Starting phenix.real_space_refine
on Wed Aug  5 08:19:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qrn_53320/08_2026/9qrn_53320_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qrn_53320/08_2026/9qrn_53320.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qrn_53320/08_2026/9qrn_53320_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qrn_53320/08_2026/9qrn_53320_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qrn_53320/08_2026/9qrn_53320.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qrn_53320/08_2026/9qrn_53320.map"
  }
  resolution = 3.1
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     P       3      5.49       5
     Mg      2      5.21       5
     S      43      5.16       5
     C    5614      2.51       5
     N    1476      2.21       5
     O    1700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8842
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1113, 8773
          Classifications: {'peptide': 1113}
          Link IDs: {'PTRANS': 45, 'TRANS': 1067}
          Chain breaks: 7
    Chain: "E"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 62
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Unusual residues: {' MG': 2, ' ZN': 4}
          Classifications: {'undetermined': 6, 'water': 1}
          Link IDs: {None: 6}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2789  SG  CYS A 669      63.541  44.507  76.015  1.00 16.38           S
  ATOM   4758  SG  CYS A 918      50.687  86.277  11.236  1.00 69.39           S
  ATOM   4780  SG  CYS A 921      51.371  86.111   8.106  1.00 57.80           S
  ATOM   4942  SG  CYS A 943      51.965  89.264  10.228  1.00 55.87           S
  ATOM   4964  SG  CYS A 946      48.948  87.525   8.563  1.00 76.87           S

  Time building chain proxies: 1.85, per 1000 atoms: 0.21
  Number of scatterers: 8842
  At special positions: 0
  Unit cell: (101.156, 116.204, 119.548, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      4     29.99
     S      43     16.00
     P       3     15.00
     Mg      2     11.99
     O    1700      8.00
     N    1476      7.00
     C    5614      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: 0.66
  Conformation dependent library (CDL) restraints added in 362.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1501 "
        pdb="ZN    ZN A1501 " - pdb=" NE2 HIS A 346 "
        pdb="ZN    ZN A1501 " - pdb=" NE2 HIS A 344 "
      pdb="  ZN A1502 "
        pdb="ZN    ZN A1502 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A1502 " - pdb=" NE2 HIS A 744 "
      pdb="  ZN A1503 "
        pdb="ZN    ZN A1503 " - pdb=" ND1 HIS A 619 "
        pdb="ZN    ZN A1503 " - pdb=" SG  CYS A 669 "
      pdb="  ZN A1504 "
        pdb="ZN    ZN A1504 " - pdb=" SG  CYS A 918 "
        pdb="ZN    ZN A1504 " - pdb=" SG  CYS A 921 "
        pdb="ZN    ZN A1504 " - pdb=" SG  CYS A 946 "
        pdb="ZN    ZN A1504 " - pdb=" SG  CYS A 943 "
      Number of angles added : 6


  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2062

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 9 sheets defined
      53.9% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 357 through 369
    Processing helix  chain 'A' and resid 383 through 395
    Processing helix  chain 'A' and resid 472 through 479
    Processing helix  chain 'A' and resid 491 through 503
    Processing helix  chain 'A' and resid 512 through 527
      removed outlier: 3.675A  pdb=" N   TYR A 527 " --> pdb=" O   SER A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 547
    Processing helix  chain 'A' and resid 554 through 562
    Processing helix  chain 'A' and resid 571 through 593
      removed outlier: 4.217A  pdb=" N   ILE A 585 " --> pdb=" O   HIS A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 604
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 3.618A  pdb=" N   ARG A 614 " --> pdb=" O   ASP A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 643
    Processing helix  chain 'A' and resid 653 through 659
    Processing helix  chain 'A' and resid 672 through 681
    Processing helix  chain 'A' and resid 682 through 690
    Processing helix  chain 'A' and resid 691 through 693
      No H-bonds generated for 'chain 'A' and resid 691 through 693'
    Processing helix  chain 'A' and resid 704 through 710
      removed outlier: 3.835A  pdb=" N   ILE A 708 " --> pdb=" O   TYR A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 733
    Processing helix  chain 'A' and resid 750 through 759
    Processing helix  chain 'A' and resid 760 through 770
      removed outlier: 6.328A  pdb=" N   GLY A 763 " --> pdb=" O   SER A 760 " (cutoff:3.500A)
      Proline residue:  A 766  - end of helix
    Processing helix  chain 'A' and resid 779 through 788
    Processing helix  chain 'A' and resid 794 through 800
    Processing helix  chain 'A' and resid 800 through 810
      removed outlier: 3.506A  pdb=" N   CYS A 810 " --> pdb=" O   ILE A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 845
    Processing helix  chain 'A' and resid 849 through 866
    Processing helix  chain 'A' and resid 868 through 886
      removed outlier: 3.518A  pdb=" N   TYR A 872 " --> pdb=" O   PHE A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 897
    Processing helix  chain 'A' and resid 898 through 904
    Processing helix  chain 'A' and resid 934 through 938
    Processing helix  chain 'A' and resid 959 through 964
    Processing helix  chain 'A' and resid 965 through 968
      removed outlier: 4.081A  pdb=" N   ASP A 968 " --> pdb=" O   PHE A 965 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 965 through 968'
    Processing helix  chain 'A' and resid 981 through 994
