Starting phenix.real_space_refine
on Sat Aug 23 05:41:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jqh_36572/08_2025/8jqh_36572_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jqh_36572/08_2025/8jqh_36572.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jqh_36572/08_2025/8jqh_36572.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jqh_36572/08_2025/8jqh_36572.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jqh_36572/08_2025/8jqh_36572_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jqh_36572/08_2025/8jqh_36572_neut.cif"
  }
  resolution = 4.2
  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=   0.002 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    6299      2.51       5
     N    1710      2.21       5
     O    1862      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9920
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1206, 9920
          Classifications: {'peptide': 1206}
          Link IDs: {'PTRANS': 53, 'TRANS': 1152}
          Chain breaks: 4
  Time building chain proxies: 1.96, per 1000 atoms: 0.20
  Number of scatterers: 9920
  At special positions: 0
  Unit cell: (96.8, 101.2, 118.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1862      8.00
     N    1710      7.00
     C    6299      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: 0.74
  Conformation dependent library (CDL) restraints added in 305.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2314

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 17 sheets defined
      36.5% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 25
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 3.686A  pdb=" N   GLU A  83 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 90
      removed outlier: 3.532A  pdb=" N   VAL A  88 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 115 through 136
    Processing helix  chain 'A' and resid 137 through 154
    Processing helix  chain 'A' and resid 163 through 173
      Proline residue:  A 171  - end of helix
    Processing helix  chain 'A' and resid 179 through 191
    Processing helix  chain 'A' and resid 199 through 214
    Processing helix  chain 'A' and resid 217 through 223
      removed outlier: 4.263A  pdb=" N   PHE A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.690A  pdb=" N   ILE A 229 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 253
    Processing helix  chain 'A' and resid 257 through 260
    Processing helix  chain 'A' and resid 261 through 274
      removed outlier: 3.641A  pdb=" N   VAL A 265 " --> pdb=" O   ASP A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
    Processing helix  chain 'A' and resid 296 through 300
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 3.980A  pdb=" N   TYR A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 393
    Processing helix  chain 'A' and resid 410 through 425
    Processing helix  chain 'A' and resid 426 through 429
    Processing helix  chain 'A' and resid 443 through 448
      removed outlier: 3.778A  pdb=" N   ARG A 448 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 513
    Processing helix  chain 'A' and resid 539 through 550
    Processing helix  chain 'A' and resid 609 through 620
      removed outlier: 4.004A  pdb=" N   GLN A 615 " --> pdb=" O   TYR A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 644
    Processing helix  chain 'A' and resid 652 through 663
    Processing helix  chain 'A' and resid 712 through 721
    Processing helix  chain 'A' and resid 736 through 743
    Processing helix  chain 'A' and resid 830 through 843
    Processing helix  chain 'A' and resid 892 through 909
    Processing helix  chain 'A' and resid 927 through 932
    Processing helix  chain 'A' and resid 960 through 970
    Processing helix  chain 'A' and resid 970 through 981
      removed outlier: 3.798A  pdb=" N   LEU A 974 " --> pdb=" O   LYS A 970 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LYS A 980 " --> pdb=" O   LYS A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1005
    Processing helix  chain 'A' and resid 1018 through 1034
      removed outlier: 3.919A  pdb=" N   LEU A1030 " --> pdb=" O   ALA A1026 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ASN A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   GLY A1032 " --> pdb=" O   PHE A1028 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR A1034 " --> pdb=" O   LEU A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1045
      removed outlier: 3.670A  pdb=" N   ARG A1044 " --> pdb=" O   PRO A1040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1156 through 1158
      No H-bonds generated for 'chain 'A' and resid 1156 through 1158'
    Processing helix  chain 'A' and resid 1190 through 1217
      removed outlier: 3.905A  pdb=" N   ARG A1204 " --> pdb=" O   CYS A1200 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   GLU A1209 " --> pdb=" O   ARG A1205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1230 through 1253
      removed outlier: 3.901A  pdb=" N   GLU A1234 " --> pdb=" O   ALA A1230 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63
      removed outlier: 4.289A  pdb=" N   SER A 110 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU A  72 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AA3, first strand: chain 'A' and resid 380 through 381
      removed outlier: 3.815A  pdb=" N   GLU A 357 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   VAL A1010 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   SER A 325 " --> pdb=" O   VAL A1010 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU A 982 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LYS A 938 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   SER A 957 " --> pdb=" O   LYS A 938 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 454
      removed outlier: 3.726A  pdb=" N   ILE A 356 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLU A 357 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 854
      removed outlier: 6.123A  pdb=" N   PHE A 505 " --> pdb=" O   ARG A 850 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ILE A 852 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A 503 " --> pdb=" O   ILE A 852 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   TYR A 495 " --> pdb=" O   SER A 506 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASP A 508 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   ARG A 493 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   GLU A 887 " --> pdb=" O   TRP A 484 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   VAL A 873 " --> pdb=" O   ALA A 863 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 565
    Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565
      removed outlier: 3.978A  pdb=" N   TYR A 573 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 648
      removed outlier: 4.862A  pdb=" N   ALA A 668 " --> pdb=" O   ARG A 685 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 648
    Processing sheet with id=AB1, first strand: chain 'A' and resid 695 through 698
    Processing sheet with id=AB2, first strand: chain 'A' and resid 724 through 726
      removed outlier: 3.817A  pdb=" N   TYR A 726 " --> pdb=" O   MET A 729 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 774 through 776
    Processing sheet with id=AB4, first strand: chain 'A' and resid 797 through 801
      removed outlier: 3.960A  pdb=" N   VAL A 799 " --> pdb=" O   LYS A 808 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LYS A 808 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
      removed outlier: 5.216A  pdb=" N   GLY A 809 " --> pdb=" O   GLN A 816 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1061 through 1065
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1067 through 1071
      removed outlier: 6.602A  pdb=" N   VAL A1067 " --> pdb=" O   PHE A1183 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   PHE A1183 " --> pdb=" O   VAL A1067 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLY A1069 " --> pdb=" O   LEU A1181 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   ALA A1178 " --> pdb=" O   LEU A1167 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1097 through 1100
      removed outlier: 6.633A  pdb=" N   VAL A1136 " --> pdb=" O   LEU A1148 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1097 through 1100

    427 hydrogen bonds defined for protein.
