Starting phenix.real_space_refine
on Fri Mar 14 00:42:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qo9_14087/03_2025/7qo9_14087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qo9_14087/03_2025/7qo9_14087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qo9_14087/03_2025/7qo9_14087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qo9_14087/03_2025/7qo9_14087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qo9_14087/03_2025/7qo9_14087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qo9_14087/03_2025/7qo9_14087.cif"
  }
  resolution = 3.88
  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=   0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    5830      2.51       5
     N    1523      2.21       5
     O    1782      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9180
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4568
          Classifications: {'peptide': 588}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 25, 'TRANS': 562}
          Chain breaks: 14
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 4486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 4486
          Classifications: {'peptide': 578}
          Link IDs: {'PTRANS': 26, 'TRANS': 551}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    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: "E"
      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: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 31
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2, 'water': 3}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.98, per 1000 atoms: 0.65
  Number of scatterers: 9180
  At special positions: 0
  Unit cell: (87.5022, 112.046, 122.717, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1782      8.00
     N    1523      7.00
     C    5830      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 129 " - pdb=" SG  CYS A 161 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 614 " - pdb=" SG  CYS A 646 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 659 " - pdb=" SG  CYS A 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 735 " - pdb=" SG  CYS A 757 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 740 " - pdb=" SG  CYS A 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 837 " - pdb=" SG  CYS A 848 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 376 " - pdb=" SG  CYS B 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 388 " - pdb=" SG  CYS B 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 477 " - pdb=" SG  CYS B 485 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 535 " - pdb=" SG  CYS B 587 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 614 " - pdb=" SG  CYS B 646 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 659 " - pdb=" SG  CYS B 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 735 " - pdb=" SG  CYS B 757 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 740 " - pdb=" SG  CYS B 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 837 " - pdb=" SG  CYS B 848 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A 231 "
      " NAG A1302 " - " ASN A 279 "
      " NAG C   1 " - " ASN A 160 "
      " NAG D   1 " - " ASN A 120 "
      " NAG E   1 " - " ASN A 135 "
  Time building additional restraints: 2.25
  Conformation dependent library (CDL) restraints added in 1000.0 milliseconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2188

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 17 sheets defined
      26.2% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 73
    Processing helix  chain 'A' and resid 291 through 301
    Processing helix  chain 'A' and resid 619 through 624
    Processing helix  chain 'A' and resid 734 through 740
      removed outlier: 3.661A  pdb=" N   TYR A 738 " --> pdb=" O   ASP A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 752
      removed outlier: 3.500A  pdb=" N   GLN A 752 " --> pdb=" O   ASN A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 780
    Processing helix  chain 'A' and resid 846 through 852
      removed outlier: 3.589A  pdb=" N   PHE A 852 " --> pdb=" O   CYS A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 874
    Processing helix  chain 'A' and resid 943 through 962
      removed outlier: 4.873A  pdb=" N   VAL A 948 " --> pdb=" O   LYS A 944 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL A 949 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 965
      No H-bonds generated for 'chain 'A' and resid 963 through 965'
    Processing helix  chain 'A' and resid 973 through 981
    Processing helix  chain 'A' and resid 982 through 1022
      removed outlier: 4.599A  pdb=" N   VAL A 988 " --> pdb=" O   PRO A 984 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU A 993 " --> pdb=" O   GLN A 989 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 368
      removed outlier: 3.769A  pdb=" N   TYR B 366 " --> pdb=" O   TYR B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 387
      removed outlier: 3.762A  pdb=" N   LEU B 384 " --> pdb=" O   PRO B 381 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASN B 385 " --> pdb=" O   THR B 382 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU B 387 " --> pdb=" O   LEU B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 419
