Starting phenix.real_space_refine
on Wed Aug  5 15:14:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dou_47091/08_2026/9dou_47091.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dou_47091/08_2026/9dou_47091.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dou_47091/08_2026/9dou_47091.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dou_47091/08_2026/9dou_47091.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dou_47091/08_2026/9dou_47091.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dou_47091/08_2026/9dou_47091.cif"
  }
  resolution = 3.2
  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     147      5.49       5
     Mg      1      5.21       5
     S      45      5.16       5
     C    6130      2.51       5
     N    1891      2.21       5
     O    2276      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  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: 10494
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 924, 7429
          Classifications: {'peptide': 924}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 41, 'TRANS': 882}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 530
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "P"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 267
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1599
          Classifications: {'RNA': 75}
          Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 35, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 14, 'rna3p': 60}
    Chain: "T"
      Number of atoms: 635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 635
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 34
          Unusual residues: {' MG': 1, ' ZN': 4, 'TTP': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    533  SG  CYS A 297      54.277  84.020  34.739  1.00 72.44           S
  ATOM    555  SG  CYS A 300      54.733  84.197  38.602  1.00 65.33           S
  ATOM   5995  SG  CYS A1212      85.350  71.211  92.026  1.00 58.26           S
  ATOM   6022  SG  CYS A1215      88.370  70.593  94.281  1.00 70.33           S
  ATOM   6121  SG  CYS A1229      85.570  67.836  94.055  1.00 57.38           S
  ATOM    326  SG  CYS A 262      68.772  90.617  59.398  1.00131.51           S
  ATOM    346  SG  CYS A 265      67.249  91.177  55.945  1.00145.26           S
  ATOM    481  SG  CYS A 282      70.741  91.818  56.209  1.00129.38           S
  ATOM     97  SG  CYS A 232      57.282  87.036  77.028  1.00155.87           S

  Time building chain proxies: 2.08, per 1000 atoms: 0.20
  Number of scatterers: 10494
  At special positions: 0
  Unit cell: (117.862, 102.209, 123.387, 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      45     16.00
     P     147     15.00
     Mg      1     11.99
     O    2276      8.00
     N    1891      7.00
     C    6130      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: 0.65
  Conformation dependent library (CDL) restraints added in 279.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1403 "
        pdb="ZN    ZN A1403 " - pdb=" NE2 HIS A 318 "
        pdb="ZN    ZN A1403 " - pdb=" NE2 HIS A 313 "
        pdb="ZN    ZN A1403 " - pdb=" SG  CYS A 297 "
        pdb="ZN    ZN A1403 " - pdb=" SG  CYS A 300 "
      pdb="  ZN A1404 "
        pdb="ZN    ZN A1404 " - pdb=" NE2 HIS A1224 "
        pdb="ZN    ZN A1404 " - pdb=" SG  CYS A1215 "
        pdb="ZN    ZN A1404 " - pdb=" SG  CYS A1212 "
        pdb="ZN    ZN A1404 " - pdb=" SG  CYS A1229 "
      pdb="  ZN A1405 "
        pdb="ZN    ZN A1405 " - pdb=" ND1 HIS A 278 "
        pdb="ZN    ZN A1405 " - pdb=" SG  CYS A 265 "
        pdb="ZN    ZN A1405 " - pdb=" SG  CYS A 282 "
        pdb="ZN    ZN A1405 " - pdb=" SG  CYS A 262 "
      pdb="  ZN A1406 "
        pdb="ZN    ZN A1406 " - pdb=" SG  CYS A 232 "
        pdb="ZN    ZN A1406 " - pdb=" NE2 HIS A 253 "
        pdb="ZN    ZN A1406 " - pdb=" NE2 HIS A 248 "
      Number of angles added : 8


  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1748

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 10 sheets defined
      55.7% alpha, 12.3% beta
      52 base pairs and 94 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 241 through 254
      removed outlier: 3.581A  pdb=" N   HIS A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.521A  pdb=" N   VAL A 275 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
    Processing helix  chain 'A' and resid 306 through 317
    Processing helix  chain 'A' and resid 321 through 330
    Processing helix  chain 'A' and resid 551 through 573
      removed outlier: 4.152A  pdb=" N   ASP A 555 " --> pdb=" O   LYS A 551 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   TYR A 571 " --> pdb=" O   GLN A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 584
      removed outlier: 3.992A  pdb=" N   ASP A 584 " --> pdb=" O   ILE A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 606
    Processing helix  chain 'A' and resid 624 through 629
      removed outlier: 3.654A  pdb=" N   ALA A 627 " --> pdb=" O   ASP A 624 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE A 628 " --> pdb=" O   ASN A 625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 644
    Processing helix  chain 'A' and resid 656 through 664
    Processing helix  chain 'A' and resid 667 through 681
    Processing helix  chain 'A' and resid 684 through 687
      removed outlier: 3.702A  pdb=" N   VAL A 687 " --> pdb=" O   PRO A 684 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 684 through 687'
    Processing helix  chain 'A' and resid 706 through 708
      No H-bonds generated for 'chain 'A' and resid 706 through 708'
    Processing helix  chain 'A' and resid 717 through 735
      removed outlier: 3.773A  pdb=" N   ARG A 730 " --> pdb=" O   ILE A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 767