    1158 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: 1.82

  Time building geometry restraints manager: 0.98 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: 1671
        1.31 -     1.44: 2764
        1.44 -     1.56: 5635
        1.56 -     1.69: 1
        1.69 -     1.81: 77
  Bond restraints: 10148
  Sorted by residual:
  bond pdb=" CA  ASN A1240 "
       pdb=" C   ASN A1240 "
    ideal  model  delta    sigma   weight residual
    1.524  1.435  0.089 1.26e-02 6.30e+03 5.01e+01
  bond pdb=" CA  LEU A1244 "
       pdb=" C   LEU A1244 "
    ideal  model  delta    sigma   weight residual
    1.524  1.440  0.084 1.24e-02 6.50e+03 4.60e+01
  bond pdb=" CA  GLU A 642 "
       pdb=" C   GLU A 642 "
    ideal  model  delta    sigma   weight residual
    1.523  1.450  0.073 1.34e-02 5.57e+03 3.00e+01
  bond pdb=" CA  TYR A 743 "
       pdb=" C   TYR A 743 "
    ideal  model  delta    sigma   weight residual
    1.524  1.445  0.079 1.48e-02 4.57e+03 2.86e+01
  bond pdb=" CA  LEU A1242 "
       pdb=" C   LEU A1242 "
    ideal  model  delta    sigma   weight residual
    1.525  1.458  0.067 1.29e-02 6.01e+03 2.73e+01
  ... (remaining 10143 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.69: 13542
        3.69 -     7.39: 130
        7.39 -    11.08: 18
       11.08 -    14.78: 3
       14.78 -    18.47: 1
  Bond angle restraints: 13694
  Sorted by residual:
  angle pdb=" N   ASN A 744 "
        pdb=" CA  ASN A 744 "
        pdb=" C   ASN A 744 "
      ideal   model   delta    sigma   weight residual
     111.71   99.80   11.91 1.15e+00 7.56e-01 1.07e+02
  angle pdb=" N   LYS A1233 "
        pdb=" CA  LYS A1233 "
        pdb=" C   LYS A1233 "
      ideal   model   delta    sigma   weight residual
     110.97  100.41   10.56 1.09e+00 8.42e-01 9.38e+01
  angle pdb=" N   GLU A1247 "
        pdb=" CA  GLU A1247 "
        pdb=" C   GLU A1247 "
      ideal   model   delta    sigma   weight residual
     113.20  101.57   11.63 1.21e+00 6.83e-01 9.24e+01
  angle pdb=" N   TYR A 743 "
        pdb=" CA  TYR A 743 "
        pdb=" C   TYR A 743 "
      ideal   model   delta    sigma   weight residual
     112.72  101.94   10.78 1.14e+00 7.69e-01 8.94e+01
  angle pdb=" N   HIS A 641 "
        pdb=" CA  HIS A 641 "
        pdb=" C   HIS A 641 "
      ideal   model   delta    sigma   weight residual
     111.75  102.04    9.71 1.28e+00 6.10e-01 5.75e+01
  ... (remaining 13689 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.60: 5520
       16.60 -    33.20: 511
       33.20 -    49.79: 117
       49.79 -    66.39: 16
       66.39 -    82.99: 11
  Dihedral angle restraints: 6175
    sinusoidal: 2610
      harmonic: 3565
  Sorted by residual:
  dihedral pdb=" CA  THR A 983 "
           pdb=" C   THR A 983 "
           pdb=" N   ARG A 984 "
           pdb=" CA  ARG A 984 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.17   19.83     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  ALA A1230 "
           pdb=" C   ALA A1230 "
           pdb=" N   LEU A1231 "
           pdb=" CA  LEU A1231 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.97   18.03     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  GLN A1213 "
           pdb=" C   GLN A1213 "
           pdb=" N   LEU A1214 "
           pdb=" CA  LEU A1214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.23   17.77     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 6172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1339
       0.082 -    0.163: 113
       0.163 -    0.245: 6
       0.245 -    0.326: 1
       0.326 -    0.408: 1
  Chirality restraints: 1460
  Sorted by residual:
  chirality pdb=" CA  LEU A1242 "
            pdb=" N   LEU A1242 "
            pdb=" C   LEU A1242 "
            pdb=" CB  LEU A1242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.16e+00
  chirality pdb=" CB  VAL A1237 "
            pdb=" CA  VAL A1237 "
            pdb=" CG1 VAL A1237 "
            pdb=" CG2 VAL A1237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  VAL A1232 "
            pdb=" N   VAL A1232 "
            pdb=" C   VAL A1232 "
            pdb=" CB  VAL A1232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1457 not shown)

  Planarity restraints: 1770
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 882 "   -0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   GLY A 882 "    0.058 2.00e-02 2.50e+03
        pdb=" O   GLY A 882 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP A 883 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 734 "    0.015 2.00e-02 2.50e+03   2.88e-02 8.27e+00
        pdb=" C   PRO A 734 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   PRO A 734 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 735 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A1243 "    0.014 2.00e-02 2.50e+03   2.75e-02 7.54e+00
        pdb=" C   GLN A1243 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   GLN A1243 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU A1244 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1767 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1089
        2.74 -     3.28: 11074
        3.28 -     3.82: 17583
        3.82 -     4.36: 21611
        4.36 -     4.90: 33641
  Nonbonded interactions: 84998
  Sorted by model distance:
  nonbonded pdb=" N   CYS A 624 "
            pdb=" O   PHE A 627 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OD1 ASP A 572 "
            pdb=" OG  SER A 590 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OE1 GLN A1022 "
            pdb=" NH2 ARG A1133 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" NE2 HIS A1150 "
            pdb=" O   ASN A1169 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   ARG A 164 "
            pdb=" N   LYS A 167 "
     model   vdw
     2.245 3.120
  ... (remaining 84993 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.02 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.560
  Find NCS groups from input model:        0.040
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   11.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.140  10148  Z= 0.375
  Angle     :  0.982  18.470  13694  Z= 0.626
  Chirality :  0.048   0.408   1460
  Planarity :  0.006   0.082   1770
  Dihedral  : 13.855  82.988   3861
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 31.35
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.43 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.64 %
    Favored  : 98.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.95 (0.24), residues: 1196
  helix: -0.77 (0.26), residues: 375
  sheet: -1.99 (0.30), residues: 240