    Processing helix  chain 'B' and resid 734 through 739
    Processing helix  chain 'B' and resid 743 through 751
    Processing helix  chain 'B' and resid 752 through 754
      No H-bonds generated for 'chain 'B' and resid 752 through 754'
    Processing helix  chain 'B' and resid 757 through 779
      removed outlier: 3.565A  pdb=" N   ILE B 767 " --> pdb=" O   ALA B 763 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B 772 " --> pdb=" O   ALA B 768 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS B 773 " --> pdb=" O   VAL B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 824
    Processing helix  chain 'B' and resid 825 through 827
      No H-bonds generated for 'chain 'B' and resid 825 through 827'
    Processing helix  chain 'B' and resid 863 through 864
      No H-bonds generated for 'chain 'B' and resid 863 through 864'
    Processing helix  chain 'B' and resid 866 through 868
      No H-bonds generated for 'chain 'B' and resid 866 through 868'
    Processing helix  chain 'B' and resid 942 through 962
      removed outlier: 3.739A  pdb=" N   GLN B 946 " --> pdb=" O   LEU B 942 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL B 948 " --> pdb=" O   LYS B 944 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL B 949 " --> pdb=" O   LEU B 945 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 963 through 965
      No H-bonds generated for 'chain 'B' and resid 963 through 965'
    Processing helix  chain 'B' and resid 973 through 980
    Processing helix  chain 'B' and resid 982 through 1022
      removed outlier: 4.466A  pdb=" N   VAL B 988 " --> pdb=" O   PRO B 984 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37
      removed outlier: 7.205A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   SER A 200 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55
      removed outlier: 4.508A  pdb=" N   ASP A 284 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68
    Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83
    Processing sheet with id=AA6, first strand: chain 'A' and resid 104 through 105
      removed outlier: 3.861A  pdb=" N   SER A 114 " --> pdb=" O   CYS A 129 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   CYS A 129 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ILE A 126 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   PHE A 163 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   VAL A 128 " --> pdb=" O   CYS A 161 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   CYS A 161 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   SER A 157 " --> pdb=" O   GLN A 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316
      removed outlier: 5.626A  pdb=" N   ILE A 309 " --> pdb=" O   THR A 596 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   THR A 596 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   GLN A 311 " --> pdb=" O   VAL A 594 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL A 594 " --> pdb=" O   GLN A 311 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER A 313 " --> pdb=" O   VAL A 592 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLY A 591 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 651 through 657
      removed outlier: 6.058A  pdb=" N   THR A 693 " --> pdb=" O   VAL A 653 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ASN A 655 " --> pdb=" O   THR A 693 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ALA A 669 " --> pdb=" O   PRO A 662 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 724 through 725
    Processing sheet with id=AB1, first strand: chain 'A' and resid 732 through 733
    Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 316
      removed outlier: 3.807A  pdb=" N   THR B 312 " --> pdb=" O   VAL B 592 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   VAL B 592 " --> pdb=" O   THR B 312 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ASN B 314 " --> pdb=" O   GLY B 590 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLY B 590 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLY B 591 " --> pdb=" O   GLN B 610 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 322 through 323
      removed outlier: 3.500A  pdb=" N   ASN B 539 " --> pdb=" O   ILE B 323 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   PHE B 540 " --> pdb=" O   LEU B 543 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 355
      removed outlier: 3.836A  pdb=" N   VAL B 392 " --> pdb=" O   ILE B 355 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 359
      removed outlier: 6.547A  pdb=" N   CYS B 358 " --> pdb=" O   CYS B 522 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 430 through 434
      removed outlier: 3.708A  pdb=" N   ARG B 506 " --> pdb=" O   TRP B 433 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 651 through 652
      removed outlier: 6.593A  pdb=" N   GLU B 651 " --> pdb=" O   ALA B 691 " (cutoff:3.500A)
      removed outlier: 9.132A  pdb=" N   THR B 693 " --> pdb=" O   GLU B 651 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 732 through 733

    300 hydrogen bonds defined for protein.
