     model   vdw
     2.450 3.120
  ... (remaining 72956 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
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=1.00 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:             1.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.470
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:14.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
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      :  0.013   0.051   8792  Z= 0.854
  Angle     :  1.798  10.657  11974  Z= 1.370
  Chirality :  0.087   0.386   1434
  Planarity :  0.012   0.277   1408
  Dihedral  : 14.464  97.319   3738
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.87 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.47 %
    Favored  : 94.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.22), residues: 1022
  helix: -1.56 (0.16), residues: 670
  sheet:  None (None), residues: 0
  loop : -1.93 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 492 
 HIS   0.005   0.002   HIS A 819 
 PHE   0.016   0.002   PHE B 451 
 TYR   0.013   0.002   TYR B 628 
 ARG   0.003   0.000   ARG B 730 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  482 ASN cc_start: 0.8611 (m-40) cc_final: 0.8260 (m110)
REVERT: A  498 ILE cc_start: 0.9632 (mt) cc_final: 0.9415 (mp)
REVERT: A  681 GLU cc_start: 0.8803 (tt0) cc_final: 0.8347 (tt0)
REVERT: A  741 MET cc_start: 0.9316 (mmm) cc_final: 0.8973 (mmm)
REVERT: A  880 ASN cc_start: 0.9250 (p0) cc_final: 0.9047 (t0)
REVERT: B  433 ASN cc_start: 0.9395 (m-40) cc_final: 0.9174 (m-40)
REVERT: B  482 ASN cc_start: 0.8615 (m-40) cc_final: 0.8244 (m110)
REVERT: B  498 ILE cc_start: 0.9630 (mt) cc_final: 0.9424 (mp)
REVERT: B  681 GLU cc_start: 0.8808 (tt0) cc_final: 0.8352 (tt0)
REVERT: B  741 MET cc_start: 0.9318 (mmm) cc_final: 0.8974 (mmm)
REVERT: B  880 ASN cc_start: 0.9252 (p0) cc_final: 0.9038 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 130
  average time/residue: 0.9647
  time to fit residues: 135.9372
Evaluate side-chains
  73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain B residue  511 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0870
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 433 ASN
A 457 GLN
A 545 GLN
A 683 GLN
B 457 GLN
B 545 GLN
B 564 GLN
B 683 GLN
B 834 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.059646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.050410 restraints weight = 28351.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 3.23
r_work: 0.2671 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8792  Z= 0.204
  Angle     :  0.650   8.528  11974  Z= 0.312
  Chirality :  0.040   0.146   1434
  Planarity :  0.005   0.042   1408
  Dihedral  : 10.134  67.469   1840
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 10.27 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.25), residues: 1022
  helix:  1.33 (0.19), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.31 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 662 
 HIS   0.002   0.001   HIS A 734 
 PHE   0.019   0.001   PHE A 411 
 TYR   0.009   0.001   TYR A 824 
 ARG   0.007   0.001   ARG B 603 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8793 (pp)
REVERT: A  498 ILE cc_start: 0.9303 (mt) cc_final: 0.9102 (mp)
REVERT: A  554 ASN cc_start: 0.8463 (t0) cc_final: 0.8119 (t0)
REVERT: A  681 GLU cc_start: 0.8935 (tt0) cc_final: 0.8120 (tm-30)
REVERT: A  696 MET cc_start: 0.8563 (mmm) cc_final: 0.8236 (mmm)
REVERT: A  721 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8545 (mtp)
REVERT: A  759 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8315 (pm20)
REVERT: B  386 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8773 (pp)
REVERT: B  554 ASN cc_start: 0.8363 (t0) cc_final: 0.7907 (t0)
REVERT: B  681 GLU cc_start: 0.8944 (tt0) cc_final: 0.8153 (tm-30)
REVERT: B  721 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8470 (mtp)
REVERT: B  759 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8409 (pm20)
  outliers start: 23
  outliers final: 0
  residues processed: 97
  average time/residue: 0.8689
  time to fit residues: 92.7661
Evaluate side-chains
  75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain B residue  386 ILE
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  759 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    0.0470