    Processing helix  chain 'A' and resid 1008 through 1023
    Processing helix  chain 'A' and resid 1028 through 1037
    Processing helix  chain 'A' and resid 1061 through 1065
    Processing helix  chain 'A' and resid 1070 through 1074
    Processing helix  chain 'A' and resid 1085 through 1090
    Processing helix  chain 'A' and resid 1102 through 1115
    Processing helix  chain 'A' and resid 1127 through 1134
    Processing helix  chain 'A' and resid 1141 through 1146
    Processing helix  chain 'A' and resid 1159 through 1170
    Processing helix  chain 'A' and resid 1173 through 1185
    Processing helix  chain 'A' and resid 1195 through 1200
    Processing helix  chain 'A' and resid 1211 through 1222
    Processing helix  chain 'A' and resid 1225 through 1238
    Processing helix  chain 'A' and resid 1245 through 1259
    Processing helix  chain 'A' and resid 1262 through 1271
      removed outlier: 3.839A  pdb=" N   ILE A1266 " --> pdb=" O   PRO A1262 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS A1271 " --> pdb=" O   ASP A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1298
    Processing helix  chain 'A' and resid 1298 through 1311
    Processing helix  chain 'A' and resid 1315 through 1322
      removed outlier: 3.672A  pdb=" N   GLY A1322 " --> pdb=" O   SER A1318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1322 through 1336
      removed outlier: 3.770A  pdb=" N   VAL A1326 " --> pdb=" O   GLY A1322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1341 through 1360
    Processing helix  chain 'A' and resid 1387 through 1391
    Processing helix  chain 'A' and resid 1396 through 1405
    Processing helix  chain 'A' and resid 1414 through 1422
    Processing helix  chain 'A' and resid 1425 through 1435
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270
    Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 378
      removed outlier: 6.543A  pdb=" N   ILE A 373 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   GLY A 401 " --> pdb=" O   ILE A 373 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   ILE A 375 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   GLU A 403 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   ASP A 377 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   ASN A 405 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   ILE A 651 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ASN A 405 " --> pdb=" O   ILE A 651 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 378
      removed outlier: 6.543A  pdb=" N   ILE A 373 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   GLY A 401 " --> pdb=" O   ILE A 373 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   ILE A 375 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   GLU A 403 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   ASP A 377 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   ASN A 405 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   TYR A 400 " --> pdb=" O   ALA A 624 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 456 through 464
      removed outlier: 6.587A  pdb=" N   LYS A 451 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   SER A 460 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ALA A 449 " --> pdb=" O   SER A 460 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ASP A 462 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LEU A 447 " --> pdb=" O   ASP A 462 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   PHE A 464 " --> pdb=" O   ILE A 445 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   ILE A 445 " --> pdb=" O   PHE A 464 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   THR A 426 " --> pdb=" O   ILE A 507 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   VAL A 509 " --> pdb=" O   THR A 426 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   VAL A 428 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 695 through 698
    Processing sheet with id=AA6, first strand: chain 'A' and resid 890 through 892
      removed outlier: 3.907A  pdb=" N   ASP A 974 " --> pdb=" O   ARG A 892 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU A1094 " --> pdb=" O   VAL A1055 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   GLY A1051 " --> pdb=" O   ILE A1098 " (cutoff:3.500A)
      removed outlier: 8.967A  pdb=" N   GLY A1100 " --> pdb=" O   HIS A1049 " (cutoff:3.500A)
      removed outlier: 12.684A  pdb=" N   HIS A1049 " --> pdb=" O   GLY A1100 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   ALA A1001 " --> pdb=" O   HIS A1049 " (cutoff:3.500A)
      removed outlier: 9.851A  pdb=" N   GLY A1051 " --> pdb=" O   TYR A 999 " (cutoff:3.500A)
      removed outlier: 10.107A  pdb=" N   TYR A 999 " --> pdb=" O   GLY A1051 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 924 through 926
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1068 through 1069
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1363 through 1364
      removed outlier: 7.568A  pdb=" N   LYS A1363 " --> pdb=" O   LEU A1384 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1218 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: 1.55

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1521
        1.31 -     1.43: 2341
        1.43 -     1.56: 5085
        1.56 -     1.69: 5
        1.69 -     1.82: 76
  Bond restraints: 9028
  Sorted by residual:
  bond pdb=" C   GLY A1115 "
       pdb=" N   ILE A1116 "
    ideal  model  delta    sigma   weight residual
    1.333  1.449 -0.116 1.23e-02 6.61e+03 8.95e+01
  bond pdb=" C   LEU A1110 "
       pdb=" N   GLN A1111 "