    819 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: 2.55

  Time building geometry restraints manager: 2.68 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: 1899
        1.33 -     1.45: 2235
        1.45 -     1.58: 5160
        1.58 -     1.70: 0
        1.70 -     1.82: 55
  Bond restraints: 9349
  Sorted by residual:
  bond pdb=" N   GLN A 625 "
       pdb=" CA  GLN A 625 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.047 1.29e-02 6.01e+03 1.31e+01
  bond pdb=" CA  SER B 491 "
       pdb=" CB  SER B 491 "
    ideal  model  delta    sigma   weight residual
    1.530  1.480  0.050 1.39e-02 5.18e+03 1.30e+01
  bond pdb=" N   VAL B 480 "
       pdb=" CA  VAL B 480 "
    ideal  model  delta    sigma   weight residual
    1.459  1.504 -0.045 1.25e-02 6.40e+03 1.29e+01
  bond pdb=" N   ASP A 624 "
       pdb=" CA  ASP A 624 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.20e-02 6.94e+03 9.24e+00
  bond pdb=" N   CYS B 485 "
       pdb=" CA  CYS B 485 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.035 1.26e-02 6.30e+03 7.82e+00
  ... (remaining 9344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 12443
        2.37 -     4.74: 203
        4.74 -     7.10: 37
        7.10 -     9.47: 3
        9.47 -    11.84: 4
  Bond angle restraints: 12690
  Sorted by residual:
  angle pdb=" N   PRO A 628 "
        pdb=" CA  PRO A 628 "
        pdb=" CB  PRO A 628 "
      ideal   model   delta    sigma   weight residual
     103.25   92.75   10.50 1.05e+00 9.07e-01 1.00e+02
  angle pdb=" C   TYR B 448 "
        pdb=" CA  TYR B 448 "
        pdb=" CB  TYR B 448 "
      ideal   model   delta    sigma   weight residual
     110.88   99.97   10.91 1.57e+00 4.06e-01 4.83e+01
  angle pdb=" C   TYR B 486 "
        pdb=" CA  TYR B 486 "
        pdb=" CB  TYR B 486 "
      ideal   model   delta    sigma   weight residual
     109.83   97.99   11.84 1.75e+00 3.27e-01 4.58e+01
  angle pdb=" C   TYR B 446 "
        pdb=" CA  TYR B 446 "
        pdb=" CB  TYR B 446 "
      ideal   model   delta    sigma   weight residual
     114.87  104.90    9.97 1.51e+00 4.39e-01 4.36e+01
  angle pdb=" CA  ASP A 624 "
        pdb=" C   ASP A 624 "
        pdb=" O   ASP A 624 "
      ideal   model   delta    sigma   weight residual
     121.31  116.01    5.30 1.07e+00 8.73e-01 2.45e+01
  ... (remaining 12685 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.74: 5320
       23.74 -    47.48: 327
       47.48 -    71.21: 45
       71.21 -    94.95: 24
       94.95 -   118.69: 13
  Dihedral angle restraints: 5729
    sinusoidal: 2346
      harmonic: 3383
  Sorted by residual:
  dihedral pdb=" CB  CYS A 288 "
           pdb=" SG  CYS A 288 "
           pdb=" SG  CYS A 298 "
           pdb=" CB  CYS A 298 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.55   81.55     1      1.00e+01 1.00e-02 8.19e+01
  dihedral pdb=" CB  CYS B 535 "
           pdb=" SG  CYS B 535 "
           pdb=" SG  CYS B 587 "
           pdb=" CB  CYS B 587 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.51  -80.49     1      1.00e+01 1.00e-02 8.01e+01
  dihedral pdb=" CB  CYS A 659 "
           pdb=" SG  CYS A 659 "
           pdb=" SG  CYS A 668 "
           pdb=" CB  CYS A 668 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -11.72  -74.28     1      1.00e+01 1.00e-02 7.00e+01
  ... (remaining 5726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1436
       0.110 -    0.219: 48
       0.219 -    0.329: 8
       0.329 -    0.438: 3
       0.438 -    0.548: 3
  Chirality restraints: 1498
  Sorted by residual:
  chirality pdb=" CA  TYR B 448 "
            pdb=" N   TYR B 448 "
            pdb=" C   TYR B 448 "
            pdb=" CB  TYR B 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.06   -0.55 2.00e-01 2.50e+01 7.50e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 160 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.91   -0.49 2.00e-01 2.50e+01 6.12e+00
  chirality pdb=" CA  TYR B 446 "
            pdb=" N   TYR B 446 "
            pdb=" C   TYR B 446 "
            pdb=" CB  TYR B 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.96   -0.45 2.00e-01 2.50e+01 4.96e+00
  ... (remaining 1495 not shown)

  Planarity restraints: 1620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 627 "    0.016 2.00e-02 2.50e+03   3.16e-02 9.99e+00
        pdb=" C   THR A 627 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR A 627 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO A 628 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 226 "    0.043 5.00e-02 4.00e+02   6.61e-02 6.98e+00
        pdb=" N   PRO A 227 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 227 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 227 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  79 "    0.042 5.00e-02 4.00e+02   6.32e-02 6.39e+00
        pdb=" N   PRO A  80 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A  80 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  80 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1617 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 528
        2.72 -     3.27: 9666
        3.27 -     3.81: 14147
        3.81 -     4.36: 16230
        4.36 -     4.90: 27275
  Nonbonded interactions: 67846
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  89 "
            pdb=" OE1 GLU A 186 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   THR B 863 "
            pdb=" N   MET B 866 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" O   VAL A 619 "
            pdb=" ND1 HIS A 622 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OG  SER A 110 "