  loop : -1.21 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 968 
 TYR   0.028   0.002   TYR A1036 
 PHE   0.026   0.002   PHE A 399 
 TRP   0.023   0.002   TRP A 322 
 HIS   0.007   0.001   HIS A1072 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 (10148)
  covalent geometry    : angle       0.98152 (13694)
  hydrogen bonds       : bond        0.17395 (  410)
  hydrogen bonds       : angle       8.29228 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8170 (tpt) cc_final: 0.7860 (tpp)
REVERT: A   49 THR cc_start: 0.9376 (p) cc_final: 0.9138 (t)
REVERT: A  306 TYR cc_start: 0.8068 (m-10) cc_final: 0.7792 (m-10)
REVERT: A  313 ASP cc_start: 0.8318 (m-30) cc_final: 0.7840 (m-30)
REVERT: A  348 CYS cc_start: 0.9046 (m) cc_final: 0.8594 (m)
REVERT: A  391 ASP cc_start: 0.8946 (t0) cc_final: 0.8144 (t0)
REVERT: A  481 LEU cc_start: 0.8674 (mt) cc_final: 0.7684 (mt)
REVERT: A  483 MET cc_start: 0.7530 (tmm) cc_final: 0.7299 (tmm)
REVERT: A  496 CYS cc_start: 0.9191 (m) cc_final: 0.8565 (m)
REVERT: A  507 ASP cc_start: 0.8252 (t0) cc_final: 0.7642 (t0)
REVERT: A  710 PHE cc_start: 0.8082 (m-10) cc_final: 0.7684 (m-10)
REVERT: A  825 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7504 (tm-30)
REVERT: A  938 LYS cc_start: 0.9216 (pttt) cc_final: 0.8847 (pptt)
REVERT: A  994 SER cc_start: 0.8861 (t) cc_final: 0.8347 (m)
REVERT: A 1027 LEU cc_start: 0.9689 (tp) cc_final: 0.9331 (tt)
REVERT: A 1036 TYR cc_start: 0.8433 (m-80) cc_final: 0.8201 (m-10)
REVERT: A 1088 GLU cc_start: 0.8103 (pp20) cc_final: 0.7519 (pp20)
REVERT: A 1107 ASN cc_start: 0.8782 (t0) cc_final: 0.8338 (t0)
REVERT: A 1202 GLN cc_start: 0.9532 (mt0) cc_final: 0.9263 (tt0)
REVERT: A 1205 ARG cc_start: 0.8978 (tmt170) cc_final: 0.8675 (tpt90)
REVERT: A 1245 TYR cc_start: 0.9099 (m-80) cc_final: 0.8873 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 264
  average time/residue: 0.0942
  time to fit residues: 34.1240
Evaluate side-chains
  191 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1238 ASN
A1241 GLN
A1243 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.098203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.074470 restraints weight = 34079.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.077129 restraints weight = 18731.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.078898 restraints weight = 12483.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.080062 restraints weight = 9435.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.080768 restraints weight = 7843.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3356
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10148  Z= 0.157
  Angle     :  0.683  16.332  13694  Z= 0.349
  Chirality :  0.043   0.198   1460
  Planarity :  0.005   0.048   1770
  Dihedral  :  5.069  18.928   1330
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.82 %
    Favored  : 95.00 %
  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 aren not related in a simple way.
  whole: -1.50 (0.24), residues: 1196
  helix: -0.15 (0.26), residues: 392
  sheet: -1.96 (0.29), residues: 239
  loop : -1.04 (0.27), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 784 
 TYR   0.016   0.002   TYR A 151 
 PHE   0.016   0.002   PHE A 228 
 TRP   0.017   0.002   TRP A 322 
 HIS   0.006   0.001   HIS A 797 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10148)
  covalent geometry    : angle       0.68303 (13694)
  hydrogen bonds       : bond        0.04592 (  410)
  hydrogen bonds       : angle       6.45289 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 246
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8572 (tpt) cc_final: 0.8020 (tpp)
REVERT: A   49 THR cc_start: 0.9478 (p) cc_final: 0.9165 (t)
REVERT: A  306 TYR cc_start: 0.8279 (m-10) cc_final: 0.7564 (m-10)
REVERT: A  313 ASP cc_start: 0.8362 (m-30) cc_final: 0.7920 (m-30)
REVERT: A  481 LEU cc_start: 0.8712 (mt) cc_final: 0.7750 (mt)
REVERT: A  496 CYS cc_start: 0.9269 (m) cc_final: 0.8724 (m)
REVERT: A  507 ASP cc_start: 0.8353 (t0) cc_final: 0.7901 (t70)
REVERT: A  661 MET cc_start: 0.9524 (mmp) cc_final: 0.9201 (mmm)
REVERT: A  671 ILE cc_start: 0.8991 (mt) cc_final: 0.8658 (tp)
REVERT: A  683 THR cc_start: 0.8700 (m) cc_final: 0.8428 (m)
REVERT: A  710 PHE cc_start: 0.8169 (m-10) cc_final: 0.7794 (m-10)
REVERT: A  729 MET cc_start: 0.8685 (tmm) cc_final: 0.8470 (tmm)
REVERT: A  825 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: A  841 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8445 (mt-10)
REVERT: A 1009 MET cc_start: 0.7903 (ttm) cc_final: 0.7288 (ttm)
REVERT: A 1015 GLN cc_start: 0.9030 (pm20) cc_final: 0.8588 (pm20)
REVERT: A 1027 LEU cc_start: 0.9720 (tp) cc_final: 0.9440 (tt)
REVERT: A 1088 GLU cc_start: 0.8356 (pp20) cc_final: 0.7807 (pp20)
REVERT: A 1104 VAL cc_start: 0.8365 (t) cc_final: 0.7994 (t)
REVERT: A 1107 ASN cc_start: 0.8776 (t0) cc_final: 0.8430 (t0)
REVERT: A 1184 CYS cc_start: 0.8923 (t) cc_final: 0.8712 (t)
REVERT: A 1202 GLN cc_start: 0.9498 (mt0) cc_final: 0.9255 (tt0)
REVERT: A 1205 ARG cc_start: 0.8958 (tmt170) cc_final: 0.8585 (tpt90)
REVERT: A 1212 ASN cc_start: 0.9266 (t0) cc_final: 0.9063 (t0)
REVERT: A 1228 ARG cc_start: 0.7120 (ptt180) cc_final: 0.6696 (pmt170)
REVERT: A 1245 TYR cc_start: 0.8942 (m-80) cc_final: 0.8522 (m-80)
REVERT: A 1250 ASN cc_start: 0.9245 (m110) cc_final: 0.9043 (m110)
  outliers start: 2
  outliers final: 0
  residues processed: 247
  average time/residue: 0.0870
  time to fit residues: 30.3375
Evaluate side-chains
  180 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0570
   chunk 94 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0670
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.100674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.076813 restraints weight = 33538.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.079580 restraints weight = 18035.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.081387 restraints weight = 11809.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.082544 restraints weight = 8842.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.083435 restraints weight = 7323.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
r_final: 0.3399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10148  Z= 0.121
  Angle     :  0.612  10.199  13694  Z= 0.315
  Chirality :  0.042   0.166   1460
  Planarity :  0.004   0.050   1770
  Dihedral  :  4.859  18.350   1330
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.18 %
    Favored  : 96.63 %
  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 aren not related in a simple way.