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.7680

-------------------------------------------------------------------------------
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 = 0.3045 r_free = 0.3045 target = 0.058450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.049503 restraints weight = 29602.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 3.29
r_work: 0.2653 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8792  Z= 0.205
  Angle     :  0.590   7.892  11974  Z= 0.280
  Chirality :  0.039   0.140   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  9.472  61.381   1836
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 11.27 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.26), residues: 1022
  helix:  1.93 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.98 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 662 
 HIS   0.002   0.001   HIS A 651 
 PHE   0.013   0.001   PHE A 411 
 TYR   0.012   0.001   TYR A 824 
 ARG   0.005   0.001   ARG B 656 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 ILE cc_start: 0.9272 (mt) cc_final: 0.9035 (mp)
REVERT: A  554 ASN cc_start: 0.8765 (t0) cc_final: 0.8376 (t0)
REVERT: A  681 GLU cc_start: 0.8911 (tt0) cc_final: 0.8142 (tm-30)
REVERT: A  696 MET cc_start: 0.8648 (mmm) cc_final: 0.8004 (mmm)
REVERT: A  721 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8418 (mpp)
REVERT: B  554 ASN cc_start: 0.8802 (t0) cc_final: 0.8291 (t0)
REVERT: B  681 GLU cc_start: 0.8926 (tt0) cc_final: 0.8162 (tm-30)
REVERT: B  721 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8689 (mmm)
  outliers start: 22
  outliers final: 3
  residues processed: 86
  average time/residue: 0.8567
  time to fit residues: 81.4332
Evaluate side-chains
  71 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  721 MET
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0870
   chunk 86 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0470
   chunk 95 optimal weight:    5.9990
   chunk 89 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.5456

-------------------------------------------------------------------------------
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 = 0.3047 r_free = 0.3047 target = 0.058457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.049680 restraints weight = 29638.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 3.28
r_work: 0.2656 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8792  Z= 0.168
  Angle     :  0.572   9.441  11974  Z= 0.268
  Chirality :  0.039   0.134   1434
  Planarity :  0.005   0.048   1408
  Dihedral  :  9.200  59.710   1836
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.94 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.26), residues: 1022
  helix:  2.09 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.80 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 662 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.013   0.001   PHE A 471 
 TYR   0.013   0.001   TYR A 824 
 ARG   0.005   0.001   ARG A 656 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 ASN cc_start: 0.8810 (t0) cc_final: 0.8369 (t0)
REVERT: A  559 MET cc_start: 0.8783 (mtm) cc_final: 0.8271 (mtt)
REVERT: A  681 GLU cc_start: 0.8900 (tt0) cc_final: 0.8130 (tm-30)
REVERT: A  759 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8285 (pm20)
REVERT: B  433 ASN cc_start: 0.9568 (m110) cc_final: 0.9282 (m110)
REVERT: B  522 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9025 (mm-30)
REVERT: B  554 ASN cc_start: 0.8907 (t0) cc_final: 0.8461 (t0)
REVERT: B  559 MET cc_start: 0.8765 (mtm) cc_final: 0.8280 (mtt)
REVERT: B  681 GLU cc_start: 0.8911 (tt0) cc_final: 0.8139 (tm-30)
REVERT: B  759 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8479 (pm20)
  outliers start: 15
  outliers final: 7
  residues processed: 82
  average time/residue: 0.8876
  time to fit residues: 80.5290
Evaluate side-chains
  74 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0060
   chunk 52 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.9398

-------------------------------------------------------------------------------
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 = 0.3027 r_free = 0.3027 target = 0.057361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.048559 restraints weight = 29905.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.2768 rms_B_bonded: 3.28