            pdb=" OE1 GLN A 132 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG  SER A 755 "
            pdb=" OG1 THR A 758 "
     model   vdw
     2.251 3.040
  ... (remaining 67841 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 'C'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.850
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.340
  Find NCS groups from input model:        0.270
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9349  Z= 0.271
  Angle     :  0.757  11.839  12690  Z= 0.435
  Chirality :  0.056   0.548   1498
  Planarity :  0.005   0.066   1615
  Dihedral  : 16.656 118.691   3490
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.16 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  0.50 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.55 %
  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: -1.18 (0.25), residues: 1124
  helix:  1.37 (0.33), residues: 272
  sheet: -0.07 (0.39), residues: 181
  loop : -2.05 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 433 
 HIS   0.004   0.001   HIS B 951 
 PHE   0.037   0.001   PHE B 371 
 TYR   0.031   0.001   TYR B 450 
 ARG   0.015   0.001   ARG B1016 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A  290 LEU cc_start: 0.8808 (tt) cc_final: 0.8282 (tt)
REVERT: B  446 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6471 (t80)
REVERT: B  490 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7178 (tpm170)
REVERT: B  770 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6274 (tm-30)
REVERT: B  999 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7871 (tm-30)
  outliers start: 13
  outliers final: 4
  residues processed: 120
  average time/residue: 0.1982
  time to fit residues: 33.9655
Evaluate side-chains
  75 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  628 PRO
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  491 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 104 optimal weight:   10.0000
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN
B 687 GLN
B 962 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.113845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.088519 restraints weight = 28483.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.087876 restraints weight = 20001.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.088756 restraints weight = 16222.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   9349  Z= 0.406
  Angle     :  0.774  11.451  12690  Z= 0.397
  Chirality :  0.049   0.339   1498
  Planarity :  0.005   0.074   1615
  Dihedral  : 12.876 112.316   1434
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.68 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.80 %
    Favored  : 87.71 %
  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: -1.66 (0.24), residues: 1124
  helix:  1.20 (0.31), residues: 269
  sheet: -0.30 (0.39), residues: 170
  loop : -2.45 (0.21), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A 630 
 HIS   0.008   0.001   HIS A 622 
 PHE   0.030   0.002   PHE B 556 
 TYR   0.017   0.002   TYR A 276 
 ARG   0.005   0.001   ARG A 997 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: A  629 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8090 (t)
REVERT: A  773 LYS cc_start: 0.9138 (tptt) cc_final: 0.8890 (tptp)
REVERT: A  833 GLN cc_start: 0.8283 (tp-100) cc_final: 0.8059 (tp-100)
REVERT: B  446 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6692 (t80)
REVERT: B  449 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7859 (pp)
REVERT: B  490 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7037 (tpm170)
REVERT: B  999 GLN cc_start: 0.8607 (tm-30) cc_final: 0.7989 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8992 (mt)
  outliers start: 15
  outliers final: 6
  residues processed: 89
  average time/residue: 0.1968
  time to fit residues: 25.7977
Evaluate side-chains
  77 residues out of total 1015 (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  191 ASN
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue  742 ASP
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0370
   chunk 49 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.2064

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.115811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.090655 restraints weight = 28793.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.090645 restraints weight = 18764.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.091168 restraints weight = 15327.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9349  Z= 0.213
  Angle     :  0.655   9.738  12690  Z= 0.330
  Chirality :  0.046   0.367   1498
  Planarity :  0.004   0.059   1615
  Dihedral  : 11.915 112.373   1428
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.25 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.97 %
    Favored  : 83.15 %
  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: -1.35 (0.25), residues: 1124
  helix:  1.62 (0.32), residues: 263
  sheet: -0.08 (0.41), residues: 160
  loop : -2.27 (0.22), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 630 
 HIS   0.003   0.001   HIS A 622 
 PHE   0.014   0.001   PHE B 371 
 TYR   0.015   0.001   TYR B 492 
 ARG   0.005   0.000   ARG A 762 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: A  737 MET cc_start: 0.7709 (ttm) cc_final: 0.7230 (tpp)
REVERT: A  770 GLU cc_start: 0.8634 (tt0) cc_final: 0.7860 (tt0)
REVERT: A  833 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7890 (tp-100)
REVERT: B  446 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6532 (t80)
