Starting phenix.real_space_refine
on Fri Jul  3 13:49:33 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8pjb_17703/07_2026/8pjb_17703.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pjb_17703/07_2026/8pjb_17703.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pjb_17703/07_2026/8pjb_17703.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pjb_17703/07_2026/8pjb_17703.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8pjb_17703/07_2026/8pjb_17703.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8pjb_17703/07_2026/8pjb_17703.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pjb_17703/07_2026/8pjb_17703.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pjb_17703/07_2026/8pjb_17703.map"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7765 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     Mg      1      5.21       5
     S      48      5.16       5
     C    4933      2.51       5
     N    1357      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7840
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7632
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 962, 7621
          Classifications: {'peptide': 962}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 915}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 962, 7621
          Classifications: {'peptide': 962}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 915}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 7754
    Chain: "C"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'RNA': 9}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 1, 'rna3p': 7}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.34, per 1000 atoms: 0.43
  Number of scatterers: 7840
  At special positions: 0
  Unit cell: (87.132, 96.174, 104.394, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P      11     15.00
     Mg      1     11.99
     O    1490      8.00
     N    1357      7.00
     C    4933      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 645.9 milliseconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1840

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 7 sheets defined
      52.1% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 146 through 154
      removed outlier: 3.812A  pdb=" N   ASN A 150 " --> pdb=" O   GLN A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 181
      removed outlier: 4.085A  pdb=" N   LYS A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   GLU A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 242
      removed outlier: 3.581A  pdb=" N   ALA A 227 " --> pdb=" O   ASN A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 282
    Processing helix  chain 'A' and resid 352 through 371
    Processing helix  chain 'A' and resid 371 through 382
      removed outlier: 3.702A  pdb=" N   ARG A 375 " --> pdb=" O   ASP A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 4.132A  pdb=" N   ALA A 388 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET A 389 " --> pdb=" O   PRO A 385 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   SER A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   GLU A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 428
      removed outlier: 4.281A  pdb=" N   ALA A 418 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   GLN A 419 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 433
    Processing helix  chain 'A' and resid 442 through 457
    Processing helix  chain 'A' and resid 487 through 494
    Processing helix  chain 'A' and resid 495 through 497
      No H-bonds generated for 'chain 'A' and resid 495 through 497'
    Processing helix  chain 'A' and resid 509 through 512
      removed outlier: 3.589A  pdb=" N   ARG A 512 " --> pdb=" O   ILE A 509 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 509 through 512'
    Processing helix  chain 'A' and resid 513 through 530
    Processing helix  chain 'A' and resid 543 through 551
      removed outlier: 3.567A  pdb=" N   PHE A 551 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 579
    Processing helix  chain 'A' and resid 583 through 590
    Processing helix  chain 'A' and resid 610 through 614
      removed outlier: 3.554A  pdb=" N   LYS A 613 " --> pdb=" O   ASN A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 630
      removed outlier: 3.614A  pdb=" N   LEU A 630 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 651
      removed outlier: 3.587A  pdb=" N   ASN A 651 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 676
      removed outlier: 3.705A  pdb=" N   THR A 676 " --> pdb=" O   PHE A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 701
    Processing helix  chain 'A' and resid 718 through 721
    Processing helix  chain 'A' and resid 758 through 768
    Processing helix  chain 'A' and resid 782 through 789
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 802 through 813
    Processing helix  chain 'A' and resid 816 through 823
    Processing helix  chain 'A' and resid 829 through 843
    Processing helix  chain 'A' and resid 853 through 862
    Processing helix  chain 'A' and resid 865 through 878
    Processing helix  chain 'A' and resid 880 through 890
    Processing helix  chain 'A' and resid 910 through 915
      removed outlier: 3.881A  pdb=" N   LEU A 914 " --> pdb=" O   HIS A 910 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER A 915 " --> pdb=" O   GLN A 911 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 910 through 915'
    Processing helix  chain 'A' and resid 916 through 919
    Processing helix  chain 'A' and resid 920 through 939
      removed outlier: 3.505A  pdb=" N   ARG A 934 " --> pdb=" O   GLN A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 951
    Processing helix  chain 'A' and resid 953 through 975
      removed outlier: 3.639A  pdb=" N   GLY A 975 " --> pdb=" O   LEU A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 982
      removed outlier: 4.125A  pdb=" N   ILE A 982 " --> pdb=" O   GLU A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1008