      removed outlier: 3.514A  pdb=" N   GLU A 752 " --> pdb=" O   ALA A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 785
      removed outlier: 3.936A  pdb=" N   VAL A 785 " --> pdb=" O   ALA A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 797
      removed outlier: 3.565A  pdb=" N   ARG A 797 " --> pdb=" O   ALA A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 811
      removed outlier: 3.634A  pdb=" N   TYR A 811 " --> pdb=" O   VAL A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 861
      Proline residue:  A 852  - end of helix
    Processing helix  chain 'A' and resid 886 through 905
      removed outlier: 3.678A  pdb=" N   MET A 890 " --> pdb=" O   SER A 886 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ASN A 891 " --> pdb=" O   TRP A 887 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   THR A 892 " --> pdb=" O   GLU A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 912
    Processing helix  chain 'A' and resid 966 through 980
      removed outlier: 3.704A  pdb=" N   LYS A 970 " --> pdb=" O   GLY A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 995
    Processing helix  chain 'A' and resid 996 through 999
    Processing helix  chain 'A' and resid 1000 through 1007
    Processing helix  chain 'A' and resid 1010 through 1029
      removed outlier: 3.652A  pdb=" N   LEU A1014 " --> pdb=" O   LYS A1010 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1042
    Processing helix  chain 'A' and resid 1043 through 1047
    Processing helix  chain 'A' and resid 1053 through 1071
      Proline residue:  A1059  - end of helix
    Processing helix  chain 'A' and resid 1082 through 1097
    Processing helix  chain 'A' and resid 1100 through 1104
      removed outlier: 3.628A  pdb=" N   ASN A1103 " --> pdb=" O   ASP A1100 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ILE A1104 " --> pdb=" O   ARG A1101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1100 through 1104'
    Processing helix  chain 'A' and resid 1140 through 1151
    Processing helix  chain 'A' and resid 1158 through 1163
      removed outlier: 3.515A  pdb=" N   ASN A1161 " --> pdb=" O   GLY A1158 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLU A1163 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1174
      removed outlier: 4.332A  pdb=" N   GLN A1173 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1179 through 1192
    Processing helix  chain 'A' and resid 1196 through 1202
    Processing helix  chain 'A' and resid 1221 through 1228
    Processing helix  chain 'A' and resid 1229 through 1231
      No H-bonds generated for 'chain 'A' and resid 1229 through 1231'
    Processing helix  chain 'A' and resid 1232 through 1254
      removed outlier: 3.647A  pdb=" N   GLU A1250 " --> pdb=" O   LEU A1246 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LYS A1254 " --> pdb=" O   GLU A1250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1298 through 1310
    Processing helix  chain 'A' and resid 1311 through 1313
      No H-bonds generated for 'chain 'A' and resid 1311 through 1313'
    Processing helix  chain 'A' and resid 1314 through 1323
    Processing helix  chain 'A' and resid 1343 through 1351
      removed outlier: 4.125A  pdb=" N   LEU A1347 " --> pdb=" O   ASP A1343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1354 through 1386
      removed outlier: 3.792A  pdb=" N   VAL A1359 " --> pdb=" O   LYS A1355 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 221 through 224
      removed outlier: 6.133A  pdb=" N   VAL A 221 " --> pdb=" O   CYS A 259 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ARG A 261 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL A 223 " --> pdb=" O   ARG A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296
    Processing sheet with id=AA3, first strand: chain 'A' and resid 710 through 715
      removed outlier: 7.032A  pdb=" N   CYS A 690 " --> pdb=" O   TYR A 817 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   THR A 819 " --> pdb=" O   CYS A 690 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   THR A 692 " --> pdb=" O   THR A 819 " (cutoff:3.500A)
      removed outlier: 5.593A  pdb=" N   ILE A 818 " --> pdb=" O   ASP A 827 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   ASP A 827 " --> pdb=" O   ILE A 818 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   THR A 820 " --> pdb=" O   HIS A 825 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   HIS A 825 " --> pdb=" O   THR A 820 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 873 through 876
    Processing sheet with id=AA5, first strand: chain 'A' and resid 873 through 876
    Processing sheet with id=AA6, first strand: chain 'A' and resid 864 through 866
    Processing sheet with id=AA7, first strand: chain 'A' and resid 934 through 935
      removed outlier: 3.651A  pdb=" N   THR A 938 " --> pdb=" O   ILE A 935 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 951
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1257 through 1260
      removed outlier: 6.445A  pdb=" N   ALA A1284 " --> pdb=" O   THR A1328 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   VAL A1330 " --> pdb=" O   ALA A1284 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   VAL A1286 " --> pdb=" O   VAL A1330 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   PHE A1332 " --> pdb=" O   VAL A1286 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   ASP A1288 " --> pdb=" O   PHE A1332 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   LEU A1334 " --> pdb=" O   ASP A1288 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   THR A1290 " --> pdb=" O   LEU A1334 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1264 through 1265

    383 hydrogen bonds defined for protein.