  whole: -1.23 (0.24), residues: 1196
  helix:  0.22 (0.26), residues: 386
  sheet: -1.76 (0.30), residues: 235
  loop : -1.02 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1204 
 TYR   0.014   0.001   TYR A 206 
 PHE   0.013   0.001   PHE A 874 
 TRP   0.012   0.001   TRP A  54 
 HIS   0.009   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10148)
  covalent geometry    : angle       0.61209 (13694)
  hydrogen bonds       : bond        0.03982 (  410)
  hydrogen bonds       : angle       6.03877 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 236
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7940 (tpp)
REVERT: A   49 THR cc_start: 0.9352 (p) cc_final: 0.9042 (t)
REVERT: A   59 ASP cc_start: 0.8722 (p0) cc_final: 0.8297 (p0)
REVERT: A   71 LYS cc_start: 0.8921 (mptt) cc_final: 0.8537 (mptt)
REVERT: A  216 SER cc_start: 0.9202 (m) cc_final: 0.8707 (p)
REVERT: A  306 TYR cc_start: 0.8232 (m-10) cc_final: 0.7612 (m-10)
REVERT: A  313 ASP cc_start: 0.8430 (m-30) cc_final: 0.7930 (m-30)
REVERT: A  454 LYS cc_start: 0.9261 (tmmt) cc_final: 0.8681 (ttpp)
REVERT: A  481 LEU cc_start: 0.8599 (mt) cc_final: 0.7730 (mt)
REVERT: A  496 CYS cc_start: 0.9257 (m) cc_final: 0.8698 (m)
REVERT: A  507 ASP cc_start: 0.8505 (t0) cc_final: 0.7998 (t70)
REVERT: A  661 MET cc_start: 0.9499 (mmp) cc_final: 0.9187 (mmm)
REVERT: A  683 THR cc_start: 0.8658 (m) cc_final: 0.8329 (m)
REVERT: A  710 PHE cc_start: 0.8444 (m-10) cc_final: 0.8107 (m-10)
REVERT: A  729 MET cc_start: 0.8743 (tmm) cc_final: 0.8150 (tmm)
REVERT: A  825 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7763 (tm-30)
REVERT: A  841 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8437 (mt-10)
REVERT: A  984 ARG cc_start: 0.9013 (mmm-85) cc_final: 0.8297 (mmm-85)
REVERT: A  993 ASP cc_start: 0.8905 (p0) cc_final: 0.8605 (p0)
REVERT: A 1009 MET cc_start: 0.7934 (ttm) cc_final: 0.7193 (ttm)
REVERT: A 1015 GLN cc_start: 0.9016 (pm20) cc_final: 0.8621 (pm20)
REVERT: A 1027 LEU cc_start: 0.9756 (tp) cc_final: 0.9513 (tt)
REVERT: A 1104 VAL cc_start: 0.8271 (t) cc_final: 0.8004 (t)
REVERT: A 1107 ASN cc_start: 0.8694 (t0) cc_final: 0.8316 (t0)
REVERT: A 1138 GLU cc_start: 0.8070 (pp20) cc_final: 0.7654 (pp20)
REVERT: A 1184 CYS cc_start: 0.8838 (t) cc_final: 0.8615 (t)
REVERT: A 1212 ASN cc_start: 0.9222 (t0) cc_final: 0.9008 (t0)
REVERT: A 1228 ARG cc_start: 0.6975 (ptt180) cc_final: 0.6320 (ptt90)
REVERT: A 1240 ASN cc_start: 0.9673 (t0) cc_final: 0.9311 (m110)
REVERT: A 1244 LEU cc_start: 0.9203 (tt) cc_final: 0.8837 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0910
  time to fit residues: 30.2961
Evaluate side-chains
  181 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0060
   chunk 9 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 110 optimal weight:    3.9990
   chunk 88 optimal weight:    9.9990
   chunk 83 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    2.9202

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1243 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.094120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.069972 restraints weight = 34820.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.072438 restraints weight = 18993.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.074085 restraints weight = 12703.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.075172 restraints weight = 9694.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.075897 restraints weight = 8120.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3252
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
r_final: 0.3252
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10148  Z= 0.224
  Angle     :  0.682  10.207  13694  Z= 0.355
  Chirality :  0.044   0.182   1460
  Planarity :  0.005   0.102   1770
  Dihedral  :  4.938  17.147   1330
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.28 %
    Favored  : 95.63 %
  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 aren not related in a simple way.