    ideal  model  delta    sigma   weight residual
    1.334  1.448 -0.114 1.33e-02 5.65e+03 7.30e+01
  bond pdb=" C   PHE A 430 "
       pdb=" N   ALA A 431 "
    ideal  model  delta    sigma   weight residual
    1.330  1.435 -0.105 1.26e-02 6.30e+03 6.97e+01
  bond pdb=" C   LYS A 561 "
       pdb=" N   PHE A 562 "
    ideal  model  delta    sigma   weight residual
    1.333  1.221  0.112 1.36e-02 5.41e+03 6.73e+01
  bond pdb=" C   TYR A 704 "
       pdb=" N   ALA A 705 "
    ideal  model  delta    sigma   weight residual
    1.332  1.434 -0.102 1.33e-02 5.65e+03 5.93e+01
  ... (remaining 9023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 10290
        1.93 -     3.87: 1706
        3.87 -     5.80: 196
        5.80 -     7.73: 20
        7.73 -     9.67: 7
  Bond angle restraints: 12219
  Sorted by residual:
  angle pdb=" N   HIS A1221 "
        pdb=" CA  HIS A1221 "
        pdb=" C   HIS A1221 "
      ideal   model   delta    sigma   weight residual
     111.28  103.38    7.90 1.09e+00 8.42e-01 5.25e+01
  angle pdb=" N   ARG A 647 "
        pdb=" CA  ARG A 647 "
        pdb=" C   ARG A 647 "
      ideal   model   delta    sigma   weight residual
     112.88  104.09    8.79 1.29e+00 6.01e-01 4.65e+01
  angle pdb=" C   ILE A 752 "
        pdb=" N   TYR A 753 "
        pdb=" CA  TYR A 753 "
      ideal   model   delta    sigma   weight residual
     120.54  111.47    9.07 1.35e+00 5.49e-01 4.51e+01
  angle pdb=" N   ARG A1044 "
        pdb=" CA  ARG A1044 "
        pdb=" C   ARG A1044 "
      ideal   model   delta    sigma   weight residual
     114.04  106.20    7.84 1.24e+00 6.50e-01 4.00e+01
  angle pdb=" N   ASP A1315 "
        pdb=" CA  ASP A1315 "
        pdb=" C   ASP A1315 "
      ideal   model   delta    sigma   weight residual
     109.39   99.72    9.67 1.59e+00 3.96e-01 3.70e+01
  ... (remaining 12214 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4501
       17.95 -    35.90: 537
       35.90 -    53.86: 266
       53.86 -    71.81: 80
       71.81 -    89.76: 16
  Dihedral angle restraints: 5400
    sinusoidal: 2180
      harmonic: 3220
  Sorted by residual:
  dihedral pdb=" CA  THR A1066 "
           pdb=" C   THR A1066 "
           pdb=" N   PRO A1067 "
           pdb=" CA  PRO A1067 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.27   18.73     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  ASN A 759 "
           pdb=" CB  ASN A 759 "
           pdb=" CG  ASN A 759 "
           pdb=" OD1 ASN A 759 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -163.30   73.30     2      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CA  HIS A 511 "
           pdb=" C   HIS A 511 "
           pdb=" N   ASN A 512 "
           pdb=" CA  ASN A 512 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.54  -16.46     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.128: 1141
       0.128 -    0.256: 200
       0.256 -    0.384: 2
       0.384 -    0.512: 1
       0.512 -    0.640: 1
  Chirality restraints: 1345
  Sorted by residual:
  chirality pdb=" P    DT E   1 "
            pdb=" OP1  DT E   1 "
            pdb=" OP2  DT E   1 "
            pdb=" O5'  DT E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.98   -0.64 2.00e-01 2.50e+01 1.02e+01
  chirality pdb=" P    DA E   2 "
            pdb=" OP1  DA E   2 "
            pdb=" OP2  DA E   2 "
            pdb=" O5'  DA E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.83   -0.50 2.00e-01 2.50e+01 6.19e+00
  chirality pdb=" CA  ILE A 871 "
            pdb=" N   ILE A 871 "
            pdb=" C   ILE A 871 "
            pdb=" CB  ILE A 871 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 1342 not shown)

  Planarity restraints: 1575
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 758 "   -0.025 2.00e-02 2.50e+03   4.99e-02 2.49e+01
        pdb=" C   ILE A 758 "    0.086 2.00e-02 2.50e+03
        pdb=" O   ILE A 758 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   ASN A 759 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 778 "    0.022 2.00e-02 2.50e+03   4.30e-02 1.85e+01
        pdb=" C   ARG A 778 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   ARG A 778 "    0.027 2.00e-02 2.50e+03
        pdb=" N   THR A 779 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 921 "    0.020 2.00e-02 2.50e+03   4.05e-02 1.64e+01
        pdb=" C   CYS A 921 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   CYS A 921 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLN A 922 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1572 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.26: 6
        2.26 -     2.92: 4139
        2.92 -     3.58: 13170
        3.58 -     4.24: 22038
        4.24 -     4.90: 36801
  Nonbonded interactions: 76154
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A1097 "
            pdb="MG    MG A1506 "
     model   vdw
     1.595 2.170
  nonbonded pdb=" OD2 ASP A 353 "
            pdb="ZN    ZN A1502 "
     model   vdw
     1.803 2.230
  nonbonded pdb=" OD1 ASN A 742 "
            pdb="ZN    ZN A1501 "
     model   vdw
     1.831 2.230
  nonbonded pdb=" OE2 GLU A 403 "
            pdb="ZN    ZN A1503 "
     model   vdw
     1.886 2.230
  nonbonded pdb=" OD1 ASP A 972 "
            pdb="MG    MG A1506 "
     model   vdw
     2.182 2.170
  ... (remaining 76149 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.150
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.552   9038  Z= 0.850
  Angle     :  1.414  26.832  12225  Z= 1.072
  Chirality :  0.091   0.640   1345
  Planarity :  0.007   0.050   1575
  Dihedral  : 20.393  89.759   3338
  Min Nonbonded Distance : 1.595

Molprobity Statistics.