      removed outlier: 3.822A  pdb=" N   CYS A1005 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A1006 " --> pdb=" O   ALA A1002 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1078
    Processing helix  chain 'A' and resid 1086 through 1088
      No H-bonds generated for 'chain 'A' and resid 1086 through 1088'
    Processing helix  chain 'A' and resid 1101 through 1110
    Processing helix  chain 'A' and resid 1110 through 1125
      removed outlier: 4.088A  pdb=" N   ALA A1114 " --> pdb=" O   ALA A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1129
      removed outlier: 3.870A  pdb=" N   ILE A1129 " --> pdb=" O   PRO A1126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1126 through 1129'
    Processing helix  chain 'A' and resid 1133 through 1147
    Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 202
      removed outlier: 3.545A  pdb=" N   PHE A 200 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY A 221 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264
      removed outlier: 5.911A  pdb=" N   TYR A 263 " --> pdb=" O   ASP A1099 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 329
      removed outlier: 4.206A  pdb=" N   ALA A 329 " --> pdb=" O   LEU A 498 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474
      removed outlier: 3.986A  pdb=" N   THR A 486 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE A 436 " --> pdb=" O   LEU A 483 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   CYS A 485 " --> pdb=" O   ILE A 436 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   VAL A 438 " --> pdb=" O   CYS A 485 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   ASN A 435 " --> pdb=" O   HIS A 503 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   ILE A 505 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   TYR A 437 " --> pdb=" O   ILE A 505 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   ASP A 507 " --> pdb=" O   TYR A 437 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   THR A 439 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE A 504 " --> pdb=" O   ILE A 536 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   MET A 538 " --> pdb=" O   ILE A 504 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   VAL A 506 " --> pdb=" O   MET A 538 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 407 " --> pdb=" O   SER A 539 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 567 through 569
      removed outlier: 6.504A  pdb=" N   GLN A 567 " --> pdb=" O   CYS A 777 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   THR A 779 " --> pdb=" O   GLN A 567 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   PHE A 569 " --> pdb=" O   THR A 779 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL A 730 " --> pdb=" O   PHE A 776 " (cutoff:3.500A)
      removed outlier: 7.503A  pdb=" N   PHE A 778 " --> pdb=" O   VAL A 730 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   VAL A 732 " --> pdb=" O   PHE A 778 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA A 655 " --> pdb=" O   PHE A 731 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   ILE A 733 " --> pdb=" O   ALA A 655 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   LEU A 657 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 744
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1054 through 1056
      removed outlier: 8.236A  pdb=" N   CYS A1063 " --> pdb=" O   ALA A1028 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   LEU A1030 " --> pdb=" O   CYS A1063 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLU A1017 " --> pdb=" O   LYS A1020 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU A1022 " --> pdb=" O   HIS A1015 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   HIS A1015 " --> pdb=" O   LEU A1022 " (cutoff:3.500A)

    357 hydrogen bonds defined for protein.
    1017 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1295
        1.30 -     1.43: 1991
        1.43 -     1.56: 4627
        1.56 -     1.69: 20
        1.69 -     1.81: 73
  Bond restraints: 8006
  Sorted by residual:
  bond pdb=" CA  SER A 222 "
       pdb=" CB  SER A 222 "
    ideal  model  delta    sigma   weight residual
    1.533  1.458  0.075 1.60e-02 3.91e+03 2.17e+01
  bond pdb=" CA  SER A 892 "
       pdb=" CB  SER A 892 "
    ideal  model  delta    sigma   weight residual
    1.530  1.453  0.077 1.69e-02 3.50e+03 2.08e+01
  bond pdb=" C   PRO A 191 "
       pdb=" O   PRO A 191 "
    ideal  model  delta    sigma   weight residual
    1.233  1.177  0.056 1.24e-02 6.50e+03 2.06e+01
  bond pdb=" CA  ALA A 202 "
       pdb=" CB  ALA A 202 "
    ideal  model  delta    sigma   weight residual
    1.533  1.455  0.078 1.72e-02 3.38e+03 2.03e+01
  bond pdb=" CA  SER A 891 "
       pdb=" CB  SER A 891 "
    ideal  model  delta    sigma   weight residual
    1.528  1.469  0.058 1.35e-02 5.49e+03 1.85e+01
  ... (remaining 8001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.36: 10682
        3.36 -     6.72: 181
        6.72 -    10.08: 14
       10.08 -    13.44: 2
       13.44 -    16.80: 2
  Bond angle restraints: 10881
  Sorted by residual:
  angle pdb=" C3'   U C   9 "
        pdb=" O3'   U C   9 "
        pdb=" P     U C  10 "
      ideal   model   delta    sigma   weight residual
     120.20  103.40   16.80 1.50e+00 4.44e-01 1.25e+02
  angle pdb=" C3'   U C   3 "
        pdb=" O3'   U C   3 "
        pdb=" P     C C   4 "
      ideal   model   delta    sigma   weight residual
     120.20  107.33   12.87 1.50e+00 4.44e-01 7.36e+01
  angle pdb=" C3'   C C   2 "
        pdb=" O3'   C C   2 "
        pdb=" P     U C   3 "
      ideal   model   delta    sigma   weight residual
     120.20  108.63   11.57 1.50e+00 4.44e-01 5.95e+01
  angle pdb=" N   ARG A1059 "
        pdb=" CA  ARG A1059 "
        pdb=" C   ARG A1059 "
      ideal   model   delta    sigma   weight residual
     112.72  104.35    8.37 1.14e+00 7.69e-01 5.39e+01