r_work: 0.2634 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8792  Z= 0.214
  Angle     :  0.591   8.489  11974  Z= 0.274
  Chirality :  0.039   0.133   1434
  Planarity :  0.005   0.048   1408
  Dihedral  :  9.106  58.846   1836
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.94 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.27), residues: 1022
  helix:  2.17 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.61 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 662 
 HIS   0.002   0.001   HIS A 651 
 PHE   0.012   0.001   PHE B 471 
 TYR   0.013   0.001   TYR A 824 
 ARG   0.004   0.000   ARG A 656 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 ASN cc_start: 0.8917 (t0) cc_final: 0.8494 (t0)
REVERT: A  559 MET cc_start: 0.8799 (mtm) cc_final: 0.8327 (mtt)
REVERT: A  721 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8259 (mmm)
REVERT: A  759 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8287 (pm20)
REVERT: B  433 ASN cc_start: 0.9594 (m110) cc_final: 0.9280 (m110)
REVERT: B  554 ASN cc_start: 0.8993 (t0) cc_final: 0.8525 (t0)
REVERT: B  559 MET cc_start: 0.8762 (mtm) cc_final: 0.8309 (mtt)
REVERT: B  681 GLU cc_start: 0.8945 (tt0) cc_final: 0.8400 (tm-30)
REVERT: B  759 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8503 (pm20)
  outliers start: 20
  outliers final: 6
  residues processed: 83
  average time/residue: 0.9321
  time to fit residues: 85.7241
Evaluate side-chains
  73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3018 r_free = 0.3018 target = 0.056879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.048180 restraints weight = 29884.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 3.24
r_work: 0.2628 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
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      :  0.004   0.033   8792  Z= 0.228
  Angle     :  0.597   9.420  11974  Z= 0.277
  Chirality :  0.039   0.148   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  8.895  59.864   1836
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.72 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.27), residues: 1022
  helix:  2.12 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.64 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 492 
 HIS   0.002   0.001   HIS A 651 
 PHE   0.012   0.001   PHE B 471 
 TYR   0.013   0.001   TYR B 824 
 ARG   0.004   0.000   ARG A 656 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 ASN cc_start: 0.8990 (t0) cc_final: 0.8533 (t0)
REVERT: A  559 MET cc_start: 0.8793 (mtm) cc_final: 0.8301 (mtt)
REVERT: A  705 ASP cc_start: 0.9344 (m-30) cc_final: 0.9061 (m-30)
REVERT: A  721 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8287 (mpp)
REVERT: A  759 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8363 (pm20)
REVERT: B  433 ASN cc_start: 0.9561 (m110) cc_final: 0.9180 (m110)
REVERT: B  554 ASN cc_start: 0.9022 (t0) cc_final: 0.8569 (t0)
REVERT: B  559 MET cc_start: 0.8803 (mtm) cc_final: 0.8338 (mtt)
REVERT: B  681 GLU cc_start: 0.8922 (tt0) cc_final: 0.8382 (tm-30)
REVERT: B  705 ASP cc_start: 0.9355 (m-30) cc_final: 0.9073 (m-30)
REVERT: B  721 MET cc_start: 0.8661 (mmm) cc_final: 0.8418 (mmm)
REVERT: B  759 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8532 (pm20)
  outliers start: 17
  outliers final: 6
  residues processed: 80
  average time/residue: 0.9055
  time to fit residues: 79.9572
Evaluate side-chains
  74 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 521 GLN
B 819 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.057785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.049067 restraints weight = 30174.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 3.30
r_work: 0.2650 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8792  Z= 0.180
  Angle     :  0.603   9.737  11974  Z= 0.278
  Chirality :  0.039   0.160   1434
  Planarity :  0.005   0.048   1408
  Dihedral  :  8.706  59.435   1836
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.50 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.26), residues: 1022
  helix:  2.08 (0.20), residues: 698
  sheet:  None (None), residues: 0
  loop : -0.58 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 492 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.012   0.001   PHE B 471 
 TYR   0.014   0.001   TYR A 824 
 ARG   0.003   0.000   ARG A 490 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 ASN cc_start: 0.8989 (t0) cc_final: 0.8492 (t0)