  whole: -1.17 (0.24), residues: 1196
  helix:  0.26 (0.26), residues: 387
  sheet: -1.80 (0.30), residues: 235
  loop : -0.94 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1204 
 TYR   0.017   0.002   TYR A 617 
 PHE   0.020   0.002   PHE A 425 
 TRP   0.011   0.002   TRP A 122 
 HIS   0.009   0.002   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (10148)
  covalent geometry    : angle       0.68209 (13694)
  hydrogen bonds       : bond        0.04097 (  410)
  hydrogen bonds       : angle       6.06633 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9494 (p) cc_final: 0.9238 (t)
REVERT: A   59 ASP cc_start: 0.8755 (p0) cc_final: 0.8209 (p0)
REVERT: A  216 SER cc_start: 0.9345 (m) cc_final: 0.9048 (t)
REVERT: A  311 MET cc_start: 0.8860 (tpp) cc_final: 0.8583 (tpp)
REVERT: A  313 ASP cc_start: 0.8706 (m-30) cc_final: 0.8295 (m-30)
REVERT: A  343 GLU cc_start: 0.8869 (tp30) cc_final: 0.8658 (mm-30)
REVERT: A  481 LEU cc_start: 0.8913 (mt) cc_final: 0.8108 (mt)
REVERT: A  496 CYS cc_start: 0.9314 (m) cc_final: 0.8823 (m)
REVERT: A  507 ASP cc_start: 0.8640 (t0) cc_final: 0.8162 (t70)
REVERT: A  617 TYR cc_start: 0.8737 (m-80) cc_final: 0.8349 (m-80)
REVERT: A  661 MET cc_start: 0.9482 (mmp) cc_final: 0.9257 (mmm)
REVERT: A  710 PHE cc_start: 0.8365 (m-10) cc_final: 0.8081 (m-10)
REVERT: A  729 MET cc_start: 0.8583 (tmm) cc_final: 0.8130 (tmm)
REVERT: A  825 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: A  841 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8671 (mt-10)
REVERT: A  887 GLU cc_start: 0.7813 (mp0) cc_final: 0.7568 (mp0)
REVERT: A  993 ASP cc_start: 0.9095 (p0) cc_final: 0.8817 (p0)
REVERT: A 1009 MET cc_start: 0.8233 (ttm) cc_final: 0.7615 (ttm)
REVERT: A 1021 MET cc_start: 0.9605 (tpp) cc_final: 0.8685 (tpp)
REVERT: A 1043 MET cc_start: 0.8992 (mmp) cc_final: 0.8580 (mmp)
REVERT: A 1107 ASN cc_start: 0.8911 (t0) cc_final: 0.8535 (t0)
REVERT: A 1122 PHE cc_start: 0.8557 (m-80) cc_final: 0.8116 (m-80)
REVERT: A 1138 GLU cc_start: 0.7979 (pp20) cc_final: 0.7673 (pp20)
REVERT: A 1206 ARG cc_start: 0.8763 (tpp-160) cc_final: 0.8551 (tpp-160)
REVERT: A 1212 ASN cc_start: 0.9202 (t0) cc_final: 0.8993 (t0)
REVERT: A 1240 ASN cc_start: 0.9646 (t0) cc_final: 0.9166 (m110)
REVERT: A 1244 LEU cc_start: 0.9255 (tt) cc_final: 0.8907 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.0884
  time to fit residues: 24.8788
Evaluate side-chains
  157 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0980
   chunk 66 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    7.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 130 HIS
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 HIS
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1097 ASN
** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1241 GLN
A1250 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.095088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.071061 restraints weight = 34178.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.073624 restraints weight = 18397.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.075341 restraints weight = 12188.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.076495 restraints weight = 9226.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.077193 restraints weight = 7649.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3297
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3297 r_free = 0.3297    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
r_final: 0.3296
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10148  Z= 0.137
  Angle     :  0.602   9.285  13694  Z= 0.318
  Chirality :  0.043   0.240   1460
  Planarity :  0.004   0.057   1770
  Dihedral  :  4.786  16.781   1330
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.91 %
    Favored  : 96.91 %
  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 aren not related in a simple way.
  whole: -1.07 (0.24), residues: 1196
  helix:  0.38 (0.27), residues: 387
  sheet: -1.82 (0.30), residues: 220
  loop : -0.91 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 984 
 TYR   0.019   0.002   TYR A 371 
 PHE   0.013   0.001   PHE A 421 
 TRP   0.031   0.002   TRP A 361 
 HIS   0.006   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10148)
  covalent geometry    : angle       0.60208 (13694)
  hydrogen bonds       : bond        0.03855 (  410)
  hydrogen bonds       : angle       5.74768 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 202
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 THR cc_start: 0.9385 (p) cc_final: 0.9139 (t)
REVERT: A   59 ASP cc_start: 0.8734 (p0) cc_final: 0.8275 (p0)
REVERT: A  210 MET cc_start: 0.8872 (mmt) cc_final: 0.8624 (mtt)
REVERT: A  216 SER cc_start: 0.9307 (m) cc_final: 0.8805 (p)
REVERT: A  311 MET cc_start: 0.8863 (tpp) cc_final: 0.8575 (tpp)
REVERT: A  313 ASP cc_start: 0.8781 (m-30) cc_final: 0.8384 (m-30)
REVERT: A  406 GLU cc_start: 0.7400 (tt0) cc_final: 0.7139 (tt0)
REVERT: A  481 LEU cc_start: 0.8838 (mt) cc_final: 0.8149 (mt)
REVERT: A  496 CYS cc_start: 0.9287 (m) cc_final: 0.8832 (m)
REVERT: A  507 ASP cc_start: 0.8830 (t0) cc_final: 0.8363 (t70)
REVERT: A  509 ILE cc_start: 0.8882 (mt) cc_final: 0.8672 (mt)
REVERT: A  661 MET cc_start: 0.9488 (mmp) cc_final: 0.9258 (mmm)
REVERT: A  710 PHE cc_start: 0.8411 (m-10) cc_final: 0.7999 (m-10)
REVERT: A  729 MET cc_start: 0.8495 (tmm) cc_final: 0.8047 (tmm)
REVERT: A  825 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: A  841 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8648 (mt-10)
REVERT: A  954 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7786 (mm-30)
REVERT: A  993 ASP cc_start: 0.9145 (p0) cc_final: 0.8868 (p0)
REVERT: A 1009 MET cc_start: 0.7937 (ttm) cc_final: 0.7361 (ttm)
REVERT: A 1107 ASN cc_start: 0.8839 (t0) cc_final: 0.8431 (t0)
REVERT: A 1122 PHE cc_start: 0.8493 (m-80) cc_final: 0.8040 (m-80)
REVERT: A 1138 GLU cc_start: 0.7953 (pp20) cc_final: 0.7713 (pp20)
REVERT: A 1206 ARG cc_start: 0.8428 (tpp-160) cc_final: 0.8228 (tpp-160)
REVERT: A 1245 TYR cc_start: 0.8834 (m-80) cc_final: 0.8439 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0980
  time to fit residues: 27.3004
Evaluate side-chains
  166 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 58 optimal weight:   30.0000
   chunk 64 optimal weight:    8.9990
   chunk 99 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 117 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0370
   chunk 47 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    5.0066

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

Flipped N/Q/H residues before XYZ refinement:
A 131 GLN
A 135 ASN
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 260 GLN
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1097 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.087564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.063629 restraints weight = 36372.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.065853 restraints weight = 20226.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.067290 restraints weight = 13799.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.068287 restraints weight = 10765.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.068863 restraints weight = 9123.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.4694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  10148  Z= 0.347
  Angle     :  0.832  10.923  13694  Z= 0.436
  Chirality :  0.047   0.197   1460
  Planarity :  0.006   0.089   1770
  Dihedral  :  5.458  20.423   1330
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 22.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  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 aren not related in a simple way.