REVERT: B  490 ARG cc_start: 0.8037 (mtt90) cc_final: 0.6765 (tpm170)
REVERT: B  737 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7914 (tpp)
REVERT: B  999 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7926 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 92
  average time/residue: 0.1981
  time to fit residues: 26.9465
Evaluate side-chains
  78 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  569 THR
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 70 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.114713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.089229 restraints weight = 28600.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.089522 restraints weight = 18521.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.089927 restraints weight = 15909.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9349  Z= 0.264
  Angle     :  0.668   9.467  12690  Z= 0.338
  Chirality :  0.046   0.328   1498
  Planarity :  0.005   0.069   1615
  Dihedral  : 11.164 113.271   1428
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.94 %
    Favored  : 88.88 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.54 %
    Favored  : 80.38 %
  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: -1.42 (0.24), residues: 1124
  helix:  1.60 (0.32), residues: 263
  sheet:  0.10 (0.41), residues: 152
  loop : -2.36 (0.21), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 630 
 HIS   0.004   0.001   HIS A 622 
 PHE   0.016   0.001   PHE B 556 
 TYR   0.013   0.001   TYR B 348 
 ARG   0.004   0.000   ARG A 762 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A  773 LYS cc_start: 0.9178 (tptt) cc_final: 0.8434 (tptt)
REVERT: A  833 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7864 (tp-100)
REVERT: A  987 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8844 (tm-30)
REVERT: B  415 ILE cc_start: 0.8348 (mp) cc_final: 0.7880 (tp)
REVERT: B  446 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6694 (t80)
REVERT: B  490 ARG cc_start: 0.8084 (mtt90) cc_final: 0.6940 (tpm170)
REVERT: B  737 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7880 (tpp)
REVERT: B  770 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7758 (tt0)
REVERT: B  999 GLN cc_start: 0.8568 (tm-30) cc_final: 0.7921 (tm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1968
  time to fit residues: 27.0799
Evaluate side-chains
  85 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  569 THR
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 18 optimal weight:    0.4980
   chunk 48 optimal weight:    0.0040
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 37 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.117024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.091575 restraints weight = 28535.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.091705 restraints weight = 18707.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.092397 restraints weight = 15976.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9349  Z= 0.169
  Angle     :  0.624   9.978  12690  Z= 0.313
  Chirality :  0.045   0.327   1498
  Planarity :  0.004   0.053   1615
  Dihedral  : 10.478 110.390   1428
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  8.99 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 19.33 %
    Favored  : 78.69 %
  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: -1.24 (0.25), residues: 1124
  helix:  1.83 (0.33), residues: 257
  sheet:  0.31 (0.44), residues: 141
  loop : -2.24 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 630 
 HIS   0.003   0.001   HIS B 502 
 PHE   0.010   0.001   PHE B 371 
 TYR   0.009   0.001   TYR B 348 
 ARG   0.004   0.000   ARG A 762 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
REVERT: A  622 HIS cc_start: 0.4333 (p-80) cc_final: 0.3974 (p-80)
REVERT: A  833 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7605 (tp-100)
REVERT: A  987 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8852 (tm-30)
REVERT: B  412 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7448 (t)
REVERT: B  415 ILE cc_start: 0.8375 (mp) cc_final: 0.7885 (tp)
REVERT: B  446 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6678 (t80)
REVERT: B  490 ARG cc_start: 0.8022 (mtt90) cc_final: 0.6919 (tpm170)
REVERT: B  737 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7806 (tpp)
REVERT: B  770 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7790 (tt0)
REVERT: B  999 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7849 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8979 (mp)
  outliers start: 20
  outliers final: 10
  residues processed: 97
  average time/residue: 0.1994
  time to fit residues: 28.1538
Evaluate side-chains
  82 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 106 optimal weight:    0.2980
   chunk 79 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0070
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.2400

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.116021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.086877 restraints weight = 27817.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.089703 restraints weight = 17170.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.090078 restraints weight = 12117.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9349  Z= 0.213
  Angle     :  0.635  10.239  12690  Z= 0.317
  Chirality :  0.045   0.321   1498
  Planarity :  0.004   0.061   1615
  Dihedral  : 10.115 108.883   1428
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.88 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.22 %
    Favored  : 77.01 %