  angle pdb=" CA  GLY A 221 "
        pdb=" C   GLY A 221 "
        pdb=" N   SER A 222 "
      ideal   model   delta    sigma   weight residual
     114.58  120.82   -6.24 8.60e-01 1.35e+00 5.26e+01
  ... (remaining 10876 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.73: 4182
       18.73 -    37.45: 512
       37.45 -    56.18: 161
       56.18 -    74.91: 38
       74.91 -    93.63: 8
  Dihedral angle restraints: 4901
    sinusoidal: 2075
      harmonic: 2826
  Sorted by residual:
  dihedral pdb=" CD  ARG A 905 "
           pdb=" NE  ARG A 905 "
           pdb=" CZ  ARG A 905 "
           pdb=" NH1 ARG A 905 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -77.76   77.76     1      1.00e+01 1.00e-02 7.56e+01
  dihedral pdb=" CD  ARG A 590 "
           pdb=" NE  ARG A 590 "
           pdb=" CZ  ARG A 590 "
           pdb=" NH1 ARG A 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -64.26   64.26     1      1.00e+01 1.00e-02 5.43e+01
  dihedral pdb=" CD  ARG A 198 "
           pdb=" NE  ARG A 198 "
           pdb=" CZ  ARG A 198 "
           pdb=" NH1 ARG A 198 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -53.38   53.38     1      1.00e+01 1.00e-02 3.87e+01
  ... (remaining 4898 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1171
       0.112 -    0.224: 64
       0.224 -    0.336: 11
       0.336 -    0.448: 4
       0.448 -    0.561: 1
  Chirality restraints: 1251
  Sorted by residual:
  chirality pdb=" P     C C   2 "
            pdb=" OP1   C C   2 "
            pdb=" OP2   C C   2 "
            pdb=" O5'   C C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.97   -0.56 2.00e-01 2.50e+01 7.86e+00
  chirality pdb=" P     C C   4 "
            pdb=" OP1   C C   4 "
            pdb=" OP2   C C   4 "
            pdb=" O5'   C C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.77   -0.36 2.00e-01 2.50e+01 3.30e+00
  chirality pdb=" P     U C   3 "
            pdb=" OP1   U C   3 "
            pdb=" OP2   U C   3 "
            pdb=" O5'   U C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.77   -0.36 2.00e-01 2.50e+01 3.30e+00
  ... (remaining 1248 not shown)

  Planarity restraints: 1371
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 905 "    1.064 9.50e-02 1.11e+02   4.77e-01 1.37e+02
        pdb=" NE  ARG A 905 "   -0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 905 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 905 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 905 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 590 "   -0.989 9.50e-02 1.11e+02   4.43e-01 1.19e+02
        pdb=" NE  ARG A 590 "    0.059 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 590 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 590 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 590 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 198 "   -0.881 9.50e-02 1.11e+02   3.95e-01 9.45e+01
        pdb=" NE  ARG A 198 "    0.052 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 198 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 198 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 198 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1368 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 168
        2.66 -     3.22: 7370
        3.22 -     3.78: 12253
        3.78 -     4.34: 16148
        4.34 -     4.90: 26440
  Nonbonded interactions: 62379
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 414 "
            pdb=" OD2 ASP A 507 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" OE1 GLN A 621 "
            pdb=" NH2 ARG A 624 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" O   GLN A 332 "
            pdb=" OH  TYR A 479 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OE1 GLN A 440 "
            pdb=" OG  SER A 445 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OG ASER A1070 "
            pdb=" NE2 GLN A1073 "
     model   vdw
     2.316 3.120
  ... (remaining 62374 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.430
  Find NCS groups from input model:        0.040
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
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      :  0.006   0.078   8006  Z= 0.356
  Angle     :  0.985  16.796  10881  Z= 0.618
  Chirality :  0.063   0.561   1251
  Planarity :  0.026   0.477   1371
  Dihedral  : 18.417  93.633   3061
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  1.15 %
    Allowed  :  5.65 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 22.67 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.28), residues: 958
  helix:  1.03 (0.25), residues: 443
  sheet: -0.98 (0.43), residues: 148
  loop : -1.08 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 867 
 TYR   0.015   0.002   TYR A 550 
 PHE   0.029   0.002   PHE A 240 
 TRP   0.014   0.001   TRP A 932 
 HIS   0.007   0.001   HIS A 910 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00551 /  0.36 ( 8006)
  covalent geometry    : angle       0.98538 /  0.62 (10881)
  hydrogen bonds       : bond        0.12888 /  8.41 (  357)
  hydrogen bonds       : angle       5.43823 /  3.90 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 35
  outliers final: 10
  residues processed: 194
  average time/residue: 0.0889
  time to fit residues: 23.2598
Evaluate side-chains
  123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  718 ASN
Chi-restraints excluded: chain A residue  899 SER
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  905 ARG
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue 1057 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 440 GLN
A1037 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.073481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.057929 restraints weight = 47140.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.060689 restraints weight = 21098.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.062669 restraints weight = 12794.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.064025 restraints weight = 8996.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.065026 restraints weight = 6954.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8006  Z= 0.145
