Starting phenix.real_space_refine
on Thu Jul 31 03:13:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9klq_62413/07_2025/9klq_62413.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9klq_62413/07_2025/9klq_62413.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9klq_62413/07_2025/9klq_62413.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9klq_62413/07_2025/9klq_62413.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9klq_62413/07_2025/9klq_62413.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9klq_62413/07_2025/9klq_62413.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.021
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: 6
    Type Number    sf(0)   Gaussians
     P     147      5.49       5
     Mg      2      5.21       5
     S      33      5.16       5
     C    7680      2.51       5
     N    2397      2.21       5
     O    2796      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13055
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 9958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1284, 9958
          Classifications: {'peptide': 1284}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 55, 'TRANS': 1228}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 196
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 158
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 16, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 129
    Chain: "B"
      Number of atoms: 2162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 2162
          Classifications: {'RNA': 101}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 45, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 16, 'rna3p': 84}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 547
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "D"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 386
          Classifications: {'DNA': 20}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 19}
          Unresolved chain links: 1
          Unresolved chain link angles: 4
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {' DT:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 9.07, per 1000 atoms: 0.69
  Number of scatterers: 13055
  At special positions: 0
  Unit cell: (109.326, 118.916, 131.383, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      33     16.00
     P     147     15.00
     Mg      2     11.99
     O    2796      8.00
     N    2397      7.00
     C    7680      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: 4.03
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2394

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 8 sheets defined
      53.9% alpha, 8.6% beta
      29 base pairs and 73 stacking pairs defined.
    Time for finding SS restraints: 5.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 52
      removed outlier: 3.603A  pdb=" N   ALA A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 54
      No H-bonds generated for 'chain 'A' and resid 53 through 54'
    Processing helix  chain 'A' and resid 55 through 60
      removed outlier: 3.560A  pdb=" N   LEU A  58 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 85
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 106 through 126
      removed outlier: 3.573A  pdb=" N   GLY A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 139
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 3.928A  pdb=" N   LEU A 143 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 168
    Processing helix  chain 'A' and resid 176 through 185
      removed outlier: 3.659A  pdb=" N   LEU A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 186 through 192
    Processing helix  chain 'A' and resid 214 through 228
      removed outlier: 3.609A  pdb=" N   LYS A 218 " --> pdb=" O   ASP A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 252
      removed outlier: 3.772A  pdb=" N   MET A 238 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 269
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 278 through 284
      removed outlier: 3.663A  pdb=" N   VAL A 282 " --> pdb=" O   ASN A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 304
      removed outlier: 3.969A  pdb=" N   GLY A 300 " --> pdb=" O   ARG A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 330
    Processing helix  chain 'A' and resid 337 through 352
      removed outlier: 3.752A  pdb=" N   ARG A 350 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 369
    Processing helix  chain 'A' and resid 382 through 416
      removed outlier: 3.560A  pdb=" N   PHE A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 572 through 579
      removed outlier: 3.748A  pdb=" N   LYS A 579 " --> pdb=" O   GLY A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 623
    Processing helix  chain 'A' and resid 641 through 648
    Processing helix  chain 'A' and resid 674 through 686
    Processing helix  chain 'A' and resid 691 through 704
    Processing helix  chain 'A' and resid 721 through 725
    Processing helix  chain 'A' and resid 742 through 746
      removed outlier: 3.614A  pdb=" N   LYS A 746 " --> pdb=" O   ILE A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 752
      removed outlier: 3.758A  pdb=" N   LYS A 752 " --> pdb=" O   GLY A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 783 through 794
    Processing helix  chain 'A' and resid 868 through 882
      removed outlier: 3.599A  pdb=" N   VAL A 872 " --> pdb=" O   SER A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 895
    Processing helix  chain 'A' and resid 900 through 914
    Processing helix  chain 'A' and resid 936 through 966
      removed outlier: 4.322A  pdb=" N   LYS A 953 " --> pdb=" O   ARG A 949 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   TYR A 954 " --> pdb=" O   LEU A 950 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   THR A 966 " --> pdb=" O   ALA A 962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 988