    1083 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      130 hydrogen bonds
      248 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      94 stacking parallelities
  Total time for adding SS restraints: 2.63

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2314
        1.34 -     1.46: 3218
        1.46 -     1.58: 5125
        1.58 -     1.70: 290
        1.70 -     1.83: 64
  Bond restraints: 11011
  Sorted by residual:
  bond pdb=" O3B TTP A1402 "
       pdb=" PG  TTP A1402 "
    ideal  model  delta    sigma   weight residual
    1.748  1.605  0.143 2.00e-02 2.50e+03 5.14e+01
  bond pdb=" C   ILE A 997 "
       pdb=" N   PRO A 998 "
    ideal  model  delta    sigma   weight residual
    1.336  1.405 -0.070 1.08e-02 8.57e+03 4.16e+01
  bond pdb=" C3'  DT P  16 "
       pdb=" O3'  DT P  16 "
    ideal  model  delta    sigma   weight residual
    1.435  1.500 -0.065 1.30e-02 5.92e+03 2.51e+01
  bond pdb=" C3'  DA P  15 "
       pdb=" O3'  DA P  15 "
    ideal  model  delta    sigma   weight residual
    1.435  1.499 -0.064 1.30e-02 5.92e+03 2.41e+01
  bond pdb=" C3'  DG T  24 "
       pdb=" O3'  DG T  24 "
    ideal  model  delta    sigma   weight residual
    1.435  1.498 -0.063 1.30e-02 5.92e+03 2.36e+01
  ... (remaining 11006 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 14729
        2.44 -     4.89: 686
        4.89 -     7.33: 89
        7.33 -     9.78: 16
        9.78 -    12.22: 13
  Bond angle restraints: 15533
  Sorted by residual:
  angle pdb=" C2    C R 280 "
        pdb=" N1    C R 280 "
        pdb=" C6    C R 280 "
      ideal   model   delta    sigma   weight residual
     120.30  116.22    4.08 4.00e-01 6.25e+00 1.04e+02
  angle pdb=" N1    U R 263 "
        pdb=" C2    U R 263 "
        pdb=" O2    U R 263 "
      ideal   model   delta    sigma   weight residual
     122.80  128.31   -5.51 7.00e-01 2.04e+00 6.20e+01
  angle pdb=" O2    U R 263 "
        pdb=" C2    U R 263 "
        pdb=" N3    U R 263 "
      ideal   model   delta    sigma   weight residual
     122.20  116.94    5.26 7.00e-01 2.04e+00 5.65e+01
  angle pdb=" N1    C R 280 "
        pdb=" C6    C R 280 "
        pdb=" C5    C R 280 "
      ideal   model   delta    sigma   weight residual
     121.00  124.56   -3.56 5.00e-01 4.00e+00 5.08e+01
  angle pdb=" C3'   U R 282 "
        pdb=" O3'   U R 282 "
        pdb=" P     A R 283 "
      ideal   model   delta    sigma   weight residual
     119.70  127.15   -7.45 1.20e+00 6.94e-01 3.85e+01
  ... (remaining 15528 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 6060
       35.81 -    71.61: 454
       71.61 -   107.42: 32
      107.42 -   143.22: 1
      143.22 -   179.03: 6
  Dihedral angle restraints: 6553
    sinusoidal: 3864
      harmonic: 2689
  Sorted by residual:
  dihedral pdb=" CA  VAL A 225 "
           pdb=" C   VAL A 225 "
           pdb=" N   PRO A 226 "
           pdb=" CA  PRO A 226 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.79   36.21     0      5.00e+00 4.00e-02 5.25e+01
  dihedral pdb=" CA  THR A 826 "
           pdb=" C   THR A 826 "
           pdb=" N   ASP A 827 "
           pdb=" CA  ASP A 827 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.25   24.75     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  LYS A 780 "
           pdb=" C   LYS A 780 "
           pdb=" N   ALA A 781 "
           pdb=" CA  ALA A 781 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.28  -24.72     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 6550 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1517
       0.095 -    0.189: 254
       0.189 -    0.284: 14
       0.284 -    0.379: 0
       0.379 -    0.474: 2
  Chirality restraints: 1787
  Sorted by residual:
  chirality pdb=" P    DG B  49 "
            pdb=" OP1  DG B  49 "
            pdb=" OP2  DG B  49 "
            pdb=" O5'  DG B  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.81   -0.47 2.00e-01 2.50e+01 5.61e+00
  chirality pdb=" P    DT P  24 "
            pdb=" OP1  DT P  24 "
            pdb=" OP2  DT P  24 "
            pdb=" O5'  DT P  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.75   -0.41 2.00e-01 2.50e+01 4.22e+00
  chirality pdb=" C3'   U R 282 "
            pdb=" C4'   U R 282 "
            pdb=" O3'   U R 282 "
            pdb=" C2'   U R 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.21   -0.27 2.00e-01 2.50e+01 1.81e+00
  ... (remaining 1784 not shown)

  Planarity restraints: 1443
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 549 "    0.017 2.00e-02 2.50e+03   2.03e-02 7.18e+00
        pdb=" CG  PHE A 549 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 549 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 549 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 549 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 549 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 549 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A1320 "    0.020 2.00e-02 2.50e+03   2.14e-02 6.85e+00
        pdb=" CG  HIS A1320 "   -0.046 2.00e-02 2.50e+03
        pdb=" ND1 HIS A1320 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 HIS A1320 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 HIS A1320 "    0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS A1320 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT T  40 "   -0.035 2.00e-02 2.50e+03   1.63e-02 6.67e+00