  All-atom Clashscore : 23.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers : 17.92 %
    Allowed  : 20.04 %
    Favored  : 62.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.24), residues: 1097
  helix:  0.59 (0.22), residues: 519
  sheet: -0.83 (0.68), residues: 53
  loop : -0.83 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 526 
 TYR   0.023   0.002   TYR A 693 
 PHE   0.017   0.002   PHE A1230 
 TRP   0.012   0.002   TRP A1264 
 HIS   0.009   0.001   HIS A1101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01070 /  0.80 ( 9028)
  covalent geometry    : angle       1.38223 /  1.07 (12219)
  hydrogen bonds       : bond        0.16511 / 10.55 (  431)
  hydrogen bonds       : angle       7.49991 /  5.28 ( 1218)
  metal coordination   : bond        0.25697 / 15.07 (   10)
  metal coordination   : angle      13.47314 /  7.95 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  400 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 169
    poor density    : 231
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8210 (tp)
REVERT: A  419 HIS cc_start: 0.7022 (t70) cc_final: 0.6804 (t-170)
REVERT: A  481 ILE cc_start: 0.8132 (mt) cc_final: 0.7901 (mt)
REVERT: A  546 LEU cc_start: 0.7689 (mt) cc_final: 0.7393 (mt)
REVERT: A  562 PHE cc_start: 0.6956 (m-80) cc_final: 0.6610 (m-80)
REVERT: A  721 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7641 (tt0)
REVERT: A  753 TYR cc_start: 0.7859 (m-10) cc_final: 0.7512 (m-10)
REVERT: A  783 MET cc_start: 0.8336 (mmt) cc_final: 0.7793 (mmt)
REVERT: A  808 ASP cc_start: 0.7570 (m-30) cc_final: 0.7226 (m-30)
REVERT: A  888 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8353 (mt)
REVERT: A 1010 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7902 (tptt)
REVERT: A 1024 ASN cc_start: 0.7259 (t0) cc_final: 0.7008 (t0)
REVERT: A 1141 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7534 (m)
REVERT: A 1212 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6261 (ptp-170)
REVERT: A 1233 MET cc_start: 0.8461 (ttp) cc_final: 0.8150 (ttp)
REVERT: A 1234 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7247 (mm-30)
REVERT: A 1422 LYS cc_start: 0.5585 (OUTLIER) cc_final: 0.5192 (mttp)
  outliers start: 169
  outliers final: 51
  residues processed: 345
  average time/residue: 0.1021
  time to fit residues: 46.2727
Evaluate side-chains
  197 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 138
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  671 LYS
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain A residue  750 ASP
Chi-restraints excluded: chain A residue  758 ILE
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  888 LEU
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1010 LYS
Chi-restraints excluded: chain A residue 1048 GLN
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1054 ILE
Chi-restraints excluded: chain A residue 1088 SER
Chi-restraints excluded: chain A residue 1089 ILE
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1107 ILE
Chi-restraints excluded: chain A residue 1129 MET
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1159 THR
Chi-restraints excluded: chain A residue 1184 SER
Chi-restraints excluded: chain A residue 1188 ASP
Chi-restraints excluded: chain A residue 1202 ASP
Chi-restraints excluded: chain A residue 1204 THR
Chi-restraints excluded: chain A residue 1212 ARG
Chi-restraints excluded: chain A residue 1213 ASP
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1221 HIS
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1234 GLU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1275 MET
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1300 ILE
Chi-restraints excluded: chain A residue 1308 SER
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1341 SER
Chi-restraints excluded: chain A residue 1345 LYS
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1378 VAL
Chi-restraints excluded: chain A residue 1415 GLU
Chi-restraints excluded: chain A residue 1422 LYS
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0470
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.6878

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 344 HIS
A 595 ASN
A 599 HIS
A 605 HIS
A 641 ASN
A 680 GLN
** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 922 GLN
A 986 HIS
A1048 GLN
A1119 GLN
A1142 GLN
A1179 GLN
A1240 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.130834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.104789 restraints weight = 13358.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.02
r_work: 0.3220 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.776   9038  Z= 0.315
  Angle     :  0.616  10.045  12225  Z= 0.330
  Chirality :  0.043   0.186   1345
  Planarity :  0.004   0.038   1575
  Dihedral  : 11.710  68.899   1362
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 21.10 %
    Favored  : 72.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.25), residues: 1097
  helix:  1.27 (0.22), residues: 537
  sheet: -0.60 (0.51), residues: 90
  loop : -0.14 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 571 
 TYR   0.022   0.002   TYR A 844 
 PHE   0.017   0.002   PHE A1027 
 TRP   0.004   0.001   TRP A1264 
 HIS   0.005   0.001   HIS A 744 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.16 ( 9028)
  covalent geometry    : angle       0.59948 /  0.33 (12219)
  hydrogen bonds       : bond        0.05254 /  3.48 (  431)
  hydrogen bonds       : angle       5.71843 /  4.05 ( 1218)
  metal coordination   : bond        0.24588 / 12.94 (   10)
  metal coordination   : angle       6.35006 /  3.91 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 150
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8607 (tp)
REVERT: A  463 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6456 (mp0)
REVERT: A  485 MET cc_start: 0.6963 (tpp) cc_final: 0.6574 (ttm)
REVERT: A  502 PHE cc_start: 0.7419 (t80) cc_final: 0.7198 (t80)
REVERT: A  647 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6335 (mtm180)
REVERT: A  753 TYR cc_start: 0.8401 (m-10) cc_final: 0.7966 (m-80)
REVERT: A  783 MET cc_start: 0.8731 (mmt) cc_final: 0.8136 (mmt)
REVERT: A  808 ASP cc_start: 0.7850 (m-30) cc_final: 0.7579 (m-30)
REVERT: A 1010 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7803 (tptt)
REVERT: A 1024 ASN cc_start: 0.7729 (t0) cc_final: 0.7332 (t0)
REVERT: A 1028 ARG cc_start: 0.7020 (tpt170) cc_final: 0.6619 (mmp80)
REVERT: A 1214 ASP cc_start: 0.7577 (m-30) cc_final: 0.7346 (m-30)
REVERT: A 1287 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7921 (tpt)