    Processing helix  chain 'A' and resid 996 through 1015
      removed outlier: 3.517A  pdb=" N   LYS A1000 " --> pdb=" O   GLU A 996 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ASP A1001 " --> pdb=" O   ALA A 997 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   TYR A1002 " --> pdb=" O   LYS A 998 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1022 through 1031
    Processing helix  chain 'A' and resid 1032 through 1035
    Processing helix  chain 'A' and resid 1054 through 1073
      Proline residue:  A1066  - end of helix
    Processing helix  chain 'A' and resid 1075 through 1108
      removed outlier: 3.736A  pdb=" N   LYS A1098 " --> pdb=" O   ALA A1094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1111 through 1115
      removed outlier: 3.532A  pdb=" N   ALA A1114 " --> pdb=" O   GLY A1111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1116 through 1120
      removed outlier: 4.026A  pdb=" N   ILE A1119 " --> pdb=" O   THR A1116 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ARG A1120 " --> pdb=" O   PRO A1117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1116 through 1120'
    Processing helix  chain 'A' and resid 1126 through 1139
      removed outlier: 3.539A  pdb=" N   LEU A1130 " --> pdb=" O   SER A1126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1140 through 1146
    Processing helix  chain 'A' and resid 1162 through 1190
      removed outlier: 3.545A  pdb=" N   LEU A1166 " --> pdb=" O   GLY A1162 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ALA A1168 " --> pdb=" O   THR A1164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1243
      removed outlier: 3.643A  pdb=" N   ALA A1243 " --> pdb=" O   LEU A1239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1244 through 1258
    Processing helix  chain 'A' and resid 1295 through 1309
    Processing helix  chain 'A' and resid 1311 through 1323
    Processing helix  chain 'A' and resid 1328 through 1336
      removed outlier: 4.216A  pdb=" N   GLY A1336 " --> pdb=" O   GLU A1332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1355 through 1360
      removed outlier: 3.905A  pdb=" N   LYS A1359 " --> pdb=" O   PRO A1356 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLY A1360 " --> pdb=" O   ALA A1357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1362 through 1376
      removed outlier: 3.852A  pdb=" N   ASN A1366 " --> pdb=" O   GLN A1362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1457 through 1481
      removed outlier: 3.619A  pdb=" N   ARG A1480 " --> pdb=" O   GLN A1476 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASN A1481 " --> pdb=" O   LEU A1477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1481 through 1486
    Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 562
      removed outlier: 3.875A  pdb=" N   GLY A 669 " --> pdb=" O   PHE A 562 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90
    Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 357
      removed outlier: 4.552A  pdb=" N   LEU A 356 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL A 364 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 637
    Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 812
      removed outlier: 3.595A  pdb=" N   ARG A 810 " --> pdb=" O   GLU A 825 " (cutoff:3.500A)
      removed outlier: 21.668A  pdb=" N   GLU A 824 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
      removed outlier: 17.072A  pdb=" N   PHE A 854 " --> pdb=" O   GLU A 824 " (cutoff:3.500A)
      removed outlier: 13.369A  pdb=" N   SER A 826 " --> pdb=" O   ARG A 852 " (cutoff:3.500A)
      removed outlier: 9.026A  pdb=" N   ARG A 852 " --> pdb=" O   SER A 826 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   VAL A 828 " --> pdb=" O   LEU A 850 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ARG A 852 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA A 774 " --> pdb=" O   ILE A 856 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   LEU A 764 " --> pdb=" O   ILE A1218 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 969 through 972
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1338 through 1341
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1387 through 1390

    514 hydrogen bonds defined for protein.
    1467 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      73 hydrogen bonds
      142 hydrogen bond angles
      0 basepair planarities
      29 basepair parallelities
      73 stacking parallelities
  Total time for adding SS restraints: 6.41

  Time building geometry restraints manager: 4.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2919
        1.33 -     1.45: 3622
        1.45 -     1.57: 6739
        1.57 -     1.69: 289
        1.69 -     1.81: 53
  Bond restraints: 13622
  Sorted by residual:
  bond pdb=" O3'   A B  94 "
       pdb=" P     U B  95 "
    ideal  model  delta    sigma   weight residual
    1.607  1.535  0.072 1.50e-02 4.44e+03 2.33e+01
  bond pdb=" O5'   G B  93 "
       pdb=" C5'   G B  93 "
    ideal  model  delta    sigma   weight residual
    1.420  1.458 -0.038 1.50e-02 4.44e+03 6.46e+00
  bond pdb=" O5'   U B  67 "
       pdb=" C5'   U B  67 "
    ideal  model  delta    sigma   weight residual
    1.420  1.450 -0.030 1.50e-02 4.44e+03 3.94e+00
  bond pdb=" P     G B  93 "
       pdb=" O5'   G B  93 "
    ideal  model  delta    sigma   weight residual
    1.593  1.621 -0.028 1.50e-02 4.44e+03 3.61e+00
  bond pdb=" O5'   U B  95 "
       pdb=" C5'   U B  95 "
    ideal  model  delta    sigma   weight residual
    1.420  1.448 -0.028 1.50e-02 4.44e+03 3.60e+00
  ... (remaining 13617 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 18691
        2.10 -     4.21: 359
        4.21 -     6.31: 43
        6.31 -     8.41: 8
        8.41 -    10.52: 4
  Bond angle restraints: 19105
  Sorted by residual:
  angle pdb=" C   GLY A1281 "
        pdb=" N   MET A1282 "
        pdb=" CA  MET A1282 "
      ideal   model   delta    sigma   weight residual