        pdb=" N1   DT T  40 "    0.027 2.00e-02 2.50e+03
        pdb=" C2   DT T  40 "    0.004 2.00e-02 2.50e+03
        pdb=" O2   DT T  40 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DT T  40 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4   DT T  40 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4   DT T  40 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5   DT T  40 "   -0.005 2.00e-02 2.50e+03
        pdb=" C7   DT T  40 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DT T  40 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1440 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 426
        2.72 -     3.26: 8839
        3.26 -     3.81: 17697
        3.81 -     4.35: 23035
        4.35 -     4.90: 34510
  Nonbonded interactions: 84507
  Sorted by model distance:
  nonbonded pdb="MG    MG A1401 "
            pdb=" O1B TTP A1402 "
     model   vdw
     2.173 2.170
  nonbonded pdb=" OD2 ASP A 878 "
            pdb="MG    MG A1401 "
     model   vdw
     2.180 2.170
  nonbonded pdb=" OD2 ASP A 777 "
            pdb="MG    MG A1401 "
     model   vdw
     2.215 2.170
  nonbonded pdb="MG    MG A1401 "
            pdb=" O1A TTP A1402 "
     model   vdw
     2.271 2.170
  nonbonded pdb=" O   ILE A 778 "
            pdb="MG    MG A1401 "
     model   vdw
     2.333 2.170
  ... (remaining 84502 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:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.430
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
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      :  0.007   0.143  11026  Z= 0.475
  Angle     :  1.208  12.223  15541  Z= 0.886
  Chirality :  0.067   0.474   1787
  Planarity :  0.009   0.066   1443
  Dihedral  : 21.154 179.031   4805
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 1.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.16 %
    Favored  : 95.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.44 %
    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: -0.83 (0.25), residues: 914
  helix: -0.56 (0.22), residues: 435
  sheet:  0.32 (0.51), residues: 107
  loop : -0.59 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG A1383 
 TYR   0.021   0.003   TYR A 864 
 PHE   0.047   0.004   PHE A 549 
 TRP   0.035   0.003   TRP A 552 
 HIS   0.024   0.003   HIS A1320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00663 /  0.48 (11011)
  covalent geometry    : angle       1.20333 /  0.89 (15533)
  hydrogen bonds       : bond        0.14473 /  9.26 (  497)
  hydrogen bonds       : angle       6.08457 /  4.15 ( 1331)
  metal coordination   : bond        0.02382 /  1.15 (   15)
  metal coordination   : angle       4.88649 /  1.92 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8785 (mmm) cc_final: 0.8437 (mtp)
REVERT: A  686 MET cc_start: 0.7159 (ptt) cc_final: 0.6952 (ptm)
REVERT: A  777 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8503 (p0)
REVERT: A 1085 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8236 (mtpt)
REVERT: A 1294 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7710 (pm20)
REVERT: A 1350 GLU cc_start: 0.8233 (tp30) cc_final: 0.7983 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1126
  time to fit residues: 17.1572
Evaluate side-chains
  86 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  777 ASP
Chi-restraints excluded: chain A residue 1294 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 97 optimal weight:   30.0000
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:   50.0000
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.160199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.119256 restraints weight = 12574.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.42
r_work: 0.2994 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11026  Z= 0.141
  Angle     :  0.633  11.288  15541  Z= 0.366
  Chirality :  0.045   0.257   1787
  Planarity :  0.005   0.045   1443
  Dihedral  : 23.456 179.919   2929
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  6.12 %
    Favored  : 93.51 %
  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:  0.30 (0.27), residues: 914
  helix:  0.92 (0.24), residues: 441
  sheet:  0.55 (0.50), residues: 99
  loop : -0.69 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1309 
 TYR   0.012   0.001   TYR A1174 
 PHE   0.019   0.002   PHE A1371 
 TRP   0.017   0.001   TRP A 552 
 HIS   0.011   0.001   HIS A1320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.14 (11011)
  covalent geometry    : angle       0.62969 /  0.37 (15533)
  hydrogen bonds       : bond        0.06043 /  4.05 (  497)
  hydrogen bonds       : angle       4.36826 /  2.98 ( 1331)
  metal coordination   : bond        0.01378 /  0.53 (   15)
  metal coordination   : angle       3.01067 /  1.11 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8728 (mmm) cc_final: 0.8394 (mmm)
REVERT: A  686 MET cc_start: 0.7240 (ptt) cc_final: 0.7036 (ptm)
REVERT: A  810 MET cc_start: 0.7828 (mtp) cc_final: 0.7568 (mtp)
REVERT: A  911 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7737 (mm-40)
REVERT: A 1177 ARG cc_start: 0.7307 (mtm180) cc_final: 0.7091 (mmt-90)