REVERT: A  559 MET cc_start: 0.8807 (mtm) cc_final: 0.8340 (mtt)
REVERT: A  721 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8356 (mmm)
REVERT: A  759 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8366 (pm20)
REVERT: B  433 ASN cc_start: 0.9535 (m110) cc_final: 0.9117 (m110)
REVERT: B  554 ASN cc_start: 0.9032 (t0) cc_final: 0.8539 (t0)
REVERT: B  559 MET cc_start: 0.8835 (mtm) cc_final: 0.8396 (mtt)
REVERT: B  681 GLU cc_start: 0.8908 (tt0) cc_final: 0.8365 (tm-30)
REVERT: B  759 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8516 (pm20)
  outliers start: 14
  outliers final: 8
  residues processed: 84
  average time/residue: 0.8398
  time to fit residues: 77.9759
Evaluate side-chains
  76 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  435 MET
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3029 r_free = 0.3029 target = 0.057141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.048469 restraints weight = 30745.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.2774 rms_B_bonded: 3.29
r_work: 0.2640 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8792  Z= 0.219
  Angle     :  0.641   9.891  11974  Z= 0.293
  Chirality :  0.041   0.248   1434
  Planarity :  0.004   0.047   1408
  Dihedral  :  8.618  59.175   1836
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.40 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.27), residues: 1022
  helix:  2.10 (0.20), residues: 698
  sheet:  None (None), residues: 0
  loop : -0.56 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 492 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.012   0.001   PHE B 471 
 TYR   0.013   0.001   TYR A 824 
 ARG   0.003   0.000   ARG A 656 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 ASN cc_start: 0.9045 (t0) cc_final: 0.8538 (t0)
REVERT: A  559 MET cc_start: 0.8802 (mtm) cc_final: 0.8361 (mtt)
REVERT: A  681 GLU cc_start: 0.8918 (tt0) cc_final: 0.8335 (tm-30)
REVERT: A  705 ASP cc_start: 0.9360 (m-30) cc_final: 0.9143 (m-30)
REVERT: A  721 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8131 (mpp)
REVERT: A  759 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8478 (pm20)
REVERT: B  433 ASN cc_start: 0.9535 (m110) cc_final: 0.9116 (m110)
REVERT: B  554 ASN cc_start: 0.9060 (t0) cc_final: 0.8566 (t0)
REVERT: B  559 MET cc_start: 0.8837 (mtm) cc_final: 0.8402 (mtt)
REVERT: B  681 GLU cc_start: 0.8930 (tt0) cc_final: 0.8347 (tm-30)
REVERT: B  705 ASP cc_start: 0.9367 (m-30) cc_final: 0.9147 (m-30)
REVERT: B  759 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8555 (pm20)
  outliers start: 15
  outliers final: 8
  residues processed: 78
  average time/residue: 0.9072
  time to fit residues: 77.8229
Evaluate side-chains
  75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 78 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3029 r_free = 0.3029 target = 0.057188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.048612 restraints weight = 30465.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 3.27
r_work: 0.2647 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8792  Z= 0.214
  Angle     :  0.678  14.342  11974  Z= 0.307
  Chirality :  0.041   0.290   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  8.508  59.756   1836
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 14.84 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.27), residues: 1022
  helix:  2.08 (0.20), residues: 698
  sheet:  None (None), residues: 0
  loop : -0.52 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 492 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.012   0.001   PHE A 471 
 TYR   0.013   0.001   TYR A 824 
 ARG   0.002   0.000   ARG A 656 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 ILE cc_start: 0.9201 (mt) cc_final: 0.8981 (mp)
REVERT: A  554 ASN cc_start: 0.9056 (t0) cc_final: 0.8544 (t0)
REVERT: A  559 MET cc_start: 0.8807 (mtm) cc_final: 0.8374 (mtt)
REVERT: A  681 GLU cc_start: 0.8914 (tt0) cc_final: 0.8187 (tt0)
REVERT: A  705 ASP cc_start: 0.9357 (m-30) cc_final: 0.9128 (m-30)
REVERT: A  759 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8517 (pm20)
REVERT: B  433 ASN cc_start: 0.9539 (m110) cc_final: 0.9124 (m110)
REVERT: B  540 LEU cc_start: 0.9559 (tp) cc_final: 0.9321 (mm)
REVERT: B  554 ASN cc_start: 0.9025 (t0) cc_final: 0.8524 (t0)