  whole: -1.65 (0.23), residues: 1196
  helix: -0.28 (0.25), residues: 380
  sheet: -1.89 (0.31), residues: 229
  loop : -1.21 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 784 
 TYR   0.022   0.003   TYR A1217 
 PHE   0.029   0.003   PHE A1142 
 TRP   0.041   0.003   TRP A1113 
 HIS   0.012   0.003   HIS A1150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00730 (10148)
  covalent geometry    : angle       0.83222 (13694)
  hydrogen bonds       : bond        0.04767 (  410)
  hydrogen bonds       : angle       6.53104 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8389 (tmm) cc_final: 0.7854 (tmm)
REVERT: A   59 ASP cc_start: 0.8888 (p0) cc_final: 0.8531 (p0)
REVERT: A  216 SER cc_start: 0.9478 (m) cc_final: 0.9200 (t)
REVERT: A  343 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8867 (mm-30)
REVERT: A  357 GLU cc_start: 0.6991 (tt0) cc_final: 0.6765 (tt0)
REVERT: A  382 PHE cc_start: 0.8853 (t80) cc_final: 0.8363 (t80)
REVERT: A  417 MET cc_start: 0.9395 (mmm) cc_final: 0.9106 (mmm)
REVERT: A  507 ASP cc_start: 0.8946 (t0) cc_final: 0.8602 (t0)
REVERT: A  509 ILE cc_start: 0.8717 (mt) cc_final: 0.8506 (mt)
REVERT: A  532 TRP cc_start: 0.8079 (m-90) cc_final: 0.7688 (m100)
REVERT: A  659 MET cc_start: 0.9270 (ptm) cc_final: 0.9003 (ptm)
REVERT: A  661 MET cc_start: 0.9548 (mmp) cc_final: 0.9270 (mmm)
REVERT: A  710 PHE cc_start: 0.8540 (m-10) cc_final: 0.8309 (m-10)
REVERT: A  725 LEU cc_start: 0.9473 (tp) cc_final: 0.9184 (tp)
REVERT: A  729 MET cc_start: 0.8716 (tmm) cc_final: 0.8334 (tmm)
REVERT: A  841 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8724 (mt-10)
REVERT: A  887 GLU cc_start: 0.7694 (mp0) cc_final: 0.7404 (mp0)
REVERT: A  993 ASP cc_start: 0.9241 (p0) cc_final: 0.8981 (p0)
REVERT: A 1009 MET cc_start: 0.8476 (ttm) cc_final: 0.7896 (ttm)
REVERT: A 1012 LEU cc_start: 0.9364 (mt) cc_final: 0.9052 (mt)
REVERT: A 1021 MET cc_start: 0.9597 (tpp) cc_final: 0.8812 (tpp)
REVERT: A 1107 ASN cc_start: 0.9144 (t0) cc_final: 0.8797 (t0)
REVERT: A 1206 ARG cc_start: 0.8580 (tpp-160) cc_final: 0.8374 (tpp-160)
REVERT: A 1228 ARG cc_start: 0.6462 (ptt180) cc_final: 0.5850 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.0978
  time to fit residues: 21.9871
Evaluate side-chains
  124 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 109 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   chunk 106 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0670
   overall best weight:    0.7722

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

Flipped N/Q/H residues before XYZ refinement:
** A  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 ASN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** 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 = 0.3609 r_free = 0.3609 target = 0.094100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.070202 restraints weight = 33758.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.072720 restraints weight = 18100.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.074382 restraints weight = 12041.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.075479 restraints weight = 9144.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.076014 restraints weight = 7623.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       35 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.4707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10148  Z= 0.129
  Angle     :  0.632   7.928  13694  Z= 0.332
  Chirality :  0.044   0.176   1460
  Planarity :  0.004   0.045   1770
  Dihedral  :  5.054  21.974   1330
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.24), residues: 1196
  helix:  0.24 (0.26), residues: 380
  sheet: -1.79 (0.31), residues: 222
  loop : -0.96 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 984 
 TYR   0.016   0.001   TYR A1217 
 PHE   0.017   0.001   PHE A 561 
 TRP   0.012   0.001   TRP A 361 
 HIS   0.006   0.001   HIS A 797 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10148)
  covalent geometry    : angle       0.63233 (13694)
  hydrogen bonds       : bond        0.03981 (  410)
  hydrogen bonds       : angle       5.74980 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 VAL cc_start: 0.9232 (m) cc_final: 0.9014 (p)
REVERT: A   47 MET cc_start: 0.8342 (tmm) cc_final: 0.7889 (tmm)
REVERT: A   59 ASP cc_start: 0.8985 (p0) cc_final: 0.8615 (p0)
REVERT: A  210 MET cc_start: 0.8890 (mmm) cc_final: 0.8235 (mtt)
REVERT: A  406 GLU cc_start: 0.7344 (tt0) cc_final: 0.6894 (tt0)
REVERT: A  507 ASP cc_start: 0.8889 (t0) cc_final: 0.8647 (t0)
REVERT: A  509 ILE cc_start: 0.8872 (mt) cc_final: 0.8669 (mt)
REVERT: A  661 MET cc_start: 0.9509 (mmp) cc_final: 0.9219 (mmm)
REVERT: A  710 PHE cc_start: 0.8368 (m-10) cc_final: 0.8111 (m-10)