REVERT: A 1294 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7757 (pm20)
REVERT: A 1350 GLU cc_start: 0.8293 (tp30) cc_final: 0.7983 (tp30)
  outliers start: 3
  outliers final: 2
  residues processed: 89
  average time/residue: 0.0944
  time to fit residues: 11.8371
Evaluate side-chains
  80 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain A residue 1294 GLU
Chi-restraints excluded: chain A residue 1330 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 93 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 100 optimal weight:   50.0000
   chunk 49 optimal weight:    0.0010
   overall best weight:    1.9994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1030 HIS
A1320 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.157347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.116058 restraints weight = 12442.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.39
r_work: 0.2953 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11026  Z= 0.156
  Angle     :  0.611   8.253  15541  Z= 0.345
  Chirality :  0.045   0.263   1787
  Planarity :  0.005   0.044   1443
  Dihedral  : 23.298 177.997   2927
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.34 %
    Favored  : 91.68 %
  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:  0.69 (0.28), residues: 914
  helix:  1.37 (0.25), residues: 438
  sheet:  0.56 (0.51), residues: 99
  loop : -0.61 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 574 
 TYR   0.014   0.002   TYR A1174 
 PHE   0.023   0.002   PHE A1371 
 TRP   0.011   0.001   TRP A 552 
 HIS   0.013   0.002   HIS A1320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.16 (11011)
  covalent geometry    : angle       0.60781 /  0.35 (15533)
  hydrogen bonds       : bond        0.05608 /  3.85 (  497)
  hydrogen bonds       : angle       4.05229 /  2.79 ( 1331)
  metal coordination   : bond        0.01285 /  0.50 (   15)
  metal coordination   : angle       2.77892 /  0.98 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8702 (mmm) cc_final: 0.8410 (mtp)
REVERT: A  686 MET cc_start: 0.7161 (ptt) cc_final: 0.6942 (ptm)
REVERT: A  777 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8395 (p0)
REVERT: A  810 MET cc_start: 0.7975 (mtp) cc_final: 0.7753 (mtp)
REVERT: A 1177 ARG cc_start: 0.7434 (mtm180) cc_final: 0.7153 (mmt-90)
REVERT: A 1294 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7842 (pm20)
REVERT: A 1350 GLU cc_start: 0.8301 (tp30) cc_final: 0.7946 (tp30)
  outliers start: 8
  outliers final: 5
  residues processed: 91
  average time/residue: 0.1015
  time to fit residues: 13.4065
Evaluate side-chains
  89 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  653 ASP
Chi-restraints excluded: chain A residue  777 ASP
Chi-restraints excluded: chain A residue  866 ARG
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain A residue 1294 GLU
Chi-restraints excluded: chain A residue 1299 SER
Chi-restraints excluded: chain A residue 1330 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0020
   chunk 59 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0470
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.5288

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 823 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.160755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.120327 restraints weight = 12541.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.46
r_work: 0.2995 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11026  Z= 0.115
  Angle     :  0.535   9.533  15541  Z= 0.307
  Chirality :  0.041   0.262   1787
  Planarity :  0.004   0.036   1443
  Dihedral  : 23.234 179.161   2927
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.08 %
    Favored  : 91.31 %
  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:  1.00 (0.28), residues: 914
  helix:  1.70 (0.25), residues: 443
  sheet:  0.72 (0.51), residues: 99
  loop : -0.61 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 730 
 TYR   0.009   0.001   TYR A1174 
 PHE   0.018   0.001   PHE A 549 
 TRP   0.011   0.001   TRP A 552 
 HIS   0.003   0.001   HIS A 825 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00185 /  0.11 (11011)
  covalent geometry    : angle       0.53309 /  0.31 (15533)
  hydrogen bonds       : bond        0.04517 /  3.06 (  497)
  hydrogen bonds       : angle       3.78570 /  2.61 ( 1331)
  metal coordination   : bond        0.01043 /  0.38 (   15)
  metal coordination   : angle       2.20589 /  0.79 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8556 (mmm) cc_final: 0.8154 (mmm)
REVERT: A  777 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8284 (p0)
REVERT: A  810 MET cc_start: 0.7959 (mtp) cc_final: 0.7695 (mtp)
REVERT: A  823 ASN cc_start: 0.6462 (t0) cc_final: 0.6064 (t0)
REVERT: A 1132 LYS cc_start: 0.6425 (mmtt) cc_final: 0.6151 (ptmt)
REVERT: A 1177 ARG cc_start: 0.7431 (mtm180) cc_final: 0.7151 (mmt-90)
REVERT: A 1350 GLU cc_start: 0.8365 (tp30) cc_final: 0.8053 (tp30)
  outliers start: 5
  outliers final: 2
  residues processed: 90
  average time/residue: 0.1097
  time to fit residues: 13.7394
Evaluate side-chains
  84 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  653 ASP
Chi-restraints excluded: chain A residue  777 ASP