REVERT: A 1422 LYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5834 (mttp)
  outliers start: 61
  outliers final: 36
  residues processed: 196
  average time/residue: 0.0862
  time to fit residues: 23.9811
Evaluate side-chains
  167 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 126
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  466 ASP
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  750 ASP
Chi-restraints excluded: chain A residue  757 LEU
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  846 ASP
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1010 LYS
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1085 ASP
Chi-restraints excluded: chain A residue 1088 SER
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1107 ILE
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1129 MET
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1159 THR
Chi-restraints excluded: chain A residue 1188 ASP
Chi-restraints excluded: chain A residue 1204 THR
Chi-restraints excluded: chain A residue 1212 ARG
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1286 LEU
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1422 LYS
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 77 optimal weight:    0.4980
   overall best weight:    1.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 GLN
A 955 HIS
A1101 HIS
A1144 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.125133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.099394 restraints weight = 13193.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.00
r_work: 0.3140 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9038  Z= 0.177
  Angle     :  0.578   9.269  12225  Z= 0.312
  Chirality :  0.044   0.162   1345
  Planarity :  0.004   0.041   1575
  Dihedral  :  9.897  64.427   1303
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 21.31 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.26), residues: 1097
  helix:  1.38 (0.22), residues: 541
  sheet: -0.74 (0.50), residues: 96
  loop :  0.04 (0.31), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 614 
 TYR   0.016   0.002   TYR A 598 
 PHE   0.017   0.002   PHE A 461 
 TRP   0.004   0.001   TRP A1190 
 HIS   0.013   0.002   HIS A 419 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 ( 9028)
  covalent geometry    : angle       0.56771 /  0.31 (12219)
  hydrogen bonds       : bond        0.04887 /  3.27 (  431)
  hydrogen bonds       : angle       5.31537 /  3.74 ( 1218)
  metal coordination   : bond        0.01607 /  0.75 (   10)
  metal coordination   : angle       5.00471 /  3.01 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 141
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 PHE cc_start: 0.7526 (m-80) cc_final: 0.6996 (m-80)
REVERT: A  485 MET cc_start: 0.7168 (tpp) cc_final: 0.6667 (ttm)
REVERT: A  783 MET cc_start: 0.8925 (mmt) cc_final: 0.8046 (mmt)
REVERT: A  808 ASP cc_start: 0.7920 (m-30) cc_final: 0.7610 (m-30)
REVERT: A 1024 ASN cc_start: 0.7755 (t0) cc_final: 0.7346 (t0)
REVERT: A 1028 ARG cc_start: 0.7118 (tpt170) cc_final: 0.6280 (mmm-85)
REVERT: A 1129 MET cc_start: 0.7833 (mmm) cc_final: 0.7622 (mmm)
REVERT: A 1287 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8012 (tpt)
REVERT: A 1380 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7762 (pt0)
REVERT: A 1422 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5829 (mttp)
  outliers start: 45
  outliers final: 34
  residues processed: 175
  average time/residue: 0.0835
  time to fit residues: 21.1375
Evaluate side-chains
  159 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  721 GLU
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  846 ASP
Chi-restraints excluded: chain A residue  924 SER
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1020 GLU
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1088 SER
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1107 ILE
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1159 THR
Chi-restraints excluded: chain A residue 1213 ASP
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1286 LEU
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1422 LYS
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 HIS
** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1092 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.124003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.097417 restraints weight = 13284.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.04
r_work: 0.3097 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9038  Z= 0.163
  Angle     :  0.535   8.390  12225  Z= 0.290
  Chirality :  0.043   0.273   1345
  Planarity :  0.004   0.042   1575
  Dihedral  :  9.281  64.018   1278
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 21.85 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.90 (0.26), residues: 1097
  helix:  1.43 (0.22), residues: 542
  sheet: -0.73 (0.49), residues: 101
  loop :  0.02 (0.32), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 614 
 TYR   0.012   0.002   TYR A 644 
 PHE   0.014   0.002   PHE A 461 
 TRP   0.004   0.001   TRP A1079 
 HIS   0.006   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.16 ( 9028)
  covalent geometry    : angle       0.52507 /  0.29 (12219)
  hydrogen bonds       : bond        0.04513 /  3.02 (  431)
  hydrogen bonds       : angle       5.15754 /  3.62 ( 1218)
  metal coordination   : bond        0.00658 /  0.32 (   10)
  metal coordination   : angle       4.56700 /  2.74 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 130
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  464 PHE cc_start: 0.7563 (m-80) cc_final: 0.7019 (m-80)
REVERT: A  478 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7765 (tm)
REVERT: A  485 MET cc_start: 0.7450 (tpp) cc_final: 0.6902 (ttm)
REVERT: A  688 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8090 (t0)
REVERT: A  783 MET cc_start: 0.8882 (mmt) cc_final: 0.8134 (mmt)
REVERT: A  808 ASP cc_start: 0.7961 (m-30) cc_final: 0.7705 (m-30)
REVERT: A 1010 LYS cc_start: 0.8397 (mttt) cc_final: 0.7966 (tptt)
REVERT: A 1024 ASN cc_start: 0.7791 (t0) cc_final: 0.7377 (t0)
REVERT: A 1028 ARG cc_start: 0.7112 (tpm170) cc_final: 0.6310 (mmm-85)
REVERT: A 1214 ASP cc_start: 0.7558 (m-30) cc_final: 0.7303 (m-30)
REVERT: A 1287 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8097 (tpt)
REVERT: A 1422 LYS cc_start: 0.6377 (OUTLIER) cc_final: 0.5835 (mttt)
  outliers start: 39
  outliers final: 30
  residues processed: 163
  average time/residue: 0.0736
  time to fit residues: 17.7359