  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: -1.30 (0.25), residues: 1124
  helix:  1.84 (0.34), residues: 257
  sheet:  0.18 (0.44), residues: 141
  loop : -2.28 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 630 
 HIS   0.002   0.001   HIS B 502 
 PHE   0.009   0.001   PHE A 131 
 TYR   0.010   0.001   TYR B 348 
 ARG   0.006   0.000   ARG A 762 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8335 (tt)
REVERT: A  622 HIS cc_start: 0.4283 (p-80) cc_final: 0.3925 (p-80)
REVERT: A  833 GLN cc_start: 0.8022 (tp-100) cc_final: 0.7571 (tp-100)
REVERT: A  987 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8865 (tm-30)
REVERT: B  415 ILE cc_start: 0.8362 (mp) cc_final: 0.7895 (tp)
REVERT: B  446 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6853 (t80)
REVERT: B  490 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7036 (tpm170)
REVERT: B  737 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7858 (tpp)
REVERT: B  770 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7900 (tt0)
REVERT: B  999 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8039 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9010 (mp)
  outliers start: 28
  outliers final: 17
  residues processed: 96
  average time/residue: 0.1801
  time to fit residues: 25.8175
Evaluate side-chains
  87 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0980
   chunk 82 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 81 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9990
   chunk 104 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 946 GLN
B 748 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.117239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.092538 restraints weight = 28181.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.091638 restraints weight = 19203.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.092451 restraints weight = 15577.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9349  Z= 0.168
  Angle     :  0.625  11.148  12690  Z= 0.310
  Chirality :  0.045   0.326   1498
  Planarity :  0.004   0.050   1615
  Dihedral  :  9.670 107.159   1428
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.52 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.11 %
    Favored  : 76.71 %
  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: -1.25 (0.25), residues: 1124
  helix:  1.76 (0.34), residues: 263
  sheet:  0.28 (0.45), residues: 136
  loop : -2.23 (0.21), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 630 
 HIS   0.002   0.001   HIS A 202 
 PHE   0.009   0.001   PHE B 389 
 TYR   0.016   0.001   TYR B 492 
 ARG   0.007   0.000   ARG A 762 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  622 HIS cc_start: 0.4347 (OUTLIER) cc_final: 0.3985 (p-80)
REVERT: A  987 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8833 (tm-30)
REVERT: B  446 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6594 (t80)
REVERT: B  490 ARG cc_start: 0.7989 (mtt90) cc_final: 0.6987 (tpm170)
REVERT: B  737 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7790 (tpp)
REVERT: B  999 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7881 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9035 (mp)
  outliers start: 22
  outliers final: 11
  residues processed: 97
  average time/residue: 0.1907
  time to fit residues: 27.1375
Evaluate side-chains
  89 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  629 THR
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 84 optimal weight:    3.9990
   chunk 106 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   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 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.117165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.087614 restraints weight = 28253.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.090497 restraints weight = 17509.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.091849 restraints weight = 11589.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9349  Z= 0.179
  Angle     :  0.630  10.969  12690  Z= 0.312
  Chirality :  0.044   0.322   1498
  Planarity :  0.004   0.048   1615
  Dihedral  :  9.396 106.967   1428
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.07 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.70 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.24 (0.25), residues: 1124
  helix:  1.84 (0.34), residues: 257
  sheet:  0.25 (0.45), residues: 136
  loop : -2.21 (0.21), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 630 
 HIS   0.002   0.001   HIS A 202 
 PHE   0.009   0.001   PHE B 389 
 TYR   0.013   0.001   TYR B 492 
 ARG   0.007   0.000   ARG A 762 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 MET cc_start: 0.7704 (tpt) cc_final: 0.7311 (tpp)
REVERT: A  622 HIS cc_start: 0.4326 (OUTLIER) cc_final: 0.3966 (p-80)
REVERT: A  987 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8804 (tm-30)
REVERT: B  415 ILE cc_start: 0.8336 (mp) cc_final: 0.7910 (tp)
REVERT: B  446 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6643 (t80)
REVERT: B  490 ARG cc_start: 0.8017 (mtt90) cc_final: 0.7020 (tpm170)
REVERT: B  737 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7872 (tpp)
REVERT: B  999 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9020 (mp)
  outliers start: 22
  outliers final: 13
  residues processed: 95
  average time/residue: 0.2033
  time to fit residues: 28.2177
Evaluate side-chains
  91 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  694 MET
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 104 optimal weight:   10.0000