Chi-restraints excluded: chain A residue  866 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 99 optimal weight:   50.0000
   chunk 77 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 85 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 87 optimal weight:    6.9990
   chunk 100 optimal weight:   50.0000
   overall best weight:    3.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 788 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.154325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.113702 restraints weight = 12416.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.37
r_work: 0.2904 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11026  Z= 0.217
  Angle     :  0.654   8.966  15541  Z= 0.361
  Chirality :  0.048   0.276   1787
  Planarity :  0.006   0.073   1443
  Dihedral  : 23.345 178.343   2924
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  8.45 %
    Favored  : 90.09 %
  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:  0.67 (0.28), residues: 914
  helix:  1.41 (0.25), residues: 438
  sheet:  0.53 (0.51), residues: 99
  loop : -0.71 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1022 
 TYR   0.017   0.002   TYR A1174 
 PHE   0.029   0.003   PHE A1371 
 TRP   0.008   0.002   TRP A 552 
 HIS   0.006   0.002   HIS A1006 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00480 /  0.22 (11011)
  covalent geometry    : angle       0.65082 /  0.36 (15533)
  hydrogen bonds       : bond        0.06171 /  4.23 (  497)
  hydrogen bonds       : angle       3.99111 /  2.76 ( 1331)
  metal coordination   : bond        0.01437 /  0.60 (   15)
  metal coordination   : angle       2.88476 /  1.02 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8633 (mmm) cc_final: 0.8378 (mtp)
REVERT: A  777 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8484 (p0)
REVERT: A  810 MET cc_start: 0.8013 (mtp) cc_final: 0.7717 (mtp)
REVERT: A  823 ASN cc_start: 0.6326 (t0) cc_final: 0.5999 (t0)
REVERT: A 1132 LYS cc_start: 0.6419 (mmtt) cc_final: 0.6131 (ptmt)
REVERT: A 1311 TYR cc_start: 0.8465 (m-80) cc_final: 0.8079 (m-80)
REVERT: A 1320 HIS cc_start: 0.7945 (p-80) cc_final: 0.7672 (p-80)
REVERT: A 1350 GLU cc_start: 0.8347 (tp30) cc_final: 0.7937 (tp30)
  outliers start: 12
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0864
  time to fit residues: 11.1934
Evaluate side-chains
  88 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  653 ASP
Chi-restraints excluded: chain A residue  777 ASP
Chi-restraints excluded: chain A residue  866 ARG
Chi-restraints excluded: chain A residue  892 THR
Chi-restraints excluded: chain A residue  976 GLN
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1299 SER
Chi-restraints excluded: chain A residue 1330 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:   40.0000
   chunk 26 optimal weight:    0.0970
   chunk 89 optimal weight:    0.5980
   chunk 21 optimal weight:   10.0000
   chunk 92 optimal weight:   20.0000
   overall best weight:    1.2782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 248 HIS
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.157364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.116962 restraints weight = 12479.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.40
r_work: 0.2952 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.864  11026  Z= 0.302
  Angle     :  0.551   8.211  15541  Z= 0.312
  Chirality :  0.042   0.267   1787
  Planarity :  0.004   0.040   1443
  Dihedral  : 23.286 179.753   2924
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  9.79 %
    Favored  : 89.72 %
  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:  0.93 (0.28), residues: 914
  helix:  1.75 (0.25), residues: 437
  sheet:  0.56 (0.51), residues: 99
  loop : -0.71 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1204 
 TYR   0.012   0.001   TYR A1194 
 PHE   0.018   0.002   PHE A1371 
 TRP   0.026   0.001   TRP A 552 
 HIS   0.003   0.001   HIS A1240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.13 (11011)
  covalent geometry    : angle       0.54779 /  0.31 (15533)
  hydrogen bonds       : bond        0.04764 /  3.25 (  497)
  hydrogen bonds       : angle       3.77795 /  2.61 ( 1331)
  metal coordination   : bond        0.22327 / 10.63 (   15)
  metal coordination   : angle       2.57873 /  0.95 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8613 (mmm) cc_final: 0.8332 (mtp)
REVERT: A  777 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8402 (p0)
REVERT: A  810 MET cc_start: 0.7981 (mtp) cc_final: 0.7642 (mtp)
REVERT: A 1132 LYS cc_start: 0.6371 (mmtt) cc_final: 0.6098 (ptmt)
REVERT: A 1311 TYR cc_start: 0.8391 (m-80) cc_final: 0.7818 (m-80)
REVERT: A 1320 HIS cc_start: 0.7867 (p-80) cc_final: 0.7621 (p-80)
REVERT: A 1350 GLU cc_start: 0.8352 (tp30) cc_final: 0.7967 (tp30)
  outliers start: 4
  outliers final: 2
  residues processed: 86
  average time/residue: 0.0829
  time to fit residues: 10.4775
Evaluate side-chains
  81 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  653 ASP
Chi-restraints excluded: chain A residue  777 ASP
Chi-restraints excluded: chain A residue  866 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 70 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0020
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 87 optimal weight:    6.9990