Evaluate side-chains
  154 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 120
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  688 ASN
Chi-restraints excluded: chain A residue  728 GLU
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  924 SER
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1020 GLU
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1107 ILE
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1213 ASP
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1286 LEU
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1422 LYS
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0770
   chunk 4 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 55 optimal weight:    0.3980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.8944

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.124610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.098206 restraints weight = 13165.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.05
r_work: 0.3104 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9038  Z= 0.126
  Angle     :  0.490   7.329  12225  Z= 0.264
  Chirality :  0.041   0.142   1345
  Planarity :  0.004   0.036   1575
  Dihedral  :  9.077  65.026   1276
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 23.12 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.26), residues: 1097
  helix:  1.66 (0.22), residues: 542
  sheet: -0.54 (0.50), residues: 101
  loop :  0.13 (0.32), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 614 
 TYR   0.011   0.001   TYR A 916 
 PHE   0.020   0.002   PHE A 461 
 TRP   0.003   0.001   TRP A 584 
 HIS   0.006   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 ( 9028)
  covalent geometry    : angle       0.48210 /  0.26 (12219)
  hydrogen bonds       : bond        0.04152 /  2.78 (  431)
  hydrogen bonds       : angle       4.98195 /  3.49 ( 1218)
  metal coordination   : bond        0.00358 /  0.16 (   10)
  metal coordination   : angle       4.05320 /  2.43 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  464 PHE cc_start: 0.7528 (m-80) cc_final: 0.6998 (m-80)
REVERT: A  478 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7766 (tm)
REVERT: A  485 MET cc_start: 0.7458 (tpp) cc_final: 0.6911 (ttm)
REVERT: A  783 MET cc_start: 0.8873 (mmt) cc_final: 0.8148 (mmt)
REVERT: A  808 ASP cc_start: 0.7996 (m-30) cc_final: 0.7732 (m-30)
REVERT: A 1010 LYS cc_start: 0.8421 (mttt) cc_final: 0.7901 (tptt)
REVERT: A 1024 ASN cc_start: 0.7798 (t0) cc_final: 0.7385 (t0)
REVERT: A 1287 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8124 (tpt)
REVERT: A 1422 LYS cc_start: 0.6344 (OUTLIER) cc_final: 0.5839 (ttmt)
  outliers start: 39
  outliers final: 29
  residues processed: 155
  average time/residue: 0.0819
  time to fit residues: 18.2263
Evaluate side-chains
  146 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  626 ASN
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  924 SER
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1020 GLU
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1107 ILE
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1213 ASP
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1286 LEU
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1422 LYS
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 108 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 469 HIS
A 581 HIS
A 710 GLN
A 853 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.122622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.096680 restraints weight = 13357.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.02
r_work: 0.3080 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9038  Z= 0.155
  Angle     :  0.516   7.710  12225  Z= 0.277
  Chirality :  0.042   0.134   1345
  Planarity :  0.004   0.036   1575
  Dihedral  :  8.926  64.731   1273
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 22.91 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.26), residues: 1097
  helix:  1.63 (0.22), residues: 541
  sheet: -0.54 (0.49), residues: 101
  loop :  0.08 (0.32), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 614 
 TYR   0.020   0.002   TYR A 844 
 PHE   0.028   0.002   PHE A1161 
 TRP   0.004   0.001   TRP A1264 
 HIS   0.006   0.001   HIS A 581 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 ( 9028)
  covalent geometry    : angle       0.50939 /  0.28 (12219)
  hydrogen bonds       : bond        0.04282 /  2.90 (  431)
  hydrogen bonds       : angle       4.97746 /  3.49 ( 1218)
  metal coordination   : bond        0.00415 /  0.19 (   10)
  metal coordination   : angle       3.85791 /  2.29 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 128
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  464 PHE cc_start: 0.7580 (m-80) cc_final: 0.7045 (m-80)
REVERT: A  485 MET cc_start: 0.7535 (tpp) cc_final: 0.7021 (ttm)
REVERT: A  783 MET cc_start: 0.8906 (mmt) cc_final: 0.8191 (mmt)
REVERT: A  808 ASP cc_start: 0.8002 (m-30) cc_final: 0.7740 (m-30)
REVERT: A  920 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7106 (mp0)
REVERT: A 1010 LYS cc_start: 0.8461 (mttt) cc_final: 0.7899 (tptt)
REVERT: A 1024 ASN cc_start: 0.7797 (t0) cc_final: 0.7379 (t0)
REVERT: A 1214 ASP cc_start: 0.7456 (m-30) cc_final: 0.7224 (m-30)
REVERT: A 1287 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8103 (tpt)
REVERT: A 1422 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5816 (mttt)
  outliers start: 41
  outliers final: 30
  residues processed: 162
  average time/residue: 0.0762
  time to fit residues: 18.2430
Evaluate side-chains
  149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  626 ASN
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  920 GLU
Chi-restraints excluded: chain A residue  924 SER
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1020 GLU
Chi-restraints excluded: chain A residue 1032 VAL
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1107 ILE
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1159 THR
Chi-restraints excluded: chain A residue 1213 ASP
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1286 LEU
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1422 LYS
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0670
   chunk 43 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.123999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.098583 restraints weight = 13291.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.00
r_work: 0.3112 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9038  Z= 0.109
  Angle     :  0.486   7.348  12225  Z= 0.259