REVERT: A  728 LYS cc_start: 0.9352 (mmtp) cc_final: 0.9042 (mmmt)
REVERT: A  825 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7627 (tm-30)
REVERT: A  841 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8656 (mt-10)
REVERT: A  964 ASP cc_start: 0.9229 (t0) cc_final: 0.8919 (t0)
REVERT: A  974 LEU cc_start: 0.9589 (tt) cc_final: 0.9177 (tt)
REVERT: A  993 ASP cc_start: 0.9146 (p0) cc_final: 0.8907 (p0)
REVERT: A 1009 MET cc_start: 0.7966 (ttm) cc_final: 0.7112 (ttm)
REVERT: A 1086 GLU cc_start: 0.8305 (tt0) cc_final: 0.8064 (tt0)
REVERT: A 1107 ASN cc_start: 0.9076 (t0) cc_final: 0.8580 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1047
  time to fit residues: 26.1079
Evaluate side-chains
  140 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 57 optimal weight:    0.4980
   chunk 27 optimal weight:    6.9990
   chunk 105 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 90 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   chunk 115 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.093465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.069193 restraints weight = 34264.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.071644 restraints weight = 18813.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.073308 restraints weight = 12637.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.074380 restraints weight = 9712.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.074902 restraints weight = 8155.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10148  Z= 0.137
  Angle     :  0.639   7.953  13694  Z= 0.334
  Chirality :  0.043   0.180   1460
  Planarity :  0.004   0.043   1770
  Dihedral  :  4.941  18.113   1330
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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 aren not related in a simple way.
  whole: -1.14 (0.24), residues: 1196
  helix:  0.25 (0.26), residues: 383
  sheet: -1.66 (0.33), residues: 211
  loop : -1.01 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 587 
 TYR   0.019   0.002   TYR A1217 
 PHE   0.013   0.001   PHE A 561 
 TRP   0.053   0.002   TRP A 361 
 HIS   0.005   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10148)
  covalent geometry    : angle       0.63945 (13694)
  hydrogen bonds       : bond        0.03815 (  410)
  hydrogen bonds       : angle       5.70640 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8269 (tmm) cc_final: 0.7549 (tmm)
REVERT: A   59 ASP cc_start: 0.9021 (p0) cc_final: 0.8678 (p0)
REVERT: A  210 MET cc_start: 0.8871 (mmm) cc_final: 0.8582 (mmm)
REVERT: A  496 CYS cc_start: 0.9278 (m) cc_final: 0.8799 (m)
REVERT: A  661 MET cc_start: 0.9554 (mmp) cc_final: 0.9268 (mmm)
REVERT: A  710 PHE cc_start: 0.8399 (m-10) cc_final: 0.8104 (m-10)
REVERT: A  784 ARG cc_start: 0.8267 (ptm-80) cc_final: 0.8059 (ptm-80)
REVERT: A  825 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: A  841 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8655 (mt-10)
REVERT: A  964 ASP cc_start: 0.9239 (t0) cc_final: 0.8908 (t0)
REVERT: A  974 LEU cc_start: 0.9597 (tt) cc_final: 0.9142 (tt)
REVERT: A  993 ASP cc_start: 0.9177 (p0) cc_final: 0.8945 (p0)
REVERT: A 1005 CYS cc_start: 0.8921 (t) cc_final: 0.8643 (t)
REVERT: A 1107 ASN cc_start: 0.9020 (t0) cc_final: 0.8556 (t0)
REVERT: A 1228 ARG cc_start: 0.6558 (ptt180) cc_final: 0.5653 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0983
  time to fit residues: 23.4450
Evaluate side-chains
  145 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 103 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 97 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 119 optimal weight:    6.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 771 GLN
** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** 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 = 0.3594 r_free = 0.3594 target = 0.093098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.068649 restraints weight = 34347.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.071124 restraints weight = 18860.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.072763 restraints weight = 12698.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.073837 restraints weight = 9742.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.074573 restraints weight = 8169.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.5123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10148  Z= 0.142
  Angle     :  0.626   7.090  13694  Z= 0.330
  Chirality :  0.043   0.158   1460
  Planarity :  0.005   0.099   1770
  Dihedral  :  4.888  17.993   1330
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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 aren not related in a simple way.