   chunk 92 optimal weight:   20.0000
   overall best weight:    3.1394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 278 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 = 0.3733 r_free = 0.3733 target = 0.154803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.114112 restraints weight = 12360.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.45
r_work: 0.2893 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11026  Z= 0.195
  Angle     :  0.621   8.599  15541  Z= 0.344
  Chirality :  0.046   0.266   1787
  Planarity :  0.005   0.062   1443
  Dihedral  : 23.333 178.567   2924
  Min Nonbonded Distance : 1.648

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.28 %
    Favored  : 88.86 %
  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:  0.70 (0.28), residues: 914
  helix:  1.51 (0.25), residues: 437
  sheet:  0.39 (0.51), residues: 101
  loop : -0.73 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1022 
 TYR   0.014   0.002   TYR A1174 
 PHE   0.025   0.002   PHE A1371 
 TRP   0.011   0.001   TRP A 552 
 HIS   0.004   0.002   HIS A1313 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.19 (11011)
  covalent geometry    : angle       0.61767 /  0.34 (15533)
  hydrogen bonds       : bond        0.05759 /  3.94 (  497)
  hydrogen bonds       : angle       3.90643 /  2.71 ( 1331)
  metal coordination   : bond        0.01818 /  0.82 (   15)
  metal coordination   : angle       2.90038 /  1.05 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8638 (mmm) cc_final: 0.8416 (mtp)
REVERT: A  810 MET cc_start: 0.8023 (mtp) cc_final: 0.7728 (mtp)
REVERT: A 1132 LYS cc_start: 0.6415 (mmtt) cc_final: 0.6130 (ptmt)
REVERT: A 1320 HIS cc_start: 0.7879 (p-80) cc_final: 0.7626 (p-80)
REVERT: A 1321 LEU cc_start: 0.8045 (tp) cc_final: 0.7304 (mp)
REVERT: A 1350 GLU cc_start: 0.8423 (tp30) cc_final: 0.8009 (tp30)
  outliers start: 7
  outliers final: 4
  residues processed: 84
  average time/residue: 0.0976
  time to fit residues: 11.5503
Evaluate side-chains
  80 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  653 ASP
Chi-restraints excluded: chain A residue  866 ARG
Chi-restraints excluded: chain A residue  976 GLN
Chi-restraints excluded: chain A residue 1330 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 102 optimal weight:   20.0000
   chunk 41 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 83 optimal weight:    9.9990
   chunk 98 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 278 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 = 0.3751 r_free = 0.3751 target = 0.156406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.116155 restraints weight = 12389.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.45
r_work: 0.2912 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11026  Z= 0.143
  Angle     :  0.566   7.802  15541  Z= 0.318
  Chirality :  0.043   0.265   1787
  Planarity :  0.005   0.043   1443
  Dihedral  : 23.331 179.149   2924
  Min Nonbonded Distance : 1.747

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.26 %
    Favored  : 88.25 %
  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:  0.81 (0.28), residues: 914
  helix:  1.65 (0.25), residues: 437
  sheet:  0.33 (0.48), residues: 113
  loop : -0.75 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1204 
 TYR   0.012   0.001   TYR A1194 
 PHE   0.019   0.002   PHE A1371 
 TRP   0.016   0.001   TRP A 552 
 HIS   0.003   0.001   HIS A1006 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.14 (11011)
  covalent geometry    : angle       0.56293 /  0.32 (15533)
  hydrogen bonds       : bond        0.05009 /  3.42 (  497)
  hydrogen bonds       : angle       3.79723 /  2.63 ( 1331)
  metal coordination   : bond        0.01378 /  0.57 (   15)
  metal coordination   : angle       2.76815 /  1.01 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8633 (mmm) cc_final: 0.8413 (mtp)
REVERT: A  810 MET cc_start: 0.8009 (mtp) cc_final: 0.7693 (mtp)
REVERT: A 1132 LYS cc_start: 0.6401 (mmtt) cc_final: 0.6114 (ptmt)
REVERT: A 1320 HIS cc_start: 0.7895 (p-80) cc_final: 0.7674 (p-80)
REVERT: A 1321 LEU cc_start: 0.8091 (tp) cc_final: 0.7330 (mp)
REVERT: A 1350 GLU cc_start: 0.8400 (tp30) cc_final: 0.7996 (tp30)
  outliers start: 4
  outliers final: 2
  residues processed: 78
  average time/residue: 0.0976
  time to fit residues: 10.6971
Evaluate side-chains
  76 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  653 ASP
Chi-restraints excluded: chain A residue  866 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 69 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 94 optimal weight:   20.0000
   chunk 83 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 278 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 = 0.3776 r_free = 0.3776 target = 0.158683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.118445 restraints weight = 12371.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.49
r_work: 0.2966 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11026  Z= 0.116
  Angle     :  0.526   8.694  15541  Z= 0.298
  Chirality :  0.040   0.272   1787
  Planarity :  0.004   0.041   1443
  Dihedral  : 23.206 179.675   2924
  Min Nonbonded Distance : 1.754

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 11.38 %
    Favored  : 88.37 %