  Angle     :  0.783  14.281  10881  Z= 0.376
  Chirality :  0.045   0.235   1251
  Planarity :  0.006   0.136   1371
  Dihedral  :  7.873  75.331   1189
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.44 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 27.04 %
    Favored  : 69.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.27), residues: 958
  helix:  0.95 (0.24), residues: 456
  sheet: -0.51 (0.44), residues: 149
  loop : -0.74 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 362 
 TYR   0.018   0.002   TYR A 420 
 PHE   0.033   0.001   PHE A 155 
 TRP   0.036   0.002   TRP A 328 
 HIS   0.008   0.002   HIS A 503 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 8006)
  covalent geometry    : angle       0.78259 /  0.38 (10881)
  hydrogen bonds       : bond        0.03811 /  2.46 (  357)
  hydrogen bonds       : angle       4.44584 /  3.22 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 GLN cc_start: 0.8539 (mm110) cc_final: 0.7543 (mt0)
REVERT: A  525 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8572 (t0)
REVERT: A  627 MET cc_start: 0.9203 (tmm) cc_final: 0.8196 (tpp)
REVERT: A  645 MET cc_start: 0.8868 (tmm) cc_final: 0.8655 (tmm)
REVERT: A  670 MET cc_start: 0.8942 (ttm) cc_final: 0.8423 (tmm)
REVERT: A  697 ASP cc_start: 0.8991 (m-30) cc_final: 0.8670 (t0)
REVERT: A  718 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8166 (p0)
REVERT: A  884 MET cc_start: 0.8984 (tpp) cc_final: 0.8358 (mmm)
REVERT: A  954 MET cc_start: 0.8580 (ttm) cc_final: 0.8291 (tpp)
REVERT: A  957 MET cc_start: 0.9176 (mmm) cc_final: 0.8723 (tpp)
REVERT: A  969 ASP cc_start: 0.9436 (t0) cc_final: 0.9035 (m-30)
REVERT: A 1005 CYS cc_start: 0.8567 (m) cc_final: 0.8360 (m)
REVERT: A 1030 LEU cc_start: 0.9267 (mt) cc_final: 0.9049 (tp)
REVERT: A 1054 GLU cc_start: 0.8699 (tt0) cc_final: 0.8374 (tt0)
REVERT: A 1131 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8426 (ptp-110)
  outliers start: 27
  outliers final: 16
  residues processed: 145
  average time/residue: 0.0797
  time to fit residues: 16.3196
Evaluate side-chains
  133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  525 ASP
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  718 ASN
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  893 THR
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1131 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 87 optimal weight:    0.3980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.073899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.058181 restraints weight = 51909.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.061041 restraints weight = 21884.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.063084 restraints weight = 12943.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.064476 restraints weight = 8980.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.065475 restraints weight = 6873.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8006  Z= 0.129
  Angle     :  0.721  11.365  10881  Z= 0.347
  Chirality :  0.043   0.215   1251
  Planarity :  0.006   0.117   1371
  Dihedral  :  7.364  73.715   1177
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.60 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 26.45 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.28), residues: 958
  helix:  1.06 (0.24), residues: 454
  sheet: -0.43 (0.43), residues: 158
  loop : -0.70 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1080 
 TYR   0.023   0.002   TYR A 189 
 PHE   0.024   0.001   PHE A 155 
 TRP   0.020   0.002   TRP A 328 
 HIS   0.005   0.001   HIS A 910 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 8006)
  covalent geometry    : angle       0.72148 /  0.35 (10881)
  hydrogen bonds       : bond        0.03486 /  2.25 (  357)
  hydrogen bonds       : angle       4.18413 /  3.05 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8890 (mmmt)
REVERT: A  328 TRP cc_start: 0.8132 (t60) cc_final: 0.7728 (t60)
REVERT: A  440 GLN cc_start: 0.8448 (mm110) cc_final: 0.7718 (mt0)
REVERT: A  645 MET cc_start: 0.8828 (tmm) cc_final: 0.8564 (tmm)
REVERT: A  670 MET cc_start: 0.8902 (ttm) cc_final: 0.8397 (tmm)
REVERT: A  694 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8941 (tt)
REVERT: A  697 ASP cc_start: 0.8968 (m-30) cc_final: 0.8623 (p0)
REVERT: A  884 MET cc_start: 0.8928 (tpp) cc_final: 0.8464 (mmm)
REVERT: A  954 MET cc_start: 0.8537 (ttm) cc_final: 0.8323 (tpp)
REVERT: A  957 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8745 (tpp)
REVERT: A  998 ASP cc_start: 0.8593 (m-30) cc_final: 0.8303 (m-30)
REVERT: A 1054 GLU cc_start: 0.8774 (tt0) cc_final: 0.8431 (tt0)
REVERT: A 1064 LYS cc_start: 0.9302 (tptp) cc_final: 0.9070 (tppp)
REVERT: A 1131 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8693 (ptp90)
  outliers start: 28
  outliers final: 17
  residues processed: 141
  average time/residue: 0.0659
  time to fit residues: 13.5292
Evaluate side-chains
  124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  249 SER
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  957 MET
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1131 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0570
   chunk 71 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    0.7902

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.072714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.057217 restraints weight = 45559.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.059871 restraints weight = 21091.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.061775 restraints weight = 13053.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.063016 restraints weight = 9351.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.064026 restraints weight = 7372.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8006  Z= 0.127