  whole: -1.18 (0.24), residues: 1196
  helix:  0.23 (0.26), residues: 383
  sheet: -1.70 (0.33), residues: 204
  loop : -1.04 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 792 
 TYR   0.019   0.001   TYR A1217 
 PHE   0.018   0.001   PHE A 382 
 TRP   0.044   0.002   TRP A 361 
 HIS   0.006   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (10148)
  covalent geometry    : angle       0.62588 (13694)
  hydrogen bonds       : bond        0.03765 (  410)
  hydrogen bonds       : angle       5.78304 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8256 (tmm) cc_final: 0.7517 (tmm)
REVERT: A   59 ASP cc_start: 0.9021 (p0) cc_final: 0.8708 (p0)
REVERT: A  210 MET cc_start: 0.8816 (mmm) cc_final: 0.8548 (mmm)
REVERT: A  357 GLU cc_start: 0.6922 (tt0) cc_final: 0.6424 (tt0)
REVERT: A  382 PHE cc_start: 0.8518 (t80) cc_final: 0.8244 (t80)
REVERT: A  406 GLU cc_start: 0.7583 (tt0) cc_final: 0.7234 (tt0)
REVERT: A  496 CYS cc_start: 0.9307 (m) cc_final: 0.8878 (m)
REVERT: A  661 MET cc_start: 0.9531 (mmp) cc_final: 0.9229 (mmm)
REVERT: A  710 PHE cc_start: 0.8393 (m-10) cc_final: 0.8138 (m-10)
REVERT: A  784 ARG cc_start: 0.8267 (ptm-80) cc_final: 0.8059 (ptm-80)
REVERT: A  825 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: A  841 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8740 (mt-10)
REVERT: A  964 ASP cc_start: 0.9222 (t0) cc_final: 0.8896 (t0)
REVERT: A  974 LEU cc_start: 0.9562 (tt) cc_final: 0.9097 (tt)
REVERT: A  993 ASP cc_start: 0.9190 (p0) cc_final: 0.8957 (p0)
REVERT: A 1005 CYS cc_start: 0.8972 (t) cc_final: 0.8723 (t)
REVERT: A 1009 MET cc_start: 0.7496 (ttm) cc_final: 0.6802 (ttm)
REVERT: A 1107 ASN cc_start: 0.8938 (t0) cc_final: 0.8498 (t0)
REVERT: A 1150 HIS cc_start: 0.9082 (p90) cc_final: 0.8615 (p90)
REVERT: A 1228 ARG cc_start: 0.6570 (ptt180) cc_final: 0.5731 (ptt90)
REVERT: A 1233 LYS cc_start: 0.9524 (pptt) cc_final: 0.9284 (ptpt)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0944
  time to fit residues: 22.6196
Evaluate side-chains
  139 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 111 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 86 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.093566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.069253 restraints weight = 34236.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.071683 restraints weight = 18882.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.073337 restraints weight = 12747.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.074344 restraints weight = 9800.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.075119 restraints weight = 8277.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.5324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10148  Z= 0.143
  Angle     :  0.646   8.729  13694  Z= 0.341
  Chirality :  0.043   0.156   1460
  Planarity :  0.005   0.095   1770
  Dihedral  :  4.915  19.874   1330
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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 aren not related in a simple way.
  whole: -1.15 (0.24), residues: 1196
  helix:  0.21 (0.26), residues: 383
  sheet: -1.68 (0.34), residues: 201
  loop : -1.00 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 984 
 TYR   0.028   0.002   TYR A1197 
 PHE   0.021   0.001   PHE A 382 
 TRP   0.038   0.002   TRP A 361 
 HIS   0.005   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10148)
  covalent geometry    : angle       0.64607 (13694)
  hydrogen bonds       : bond        0.03804 (  410)
  hydrogen bonds       : angle       5.82317 ( 1158)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8232 (tmm) cc_final: 0.7616 (tmm)
REVERT: A   59 ASP cc_start: 0.9033 (p0) cc_final: 0.8719 (p0)
REVERT: A  210 MET cc_start: 0.8857 (mmm) cc_final: 0.8576 (mmm)
REVERT: A  348 CYS cc_start: 0.9048 (m) cc_final: 0.8350 (t)
REVERT: A  357 GLU cc_start: 0.7206 (tt0) cc_final: 0.6691 (tt0)
REVERT: A  384 ASP cc_start: 0.8911 (t70) cc_final: 0.8710 (p0)
REVERT: A  406 GLU cc_start: 0.7570 (tt0) cc_final: 0.7257 (tt0)
REVERT: A  496 CYS cc_start: 0.9320 (m) cc_final: 0.8893 (m)
REVERT: A  509 ILE cc_start: 0.9133 (mm) cc_final: 0.8684 (mt)
REVERT: A  661 MET cc_start: 0.9528 (mmp) cc_final: 0.9243 (mmm)
REVERT: A  710 PHE cc_start: 0.8418 (m-10) cc_final: 0.8169 (m-10)
REVERT: A  777 LEU cc_start: 0.8784 (mt) cc_final: 0.8560 (mt)
REVERT: A  841 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8737 (mt-10)
REVERT: A  964 ASP cc_start: 0.9230 (t0) cc_final: 0.8918 (t0)
REVERT: A  974 LEU cc_start: 0.9559 (tt) cc_final: 0.9127 (tt)
REVERT: A  993 ASP cc_start: 0.9167 (p0) cc_final: 0.8937 (p0)
REVERT: A 1005 CYS cc_start: 0.9003 (t) cc_final: 0.8759 (t)
REVERT: A 1009 MET cc_start: 0.7503 (ttm) cc_final: 0.6885 (ttm)
REVERT: A 1043 MET cc_start: 0.9080 (mmp) cc_final: 0.8785 (mmm)
REVERT: A 1107 ASN cc_start: 0.8926 (t0) cc_final: 0.8074 (m110)
REVERT: A 1150 HIS cc_start: 0.9100 (p90) cc_final: 0.8644 (p90)
REVERT: A 1205 ARG cc_start: 0.8946 (pmt-80) cc_final: 0.8330 (ptm-80)
REVERT: A 1228 ARG cc_start: 0.6569 (ptt180) cc_final: 0.5767 (ptt90)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0951
  time to fit residues: 24.1845
Evaluate side-chains
  141 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0000
   chunk 41 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 117 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 135 ASN
A 214 GLN
** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.095371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.070944 restraints weight = 34373.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.073440 restraints weight = 18938.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.075149 restraints weight = 12736.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.076205 restraints weight = 9768.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.076996 restraints weight = 8225.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3275
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.5457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10148  Z= 0.123
  Angle     :  0.629   7.967  13694  Z= 0.331
  Chirality :  0.043   0.157   1460
  Planarity :  0.004   0.089   1770
  Dihedral  :  4.811  18.337   1330
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  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 aren not related in a simple way.
  whole: -1.01 (0.24), residues: 1196
  helix:  0.36 (0.27), residues: 377
  sheet: -1.63 (0.34), residues: 202
  loop : -0.92 (0.25), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 984 
 TYR   0.034   0.001   TYR A1197 
 PHE   0.027   0.001   PHE A 382 
 TRP   0.037   0.002   TRP A 361 
 HIS   0.004   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10148)
  covalent geometry    : angle       0.62918 (13694)
  hydrogen bonds       : bond        0.03647 (  410)
  hydrogen bonds       : angle       5.63504 ( 1158)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1586.28 seconds
wall clock time: 28 minutes 24.12 seconds (1704.12 seconds total)