  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:  0.98 (0.28), residues: 914
  helix:  1.83 (0.25), residues: 444
  sheet:  0.43 (0.49), residues: 113
  loop : -0.77 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1204 
 TYR   0.009   0.001   TYR A1194 
 PHE   0.016   0.001   PHE A1329 
 TRP   0.017   0.001   TRP A 552 
 HIS   0.002   0.001   HIS A1170 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00204 /  0.12 (11011)
  covalent geometry    : angle       0.52362 /  0.30 (15533)
  hydrogen bonds       : bond        0.04372 /  2.99 (  497)
  hydrogen bonds       : angle       3.64215 /  2.52 ( 1331)
  metal coordination   : bond        0.00985 /  0.40 (   15)
  metal coordination   : angle       2.19788 /  0.77 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8609 (mmm) cc_final: 0.8314 (mtp)
REVERT: A  810 MET cc_start: 0.8000 (mtp) cc_final: 0.7651 (mtp)
REVERT: A 1132 LYS cc_start: 0.6424 (mmtt) cc_final: 0.6138 (ptmt)
REVERT: A 1350 GLU cc_start: 0.8425 (tp30) cc_final: 0.8029 (tp30)
  outliers start: 2
  outliers final: 2
  residues processed: 80
  average time/residue: 0.0929
  time to fit residues: 10.7949
Evaluate side-chains
  75 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  653 ASP
Chi-restraints excluded: chain A residue  866 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 31 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 100 optimal weight:   50.0000
   overall best weight:    1.2782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 278 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 = 0.3770 r_free = 0.3770 target = 0.158117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.117642 restraints weight = 12333.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.51
r_work: 0.2949 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11026  Z= 0.121
  Angle     :  0.536   8.207  15541  Z= 0.301
  Chirality :  0.041   0.271   1787
  Planarity :  0.004   0.040   1443
  Dihedral  : 23.164 178.935   2924
  Min Nonbonded Distance : 1.731

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 11.51 %
    Favored  : 88.25 %
  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:  1.07 (0.29), residues: 914
  helix:  1.89 (0.25), residues: 443
  sheet:  0.47 (0.49), residues: 113
  loop : -0.72 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1204 
 TYR   0.009   0.001   TYR A1194 
 PHE   0.018   0.001   PHE A1371 
 TRP   0.014   0.001   TRP A 552 
 HIS   0.005   0.001   HIS A1320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.12 (11011)
  covalent geometry    : angle       0.53325 /  0.30 (15533)
  hydrogen bonds       : bond        0.04428 /  3.04 (  497)
  hydrogen bonds       : angle       3.64198 /  2.53 ( 1331)
  metal coordination   : bond        0.00997 /  0.42 (   15)
  metal coordination   : angle       2.28903 /  0.83 (    8)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  644 MET cc_start: 0.8589 (mmm) cc_final: 0.8332 (mtp)
REVERT: A  810 MET cc_start: 0.7986 (mtp) cc_final: 0.7631 (mtp)
REVERT: A 1132 LYS cc_start: 0.6440 (mmtt) cc_final: 0.6106 (ptmt)
REVERT: A 1320 HIS cc_start: 0.7965 (p-80) cc_final: 0.7691 (p-80)
REVERT: A 1321 LEU cc_start: 0.8024 (tt) cc_final: 0.7646 (pp)
REVERT: A 1350 GLU cc_start: 0.8402 (tp30) cc_final: 0.7991 (tp30)
  outliers start: 2
  outliers final: 2
  residues processed: 79
  average time/residue: 0.0884
  time to fit residues: 10.1180
Evaluate side-chains
  80 residues out of total 817 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  653 ASP
Chi-restraints excluded: chain A residue  866 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 53 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 97 optimal weight:   30.0000
   chunk 91 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 278 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 = 0.3791 r_free = 0.3791 target = 0.159874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.120008 restraints weight = 12374.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.58
r_work: 0.2952 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11026  Z= 0.108
  Angle     :  0.516   8.918  15541  Z= 0.290
  Chirality :  0.040   0.273   1787
  Planarity :  0.004   0.040   1443
  Dihedral  : 23.048 178.618   2924
  Min Nonbonded Distance : 1.737

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 11.38 %
    Favored  : 88.25 %
  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:  1.16 (0.29), residues: 914
  helix:  2.01 (0.25), residues: 443
  sheet:  0.56 (0.50), residues: 113
  loop : -0.74 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1204 
 TYR   0.012   0.001   TYR A1311 
 PHE   0.032   0.001   PHE A 549 
 TRP   0.019   0.001   TRP A 552 
 HIS   0.005   0.001   HIS A1320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00186 /  0.11 (11011)
  covalent geometry    : angle       0.51396 /  0.29 (15533)
  hydrogen bonds       : bond        0.04046 /  2.78 (  497)
  hydrogen bonds       : angle       3.55255 /  2.46 ( 1331)
  metal coordination   : bond        0.00847 /  0.35 (   15)
  metal coordination   : angle       2.07309 /  0.73 (    8)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1981.04 seconds
wall clock time: 34 minutes 38.30 seconds (2078.30 seconds total)