  Angle     :  0.707  10.287  10881  Z= 0.341
  Chirality :  0.043   0.205   1251
  Planarity :  0.006   0.106   1371
  Dihedral  :  6.831  73.246   1171
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.50 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 26.33 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.28), residues: 958
  helix:  1.22 (0.24), residues: 453
  sheet: -0.32 (0.42), residues: 164
  loop : -0.78 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 362 
 TYR   0.034   0.002   TYR A 420 
 PHE   0.029   0.001   PHE A 898 
 TRP   0.033   0.003   TRP A 663 
 HIS   0.004   0.001   HIS A 922 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 8006)
  covalent geometry    : angle       0.70708 /  0.34 (10881)
  hydrogen bonds       : bond        0.03273 /  2.15 (  357)
  hydrogen bonds       : angle       4.13361 /  2.99 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8880 (mmmt)
REVERT: A  328 TRP cc_start: 0.7841 (t60) cc_final: 0.7331 (t60)
REVERT: A  414 THR cc_start: 0.8890 (m) cc_final: 0.8277 (p)
REVERT: A  440 GLN cc_start: 0.8430 (mm110) cc_final: 0.7699 (mt0)
REVERT: A  538 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7572 (tmm)
REVERT: A  627 MET cc_start: 0.9166 (tmm) cc_final: 0.8550 (tpp)
REVERT: A  634 ASP cc_start: 0.9095 (p0) cc_final: 0.8873 (t0)
REVERT: A  645 MET cc_start: 0.8824 (tmm) cc_final: 0.8576 (tmm)
REVERT: A  670 MET cc_start: 0.8865 (ttm) cc_final: 0.8417 (tmm)
REVERT: A  697 ASP cc_start: 0.8995 (m-30) cc_final: 0.8685 (p0)
REVERT: A  789 LEU cc_start: 0.9404 (mt) cc_final: 0.9186 (mt)
REVERT: A  884 MET cc_start: 0.8906 (tpp) cc_final: 0.8503 (mmm)
REVERT: A  905 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7856 (pmt-80)
REVERT: A  957 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8820 (tpp)
REVERT: A  969 ASP cc_start: 0.9421 (t0) cc_final: 0.8999 (m-30)
REVERT: A  998 ASP cc_start: 0.8459 (m-30) cc_final: 0.8222 (m-30)
REVERT: A 1054 GLU cc_start: 0.8888 (tt0) cc_final: 0.8533 (tt0)
REVERT: A 1131 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8737 (ptp90)
  outliers start: 26
  outliers final: 17
  residues processed: 125
  average time/residue: 0.0658
  time to fit residues: 11.8491
Evaluate side-chains
  128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  345 GLU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  538 MET
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  905 ARG
Chi-restraints excluded: chain A residue  957 MET
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1094 ASN
Chi-restraints excluded: chain A residue 1131 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.3990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.069582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.053132 restraints weight = 75689.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.056039 restraints weight = 27791.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.058090 restraints weight = 15872.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.059569 restraints weight = 10879.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.060490 restraints weight = 8294.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3053
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3053
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8006  Z= 0.191
  Angle     :  0.710  10.050  10881  Z= 0.344
  Chirality :  0.044   0.201   1251
  Planarity :  0.005   0.101   1371
  Dihedral  :  6.643  74.063   1168
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.81 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 25.86 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.28), residues: 958
  helix:  1.37 (0.24), residues: 454
  sheet: -0.32 (0.42), residues: 170
  loop : -0.78 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 587 
 TYR   0.012   0.002   TYR A 420 
 PHE   0.017   0.001   PHE A1045 
 TRP   0.024   0.002   TRP A 663 
 HIS   0.006   0.001   HIS A 503 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.19 ( 8006)
  covalent geometry    : angle       0.70966 /  0.34 (10881)
  hydrogen bonds       : bond        0.03441 /  2.27 (  357)
  hydrogen bonds       : angle       4.23233 /  3.09 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8879 (mmmt)
REVERT: A  440 GLN cc_start: 0.8548 (mm110) cc_final: 0.7739 (mt0)
REVERT: A  627 MET cc_start: 0.9159 (tmm) cc_final: 0.8540 (tpp)
REVERT: A  645 MET cc_start: 0.8839 (tmm) cc_final: 0.8636 (tmm)
REVERT: A  697 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8700 (p0)
REVERT: A  789 LEU cc_start: 0.9501 (mt) cc_final: 0.9285 (mt)
REVERT: A  884 MET cc_start: 0.8954 (tpp) cc_final: 0.8367 (mmm)
REVERT: A  898 PHE cc_start: 0.8739 (m-80) cc_final: 0.8531 (m-80)
REVERT: A  905 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7998 (pmt-80)
REVERT: A  942 MET cc_start: 0.9208 (mmp) cc_final: 0.8451 (tpt)
REVERT: A  954 MET cc_start: 0.8215 (tpp) cc_final: 0.7758 (tpp)
REVERT: A  998 ASP cc_start: 0.8527 (m-30) cc_final: 0.8286 (m-30)
REVERT: A 1054 GLU cc_start: 0.8846 (tt0) cc_final: 0.8530 (tt0)
REVERT: A 1131 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8769 (ptp90)
  outliers start: 30
  outliers final: 19
  residues processed: 123
  average time/residue: 0.0685
  time to fit residues: 12.0568
Evaluate side-chains
  120 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  697 ASP
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  905 ARG
Chi-restraints excluded: chain A residue  914 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1072 LEU
Chi-restraints excluded: chain A residue 1131 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 65 optimal weight:    0.0020