  Chirality :  0.041   0.135   1345
  Planarity :  0.004   0.036   1575
  Dihedral  :  8.736  65.549   1269
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 23.44 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.27), residues: 1097
  helix:  1.79 (0.22), residues: 542
  sheet: -0.46 (0.48), residues: 101
  loop :  0.15 (0.33), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 614 
 TYR   0.023   0.001   TYR A 844 
 PHE   0.020   0.001   PHE A 461 
 TRP   0.003   0.001   TRP A 584 
 HIS   0.004   0.001   HIS A 770 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 9028)
  covalent geometry    : angle       0.47934 /  0.26 (12219)
  hydrogen bonds       : bond        0.03933 /  2.64 (  431)
  hydrogen bonds       : angle       4.83663 /  3.39 ( 1218)
  metal coordination   : bond        0.00224 /  0.10 (   10)
  metal coordination   : angle       3.59276 /  2.15 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  434 THR cc_start: 0.8868 (m) cc_final: 0.8633 (p)
REVERT: A  454 LYS cc_start: 0.7688 (mtpp) cc_final: 0.7171 (tppt)
REVERT: A  464 PHE cc_start: 0.7540 (m-80) cc_final: 0.7042 (m-80)
REVERT: A  485 MET cc_start: 0.7551 (tpp) cc_final: 0.7045 (ttm)
REVERT: A  783 MET cc_start: 0.8880 (mmt) cc_final: 0.8267 (mmt)
REVERT: A  785 THR cc_start: 0.8837 (m) cc_final: 0.8540 (p)
REVERT: A  808 ASP cc_start: 0.8002 (m-30) cc_final: 0.7724 (m-30)
REVERT: A  920 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7377 (mm-30)
REVERT: A 1010 LYS cc_start: 0.8470 (mttt) cc_final: 0.7873 (tptt)
REVERT: A 1024 ASN cc_start: 0.7756 (t0) cc_final: 0.7342 (t0)
REVERT: A 1129 MET cc_start: 0.8016 (mmt) cc_final: 0.5017 (ptp)
REVERT: A 1214 ASP cc_start: 0.7448 (m-30) cc_final: 0.7173 (m-30)
REVERT: A 1287 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8084 (tpt)
REVERT: A 1422 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5756 (ttmt)
  outliers start: 37
  outliers final: 31
  residues processed: 153
  average time/residue: 0.0786
  time to fit residues: 17.6932
Evaluate side-chains
  150 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 116
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  357 SER
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  920 GLU
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1009 ASP
Chi-restraints excluded: chain A residue 1020 GLU
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1159 THR
Chi-restraints excluded: chain A residue 1213 ASP
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1286 LEU
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1422 LYS
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 37 optimal weight:    0.2980
   chunk 72 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.123564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.098006 restraints weight = 13445.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.04
r_work: 0.3103 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.4701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9038  Z= 0.118
  Angle     :  0.483   7.257  12225  Z= 0.257
  Chirality :  0.041   0.134   1345
  Planarity :  0.004   0.035   1575
  Dihedral  :  8.602  65.683   1267
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 23.33 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.26), residues: 1097
  helix:  1.79 (0.22), residues: 541
  sheet: -0.28 (0.51), residues: 92
  loop :  0.15 (0.32), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 614 
 TYR   0.024   0.001   TYR A 844 
 PHE   0.028   0.001   PHE A1161 
 TRP   0.003   0.001   TRP A1264 
 HIS   0.005   0.001   HIS A 581 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 9028)
  covalent geometry    : angle       0.47683 /  0.26 (12219)
  hydrogen bonds       : bond        0.03916 /  2.65 (  431)
  hydrogen bonds       : angle       4.82357 /  3.38 ( 1218)
  metal coordination   : bond        0.00276 /  0.12 (   10)
  metal coordination   : angle       3.45358 /  2.06 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 118
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  434 THR cc_start: 0.8826 (m) cc_final: 0.8611 (p)
REVERT: A  464 PHE cc_start: 0.7533 (m-80) cc_final: 0.7060 (m-80)
REVERT: A  485 MET cc_start: 0.7571 (tpp) cc_final: 0.7143 (ttm)
REVERT: A  783 MET cc_start: 0.8868 (mmt) cc_final: 0.8256 (mmt)
REVERT: A  785 THR cc_start: 0.8890 (m) cc_final: 0.8580 (p)
REVERT: A  808 ASP cc_start: 0.7983 (m-30) cc_final: 0.7713 (m-30)
REVERT: A  920 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7385 (mm-30)
REVERT: A 1010 LYS cc_start: 0.8478 (mttt) cc_final: 0.7859 (tptt)
REVERT: A 1024 ASN cc_start: 0.7788 (t0) cc_final: 0.7383 (t0)
REVERT: A 1129 MET cc_start: 0.8011 (mmt) cc_final: 0.5086 (ptp)
REVERT: A 1188 ASP cc_start: 0.8036 (t0) cc_final: 0.7345 (t0)
REVERT: A 1214 ASP cc_start: 0.7415 (m-30) cc_final: 0.7126 (m-30)
REVERT: A 1287 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8117 (tpt)
REVERT: A 1422 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5744 (ttmt)
  outliers start: 37
  outliers final: 30
  residues processed: 149
  average time/residue: 0.0781
  time to fit residues: 17.0518
Evaluate side-chains
  146 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  626 ASN
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  920 GLU
Chi-restraints excluded: chain A residue  924 SER
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1009 ASP
Chi-restraints excluded: chain A residue 1020 GLU
Chi-restraints excluded: chain A residue 1032 VAL
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1159 THR
Chi-restraints excluded: chain A residue 1213 ASP
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1286 LEU
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1422 LYS
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.121878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.095806 restraints weight = 13377.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 2.04
r_work: 0.3065 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9038  Z= 0.171
  Angle     :  0.523   7.140  12225  Z= 0.281
  Chirality :  0.043   0.225   1345
  Planarity :  0.004   0.037   1575
  Dihedral  :  8.510  64.816   1264
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 23.65 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.26), residues: 1097
  helix:  1.62 (0.22), residues: 543
  sheet: -0.44 (0.47), residues: 101
  loop :  0.02 (0.32), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 614 
 TYR   0.021   0.002   TYR A 844 
 PHE   0.017   0.002   PHE A 461 