   chunk 24 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.114945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.087923 restraints weight = 28297.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.089776 restraints weight = 16924.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.092150 restraints weight = 12565.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9349  Z= 0.274
  Angle     :  0.682  11.719  12690  Z= 0.343
  Chirality :  0.045   0.339   1498
  Planarity :  0.005   0.062   1615
  Dihedral  :  9.432 108.409   1427
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.94 %
    Favored  : 88.88 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.61 %
    Favored  : 76.02 %
  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: -1.45 (0.25), residues: 1124
  helix:  1.64 (0.33), residues: 263
  sheet:  0.05 (0.42), residues: 151
  loop : -2.40 (0.21), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 630 
 HIS   0.003   0.001   HIS A 622 
 PHE   0.023   0.001   PHE A 272 
 TYR   0.010   0.001   TYR B 492 
 ARG   0.007   0.001   ARG A 762 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8435 (tt)
REVERT: A  622 HIS cc_start: 0.4237 (OUTLIER) cc_final: 0.3890 (p-80)
REVERT: A  773 LYS cc_start: 0.9015 (tptp) cc_final: 0.8793 (tptt)
REVERT: A  987 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8671 (tm-30)
REVERT: B  415 ILE cc_start: 0.8329 (mp) cc_final: 0.7905 (tp)
REVERT: B  490 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7039 (tpm170)
REVERT: B  737 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7825 (tpp)
REVERT: B  999 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8013 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9046 (mp)
  outliers start: 24
  outliers final: 17
  residues processed: 92
  average time/residue: 0.2005
  time to fit residues: 27.0358
Evaluate side-chains
  92 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 946 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.114452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.089343 restraints weight = 29160.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.089098 restraints weight = 18865.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.090074 restraints weight = 15213.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9349  Z= 0.282
  Angle     :  0.698  11.234  12690  Z= 0.352
  Chirality :  0.046   0.347   1498
  Planarity :  0.005   0.052   1615
  Dihedral  :  9.425 108.729   1425
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.85 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 22.10 %
    Favored  : 75.82 %
  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: -1.53 (0.25), residues: 1124
  helix:  1.59 (0.33), residues: 264
  sheet: -0.02 (0.42), residues: 151
  loop : -2.47 (0.21), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 255 
 HIS   0.002   0.001   HIS A1055 
 PHE   0.021   0.002   PHE A 272 
 TYR   0.010   0.001   TYR B 448 
 ARG   0.008   0.001   ARG A 762 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8432 (tt)
REVERT: A  622 HIS cc_start: 0.4314 (OUTLIER) cc_final: 0.3938 (p-80)
REVERT: A  987 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8877 (tm-30)
REVERT: B  415 ILE cc_start: 0.8280 (mp) cc_final: 0.7860 (tp)
REVERT: B  490 ARG cc_start: 0.8228 (mtt90) cc_final: 0.7166 (tpm170)
REVERT: B  737 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7764 (tpp)
REVERT: B  999 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: B 1009 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9041 (mp)
  outliers start: 21
  outliers final: 16
  residues processed: 95
  average time/residue: 0.2130
  time to fit residues: 29.7624
Evaluate side-chains
  94 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  288 CYS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain B residue  467 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  629 THR
Chi-restraints excluded: chain B residue  726 VAL
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain B residue  737 MET
Chi-restraints excluded: chain B residue 1009 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 107 optimal weight:    0.0770
   chunk 48 optimal weight:    0.0980
   chunk 70 optimal weight:    0.0060
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0020
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.1962

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 989 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.117400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.092045 restraints weight = 28833.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.092463 restraints weight = 19076.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.092907 restraints weight = 14692.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9349  Z= 0.181
  Angle     :  0.703  15.165  12690  Z= 0.346
  Chirality :  0.046   0.349   1498
  Planarity :  0.004   0.048   1615
  Dihedral  :  9.681 105.815   1425
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.88 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 23.29 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.28 (0.25), residues: 1124
  helix:  1.70 (0.34), residues: 265
  sheet:  0.24 (0.44), residues: 144
  loop : -2.27 (0.21), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 630 
 HIS   0.003   0.001   HIS B 622 
 PHE   0.026   0.001   PHE A 756 
 TYR   0.009   0.001   TYR B 492 
 ARG   0.010   0.001   ARG B 980 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2646.90 seconds
wall clock time: 46 minutes 54.65 seconds (2814.65 seconds total)