   chunk 6 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 86 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1094 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.071868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.056100 restraints weight = 57820.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.058946 restraints weight = 23359.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.060966 restraints weight = 13650.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.062342 restraints weight = 9458.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.063362 restraints weight = 7247.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8006  Z= 0.121
  Angle     :  0.690  10.254  10881  Z= 0.334
  Chirality :  0.043   0.201   1251
  Planarity :  0.006   0.141   1371
  Dihedral  :  6.494  71.997   1168
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.81 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 26.68 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.28), residues: 958
  helix:  1.41 (0.24), residues: 454
  sheet: -0.26 (0.42), residues: 164
  loop : -0.71 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 587 
 TYR   0.015   0.001   TYR A 420 
 PHE   0.036   0.001   PHE A 155 
 TRP   0.033   0.002   TRP A 328 
 HIS   0.006   0.001   HIS A 922 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 8006)
  covalent geometry    : angle       0.69037 /  0.33 (10881)
  hydrogen bonds       : bond        0.03175 /  2.11 (  357)
  hydrogen bonds       : angle       4.15304 /  3.02 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LYS cc_start: 0.9085 (mmmt) cc_final: 0.8830 (mmmt)
REVERT: A  440 GLN cc_start: 0.8507 (mm110) cc_final: 0.7712 (mt0)
REVERT: A  508 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8013 (mm-30)
REVERT: A  526 MET cc_start: 0.9317 (mmm) cc_final: 0.8982 (mmm)
REVERT: A  538 MET cc_start: 0.7926 (tmm) cc_final: 0.6896 (tmm)
REVERT: A  627 MET cc_start: 0.9191 (tmm) cc_final: 0.8646 (tpp)
REVERT: A  641 GLU cc_start: 0.9291 (tt0) cc_final: 0.9030 (pp20)
REVERT: A  645 MET cc_start: 0.8855 (tmm) cc_final: 0.8622 (tmm)
REVERT: A  670 MET cc_start: 0.8849 (ttm) cc_final: 0.8400 (tmm)
REVERT: A  697 ASP cc_start: 0.9011 (m-30) cc_final: 0.8695 (p0)
REVERT: A  789 LEU cc_start: 0.9491 (mt) cc_final: 0.9110 (mt)
REVERT: A  884 MET cc_start: 0.8991 (tpp) cc_final: 0.8532 (mmm)
REVERT: A  905 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7969 (pmt-80)
REVERT: A  954 MET cc_start: 0.8232 (tpp) cc_final: 0.7730 (tpp)
REVERT: A  969 ASP cc_start: 0.9413 (t0) cc_final: 0.8986 (m-30)
REVERT: A  998 ASP cc_start: 0.8387 (m-30) cc_final: 0.8133 (m-30)
REVERT: A 1004 LEU cc_start: 0.9624 (tp) cc_final: 0.9423 (tt)
REVERT: A 1054 GLU cc_start: 0.8796 (tt0) cc_final: 0.8444 (tt0)
REVERT: A 1064 LYS cc_start: 0.9060 (tptm) cc_final: 0.8799 (mmmt)
REVERT: A 1131 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8753 (ptp90)
  outliers start: 23
  outliers final: 16
  residues processed: 123
  average time/residue: 0.0731
  time to fit residues: 12.7303
Evaluate side-chains
  122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  905 ARG
Chi-restraints excluded: chain A residue  914 LEU
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1094 ASN
Chi-restraints excluded: chain A residue 1131 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0270
   chunk 70 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 89 optimal weight:    8.9990
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.6838

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 332 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.072251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.056020 restraints weight = 71936.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.059020 restraints weight = 26032.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.061176 restraints weight = 14677.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.062662 restraints weight = 9914.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.063704 restraints weight = 7473.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8006  Z= 0.117
  Angle     :  0.681  10.045  10881  Z= 0.328
  Chirality :  0.043   0.217   1251
  Planarity :  0.006   0.096   1371
  Dihedral  :  6.350  71.450   1168
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.60 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 25.74 %
    Favored  : 71.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.28), residues: 958
  helix:  1.46 (0.24), residues: 454
  sheet: -0.11 (0.41), residues: 162
  loop : -0.79 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 587 
 TYR   0.013   0.001   TYR A 420 
 PHE   0.032   0.001   PHE A 155 
 TRP   0.018   0.002   TRP A 663 
 HIS   0.006   0.001   HIS A 922 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 8006)
  covalent geometry    : angle       0.68150 /  0.33 (10881)
  hydrogen bonds       : bond        0.03158 /  2.11 (  357)
  hydrogen bonds       : angle       4.09481 /  2.99 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8850 (mmmt)
REVERT: A  420 TYR cc_start: 0.8304 (m-80) cc_final: 0.7877 (m-10)
REVERT: A  440 GLN cc_start: 0.8531 (mm110) cc_final: 0.7748 (mt0)
REVERT: A  538 MET cc_start: 0.7893 (tmm) cc_final: 0.6877 (tmm)
REVERT: A  627 MET cc_start: 0.9183 (tmm) cc_final: 0.8573 (tpp)
REVERT: A  645 MET cc_start: 0.8829 (tmm) cc_final: 0.8567 (tmm)
REVERT: A  697 ASP cc_start: 0.9002 (m-30) cc_final: 0.8707 (p0)
REVERT: A  740 MET cc_start: 0.8551 (ptp) cc_final: 0.8327 (ptm)
REVERT: A  789 LEU cc_start: 0.9470 (mt) cc_final: 0.9106 (mt)
REVERT: A  884 MET cc_start: 0.8950 (tpp) cc_final: 0.8476 (mmm)
REVERT: A  905 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7910 (pmt-80)
REVERT: A  954 MET cc_start: 0.8159 (tpp) cc_final: 0.7768 (tpp)
REVERT: A  998 ASP cc_start: 0.8336 (m-30) cc_final: 0.8034 (m-30)
REVERT: A 1003 LEU cc_start: 0.9610 (mt) cc_final: 0.9388 (mp)
REVERT: A 1054 GLU cc_start: 0.8755 (tt0) cc_final: 0.8410 (tt0)
REVERT: A 1064 LYS cc_start: 0.9059 (tptm) cc_final: 0.8675 (tppt)
REVERT: A 1131 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8781 (ptp90)