 TRP   0.005   0.001   TRP A1264 
 HIS   0.006   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.17 ( 9028)
  covalent geometry    : angle       0.51773 /  0.28 (12219)
  hydrogen bonds       : bond        0.04332 /  2.96 (  431)
  hydrogen bonds       : angle       4.94187 /  3.45 ( 1218)
  metal coordination   : bond        0.00444 /  0.20 (   10)
  metal coordination   : angle       3.49218 /  2.05 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  434 THR cc_start: 0.8876 (m) cc_final: 0.8607 (p)
REVERT: A  464 PHE cc_start: 0.7649 (m-80) cc_final: 0.7162 (m-80)
REVERT: A  485 MET cc_start: 0.7613 (tpp) cc_final: 0.7168 (ttm)
REVERT: A  783 MET cc_start: 0.8878 (mmt) cc_final: 0.8166 (mmt)
REVERT: A  785 THR cc_start: 0.8862 (m) cc_final: 0.8534 (p)
REVERT: A  808 ASP cc_start: 0.8034 (m-30) cc_final: 0.7786 (m-30)
REVERT: A  920 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7106 (mp0)
REVERT: A 1010 LYS cc_start: 0.8465 (mttt) cc_final: 0.7833 (tptt)
REVERT: A 1024 ASN cc_start: 0.7754 (t0) cc_final: 0.7344 (t0)
REVERT: A 1188 ASP cc_start: 0.8013 (t0) cc_final: 0.7114 (t0)
REVERT: A 1214 ASP cc_start: 0.7623 (m-30) cc_final: 0.7358 (m-30)
REVERT: A 1287 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8110 (tpt)
  outliers start: 34
  outliers final: 29
  residues processed: 145
  average time/residue: 0.0716
  time to fit residues: 15.4510
Evaluate side-chains
  145 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  626 ASN
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  920 GLU
Chi-restraints excluded: chain A residue  924 SER
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1009 ASP
Chi-restraints excluded: chain A residue 1032 VAL
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1159 THR
Chi-restraints excluded: chain A residue 1213 ASP
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1286 LEU
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 109 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0270
   chunk 51 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    1.3244

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.121700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.097577 restraints weight = 13508.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.92
r_work: 0.3079 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9038  Z= 0.150
  Angle     :  0.508   7.350  12225  Z= 0.272
  Chirality :  0.042   0.135   1345
  Planarity :  0.004   0.037   1575
  Dihedral  :  8.346  65.133   1260
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 23.97 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.26), residues: 1097
  helix:  1.55 (0.22), residues: 549
  sheet: -0.43 (0.47), residues: 101
  loop : -0.10 (0.32), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 614 
 TYR   0.023   0.002   TYR A 844 
 PHE   0.028   0.002   PHE A1161 
 TRP   0.004   0.001   TRP A1264 
 HIS   0.004   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 9028)
  covalent geometry    : angle       0.50248 /  0.27 (12219)
  hydrogen bonds       : bond        0.04198 /  2.85 (  431)
  hydrogen bonds       : angle       4.92542 /  3.45 ( 1218)
  metal coordination   : bond        0.00351 /  0.17 (   10)
  metal coordination   : angle       3.39799 /  2.00 (    6)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 122
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  464 PHE cc_start: 0.7675 (m-80) cc_final: 0.7225 (m-80)
REVERT: A  485 MET cc_start: 0.7594 (tpp) cc_final: 0.7212 (ttm)
REVERT: A  783 MET cc_start: 0.8895 (mmt) cc_final: 0.8200 (mmt)
REVERT: A  785 THR cc_start: 0.8861 (m) cc_final: 0.8539 (p)
REVERT: A  808 ASP cc_start: 0.7985 (m-30) cc_final: 0.7732 (m-30)
REVERT: A  920 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7133 (mp0)
REVERT: A 1010 LYS cc_start: 0.8428 (mttt) cc_final: 0.7860 (tptt)
REVERT: A 1024 ASN cc_start: 0.7728 (t0) cc_final: 0.7324 (t0)
REVERT: A 1095 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7367 (tmmt)
REVERT: A 1188 ASP cc_start: 0.7971 (t0) cc_final: 0.7109 (t0)
REVERT: A 1287 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8103 (tpt)
  outliers start: 33
  outliers final: 28
  residues processed: 150
  average time/residue: 0.0753
  time to fit residues: 16.7104
Evaluate side-chains
  149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  356 ASN
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  626 ASN
Chi-restraints excluded: chain A residue  781 ASP
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  920 GLU
Chi-restraints excluded: chain A residue  924 SER
Chi-restraints excluded: chain A residue  965 PHE
Chi-restraints excluded: chain A residue 1009 ASP
Chi-restraints excluded: chain A residue 1032 VAL
Chi-restraints excluded: chain A residue 1053 ILE
Chi-restraints excluded: chain A residue 1066 THR
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1159 THR
Chi-restraints excluded: chain A residue 1213 ASP
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1286 LEU
Chi-restraints excluded: chain A residue 1287 MET
Chi-restraints excluded: chain A residue 1324 ASP
Chi-restraints excluded: chain A residue 1326 VAL
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.119966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.093919 restraints weight = 13239.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.00
r_work: 0.3034 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.4963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   9038  Z= 0.235
  Angle     :  0.581   7.130  12225  Z= 0.313
  Chirality :  0.045   0.142   1345
  Planarity :  0.004   0.038   1575
  Dihedral  :  8.516  64.082   1260
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 23.86 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.25), residues: 1097
  helix:  1.27 (0.21), residues: 549
  sheet: -0.71 (0.46), residues: 99
  loop : -0.28 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 614 
 TYR   0.022   0.002   TYR A 844 
 PHE   0.029   0.002   PHE A1161 
 TRP   0.007   0.002   TRP A 368 
 HIS   0.007   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00550 /  0.23 ( 9028)
  covalent geometry    : angle       0.57570 /  0.31 (12219)
  hydrogen bonds       : bond        0.04787 /  3.28 (  431)
  hydrogen bonds       : angle       5.11235 /  3.57 ( 1218)
  metal coordination   : bond        0.00607 /  0.28 (   10)
  metal coordination   : angle       3.56822 /  2.08 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2378.88 seconds
wall clock time: 41 minutes 21.51 seconds (2481.51 seconds total)