REVERT: B  559 MET cc_start: 0.8834 (mtm) cc_final: 0.8400 (mtt)
REVERT: B  681 GLU cc_start: 0.8921 (tt0) cc_final: 0.8335 (tm-30)
REVERT: B  705 ASP cc_start: 0.9359 (m-30) cc_final: 0.9129 (m-30)
REVERT: B  759 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8548 (pm20)
  outliers start: 13
  outliers final: 8
  residues processed: 79
  average time/residue: 0.8996
  time to fit residues: 78.3633
Evaluate side-chains
  77 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 75 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 76 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:
B 880 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.057567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.048982 restraints weight = 30517.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.2787 rms_B_bonded: 3.29
r_work: 0.2653 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8792  Z= 0.214
  Angle     :  0.677  13.420  11974  Z= 0.307
  Chirality :  0.041   0.355   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  8.383  58.352   1836
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.96 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.27), residues: 1022
  helix:  2.02 (0.20), residues: 698
  sheet:  None (None), residues: 0
  loop : -0.52 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 492 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.011   0.001   PHE A 471 
 TYR   0.012   0.001   TYR A 824 
 ARG   0.003   0.000   ARG B 490 

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 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: 11
    poor density    : 68
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 ILE cc_start: 0.9155 (mt) cc_final: 0.8952 (mp)
REVERT: A  522 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8916 (mm-30)
REVERT: A  554 ASN cc_start: 0.9054 (t0) cc_final: 0.8529 (t0)
REVERT: A  559 MET cc_start: 0.8815 (mtm) cc_final: 0.8390 (mtt)
REVERT: A  681 GLU cc_start: 0.8911 (tt0) cc_final: 0.8187 (tt0)
REVERT: A  705 ASP cc_start: 0.9345 (m-30) cc_final: 0.9118 (m-30)
REVERT: A  721 MET cc_start: 0.8842 (mmm) cc_final: 0.8117 (mpp)
REVERT: A  759 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8533 (pm20)
REVERT: B  433 ASN cc_start: 0.9531 (m110) cc_final: 0.9114 (m110)
REVERT: B  540 LEU cc_start: 0.9554 (tp) cc_final: 0.9292 (mm)
REVERT: B  554 ASN cc_start: 0.9036 (t0) cc_final: 0.8536 (t0)
REVERT: B  559 MET cc_start: 0.8875 (mtm) cc_final: 0.8430 (mtt)
REVERT: B  586 MET cc_start: 0.9464 (mmm) cc_final: 0.9227 (mmm)
REVERT: B  681 GLU cc_start: 0.8912 (tt0) cc_final: 0.8183 (tt0)
REVERT: B  705 ASP cc_start: 0.9348 (m-30) cc_final: 0.9117 (m-30)
REVERT: B  759 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8549 (pm20)
  outliers start: 11
  outliers final: 8
  residues processed: 79
  average time/residue: 0.9903
  time to fit residues: 86.3724
Evaluate side-chains
  77 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 PHE
Chi-restraints excluded: chain A residue  522 GLU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  759 GLN
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain B residue  511 PHE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  759 GLN
Chi-restraints excluded: chain B residue  864 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0870
   chunk 85 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 880 ASN
B 521 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.058208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.049677 restraints weight = 30454.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 3.29
r_work: 0.2675 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8792  Z= 0.192
  Angle     :  0.680  15.781  11974  Z= 0.307
  Chirality :  0.040   0.325   1434
  Planarity :  0.005   0.047   1408
  Dihedral  :  8.242  59.973   1836
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.18 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.27), residues: 1022
  helix:  2.00 (0.20), residues: 710
  sheet:  None (None), residues: 0
  loop : -0.44 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 492 
 HIS   0.002   0.001   HIS B 834 
 PHE   0.011   0.001   PHE A 471 
 TYR   0.013   0.001   TYR A 824 
 ARG   0.002   0.000   ARG A 656 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4141.61 seconds
wall clock time: 74 minutes 34.19 seconds (4474.19 seconds total)