  outliers start: 24
  outliers final: 16
  residues processed: 127
  average time/residue: 0.0714
  time to fit residues: 13.0453
Evaluate side-chains
  122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  905 ARG
Chi-restraints excluded: chain A residue  914 LEU
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1131 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 84 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 503 HIS
A 534 HIS
A1094 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.072279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.056259 restraints weight = 67864.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.059230 restraints weight = 25433.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.061339 restraints weight = 14478.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.062787 restraints weight = 9838.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.063766 restraints weight = 7440.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8006  Z= 0.123
  Angle     :  0.710  11.775  10881  Z= 0.342
  Chirality :  0.043   0.197   1251
  Planarity :  0.006   0.102   1371
  Dihedral  :  6.280  71.203   1168
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.92 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 27.27 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.28), residues: 958
  helix:  1.54 (0.24), residues: 453
  sheet: -0.09 (0.42), residues: 162
  loop : -0.73 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 390 
 TYR   0.019   0.001   TYR A1009 
 PHE   0.030   0.001   PHE A 155 
 TRP   0.026   0.002   TRP A 932 
 HIS   0.006   0.001   HIS A 910 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.12 ( 8006)
  covalent geometry    : angle       0.71025 /  0.34 (10881)
  hydrogen bonds       : bond        0.03068 /  2.02 (  357)
  hydrogen bonds       : angle       4.06983 /  2.97 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8808 (mmmt)
REVERT: A  420 TYR cc_start: 0.8313 (m-80) cc_final: 0.7663 (m-10)
REVERT: A  440 GLN cc_start: 0.8568 (mm110) cc_final: 0.7774 (mt0)
REVERT: A  526 MET cc_start: 0.9233 (mmm) cc_final: 0.8989 (mmm)
REVERT: A  538 MET cc_start: 0.7928 (tmm) cc_final: 0.6967 (tmm)
REVERT: A  627 MET cc_start: 0.9145 (tmm) cc_final: 0.8550 (tpp)
REVERT: A  641 GLU cc_start: 0.9262 (tt0) cc_final: 0.9049 (pp20)
REVERT: A  645 MET cc_start: 0.8810 (tmm) cc_final: 0.8548 (tmm)
REVERT: A  697 ASP cc_start: 0.8987 (m-30) cc_final: 0.8699 (p0)
REVERT: A  743 PHE cc_start: 0.9237 (t80) cc_final: 0.8997 (t80)
REVERT: A  789 LEU cc_start: 0.9466 (mt) cc_final: 0.9125 (mt)
REVERT: A  797 MET cc_start: 0.8038 (tpp) cc_final: 0.7816 (mmm)
REVERT: A  843 MET cc_start: 0.8533 (ttp) cc_final: 0.8045 (ttm)
REVERT: A  884 MET cc_start: 0.9031 (tpp) cc_final: 0.8359 (mmm)
REVERT: A  905 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7949 (pmt-80)
REVERT: A  954 MET cc_start: 0.8144 (tpp) cc_final: 0.7777 (tpp)
REVERT: A  969 ASP cc_start: 0.9369 (t0) cc_final: 0.8989 (m-30)
REVERT: A 1035 SER cc_start: 0.8810 (t) cc_final: 0.8486 (t)
REVERT: A 1054 GLU cc_start: 0.8751 (tt0) cc_final: 0.8390 (tt0)
REVERT: A 1131 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8773 (ptp90)
  outliers start: 18
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0679
  time to fit residues: 11.9315
Evaluate side-chains
  120 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  905 ARG
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1094 ASN
Chi-restraints excluded: chain A residue 1131 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.5788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.070511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.054750 restraints weight = 58829.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.057531 restraints weight = 24186.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.059533 restraints weight = 14284.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.060891 restraints weight = 9968.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.061844 restraints weight = 7657.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8006  Z= 0.148
  Angle     :  0.710  12.975  10881  Z= 0.343
  Chirality :  0.043   0.197   1251
  Planarity :  0.006   0.094   1371
  Dihedral  :  6.120  71.197   1164
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.23 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 27.04 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.28), residues: 958
  helix:  1.55 (0.24), residues: 454
  sheet: -0.16 (0.42), residues: 163
  loop : -0.68 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 390 
 TYR   0.013   0.001   TYR A 420 
 PHE   0.030   0.001   PHE A 155 
 TRP   0.030   0.002   TRP A 932 
 HIS   0.005   0.001   HIS A 910 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 ( 8006)
  covalent geometry    : angle       0.70968 /  0.34 (10881)
  hydrogen bonds       : bond        0.03220 /  2.16 (  357)
  hydrogen bonds       : angle       4.17421 /  3.08 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8845 (mmmt)
REVERT: A  420 TYR cc_start: 0.8414 (m-80) cc_final: 0.7779 (m-10)
REVERT: A  440 GLN cc_start: 0.8555 (mm110) cc_final: 0.7675 (mt0)
REVERT: A  472 GLU cc_start: 0.7233 (mp0) cc_final: 0.7006 (mp0)
REVERT: A  508 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7914 (mm-30)
REVERT: A  526 MET cc_start: 0.9289 (mmm) cc_final: 0.9050 (mmm)
REVERT: A  538 MET cc_start: 0.7931 (tmm) cc_final: 0.6953 (tmm)
REVERT: A  627 MET cc_start: 0.9140 (tmm) cc_final: 0.8532 (tpp)
REVERT: A  645 MET cc_start: 0.8835 (tmm) cc_final: 0.8586 (tmm)
REVERT: A  697 ASP cc_start: 0.9000 (m-30) cc_final: 0.8719 (p0)
REVERT: A  789 LEU cc_start: 0.9496 (mt) cc_final: 0.9165 (mt)
REVERT: A  843 MET cc_start: 0.8544 (ttp) cc_final: 0.7986 (ttm)
REVERT: A  884 MET cc_start: 0.9141 (tpp) cc_final: 0.8530 (mmm)
REVERT: A  905 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7910 (pmt-80)
REVERT: A  954 MET cc_start: 0.8025 (tpp) cc_final: 0.7786 (tpp)
REVERT: A 1054 GLU cc_start: 0.8725 (tt0) cc_final: 0.8287 (tt0)
REVERT: A 1131 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8798 (ptp90)
  outliers start: 19
  outliers final: 16
  residues processed: 119
  average time/residue: 0.0692
  time to fit residues: 12.1156
Evaluate side-chains
  119 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  905 ARG
Chi-restraints excluded: chain A residue  914 LEU
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1131 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    0.0070
   chunk 69 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0570
   chunk 29 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 31 optimal weight:    0.3980
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.4318

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.072459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.057090 restraints weight = 52353.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.059882 restraints weight = 22111.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.061835 restraints weight = 13125.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.063219 restraints weight = 9172.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.064142 restraints weight = 7050.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8006  Z= 0.121
  Angle     :  0.727  12.424  10881  Z= 0.346
  Chirality :  0.044   0.201   1251
  Planarity :  0.006   0.093   1371
  Dihedral  :  5.986  69.801   1164
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.60 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 27.39 %
    Favored  : 70.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.28), residues: 958
  helix:  1.55 (0.25), residues: 446
  sheet: -0.31 (0.42), residues: 166
  loop : -0.58 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 390 
 TYR   0.012   0.001   TYR A 420 
 PHE   0.030   0.001   PHE A 155 
 TRP   0.029   0.002   TRP A 932 
 HIS   0.004   0.001   HIS A 910 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 8006)
  covalent geometry    : angle       0.72672 /  0.35 (10881)
  hydrogen bonds       : bond        0.03058 /  2.01 (  357)
  hydrogen bonds       : angle       4.17222 /  3.06 ( 1017)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8866 (mmmt)
REVERT: A  420 TYR cc_start: 0.8292 (m-80) cc_final: 0.7638 (m-10)
REVERT: A  440 GLN cc_start: 0.8512 (mm110) cc_final: 0.7701 (mt0)
REVERT: A  472 GLU cc_start: 0.7202 (mp0) cc_final: 0.6959 (mp0)
REVERT: A  508 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7882 (mm-30)
REVERT: A  526 MET cc_start: 0.9216 (mmm) cc_final: 0.9003 (mmm)
REVERT: A  538 MET cc_start: 0.7954 (tmm) cc_final: 0.7035 (tmm)
REVERT: A  627 MET cc_start: 0.9145 (tmm) cc_final: 0.8555 (tpp)
REVERT: A  641 GLU cc_start: 0.9167 (tt0) cc_final: 0.8841 (tm-30)
REVERT: A  670 MET cc_start: 0.8780 (ttm) cc_final: 0.8536 (tmm)
REVERT: A  697 ASP cc_start: 0.8978 (m-30) cc_final: 0.8683 (p0)
REVERT: A  743 PHE cc_start: 0.9224 (t80) cc_final: 0.8996 (t80)
REVERT: A  789 LEU cc_start: 0.9482 (mt) cc_final: 0.9179 (mt)
REVERT: A  797 MET cc_start: 0.8098 (tpp) cc_final: 0.7686 (mmt)
REVERT: A  843 MET cc_start: 0.8505 (ttp) cc_final: 0.7950 (ttm)
REVERT: A  884 MET cc_start: 0.8925 (tpp) cc_final: 0.8347 (mmm)
REVERT: A  905 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7893 (pmt-80)
REVERT: A  954 MET cc_start: 0.8083 (tpp) cc_final: 0.7709 (tpp)
REVERT: A  969 ASP cc_start: 0.9351 (t0) cc_final: 0.8956 (m-30)
REVERT: A 1054 GLU cc_start: 0.8650 (tt0) cc_final: 0.8220 (tt0)
REVERT: A 1064 LYS cc_start: 0.9088 (tptm) cc_final: 0.8646 (tppt)
REVERT: A 1131 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8818 (ptp90)
  outliers start: 18
  outliers final: 14
  residues processed: 127
  average time/residue: 0.0623
  time to fit residues: 11.5154
Evaluate side-chains
  121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  905 ARG
Chi-restraints excluded: chain A residue 1051 VAL
Chi-restraints excluded: chain A residue 1131 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0870
   chunk 47 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0070
   chunk 19 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.5576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1037 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.073057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.058111 restraints weight = 44367.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.060761 restraints weight = 20322.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.062637 restraints weight = 12448.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.063878 restraints weight = 8856.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.064824 restraints weight = 6934.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.4203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8006  Z= 0.121
  Angle     :  0.725  12.559  10881  Z= 0.348
  Chirality :  0.044   0.198   1251
  Planarity :  0.005   0.091   1371
  Dihedral  :  5.875  69.515   1164
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.81 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 27.86 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.28), residues: 958
  helix:  1.51 (0.24), residues: 447
  sheet: -0.02 (0.43), residues: 159
  loop : -0.72 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 390 
 TYR   0.010   0.001   TYR A 420 
 PHE   0.029   0.001   PHE A 155 
 TRP   0.027   0.002   TRP A 932 
 HIS   0.007   0.001   HIS A 910 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 8006)
  covalent geometry    : angle       0.72521 /  0.35 (10881)
  hydrogen bonds       : bond        0.03024 /  2.00 (  357)
  hydrogen bonds       : angle       4.13640 /  2.99 ( 1017)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1475.55 seconds
wall clock time: 26 minutes 2.87 seconds (1562.87 seconds total)