     121.90  115.30    6.60 1.26e+00 6.30e-01 2.75e+01
  angle pdb=" C   MET A1282 "
        pdb=" N   ARG A1283 "
        pdb=" CA  ARG A1283 "
      ideal   model   delta    sigma   weight residual
     121.91  111.39   10.52 2.03e+00 2.43e-01 2.68e+01
  angle pdb=" C   LYS A 231 "
        pdb=" CA  LYS A 231 "
        pdb=" CB  LYS A 231 "
      ideal   model   delta    sigma   weight residual
     117.23  110.31    6.92 1.36e+00 5.41e-01 2.59e+01
  angle pdb=" C3'   G B  92 "
        pdb=" O3'   G B  92 "
        pdb=" P     G B  93 "
      ideal   model   delta    sigma   weight residual
     120.20  126.26   -6.06 1.50e+00 4.44e-01 1.63e+01
  angle pdb=" O4'   G B  92 "
        pdb=" C1'   G B  92 "
        pdb=" N9    G B  92 "
      ideal   model   delta    sigma   weight residual
     108.20  114.23   -6.03 1.50e+00 4.44e-01 1.62e+01
  ... (remaining 19100 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.70: 7706
       34.70 -    69.39: 440
       69.39 -   104.09: 39
      104.09 -   138.78: 2
      138.78 -   173.48: 1
  Dihedral angle restraints: 8188
    sinusoidal: 4492
      harmonic: 3696
  Sorted by residual:
  dihedral pdb=" O4'   C B  45 "
           pdb=" C1'   C B  45 "
           pdb=" N1    C B  45 "
           pdb=" C2    C B  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   26.52  173.48     1      1.50e+01 4.44e-03 8.51e+01
  dihedral pdb=" CA  ASP A1202 "
           pdb=" C   ASP A1202 "
           pdb=" N   PRO A1203 "
           pdb=" CA  PRO A1203 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.53  -28.47     0      5.00e+00 4.00e-02 3.24e+01
  dihedral pdb=" CA  GLN A1362 "
           pdb=" C   GLN A1362 "
           pdb=" N   ALA A1363 "
           pdb=" CA  ALA A1363 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.63  -21.37     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 8185 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 2120
       0.102 -    0.205: 44
       0.205 -    0.307: 2
       0.307 -    0.410: 1
       0.410 -    0.512: 6
  Chirality restraints: 2173
  Sorted by residual:
  chirality pdb=" P     A B 103 "
            pdb=" OP1   A B 103 "
            pdb=" OP2   A B 103 "
            pdb=" O5'   A B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.92   -0.51 2.00e-01 2.50e+01 6.55e+00
  chirality pdb=" P     U B  67 "
            pdb=" OP1   U B  67 "
            pdb=" OP2   U B  67 "
            pdb=" O5'   U B  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.92   -0.51 2.00e-01 2.50e+01 6.53e+00
  chirality pdb=" P     U B  95 "
            pdb=" OP1   U B  95 "
            pdb=" OP2   U B  95 "
            pdb=" O5'   U B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.90   -0.49 2.00e-01 2.50e+01 6.05e+00
  ... (remaining 2170 not shown)

  Planarity restraints: 1929
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1202 "   -0.086 5.00e-02 4.00e+02   1.30e-01 2.72e+01
        pdb=" N   PRO A1203 "    0.225 5.00e-02 4.00e+02
        pdb=" CA  PRO A1203 "   -0.072 5.00e-02 4.00e+02
        pdb=" CD  PRO A1203 "   -0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 177 "    0.028 2.00e-02 2.50e+03   2.55e-02 1.63e+01
        pdb=" CG  TRP A 177 "   -0.068 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 177 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 177 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 177 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 177 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 177 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 177 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 177 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 177 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 135 "    0.020 2.00e-02 2.50e+03   2.23e-02 1.25e+01
        pdb=" CG  TRP A 135 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 135 "    0.034 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 135 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 135 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 135 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 135 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 135 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 135 "    0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 135 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1926 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.54: 70
        2.54 -     3.13: 9633
        3.13 -     3.72: 20777
        3.72 -     4.31: 27615
        4.31 -     4.90: 44857
  Nonbonded interactions: 102952
  Sorted by model distance:
  nonbonded pdb=" OP2   U B  33 "
            pdb="MG    MG B 201 "
     model   vdw
     1.956 2.170
  nonbonded pdb=" OP2   U B  38 "
            pdb="MG    MG B 202 "
     model   vdw
     2.091 2.170
  nonbonded pdb=" OD2 ASP A1202 "
            pdb=" O2'   G B  87 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" OD1 ASP A 957 "
            pdb=" NH1 ARG A 960 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OG1 THR A 811 "
            pdb=" OE2 GLU A 824 "
     model   vdw
     2.207 3.040
  ... (remaining 102947 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.520
  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:          0.520
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     40.120
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
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   0.072  13622  Z= 0.266
  Angle     :  0.695  10.515  19105  Z= 0.373
  Chirality :  0.047   0.512   2173
  Planarity :  0.006   0.130   1929
  Dihedral  : 19.045 173.476   5794
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.23 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.24), residues: 1262
  helix:  1.29 (0.21), residues: 643
  sheet: -0.07 (0.47), residues: 124
  loop : -1.40 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.002   TRP A 177 
 HIS   0.013   0.002   HIS A 770 
 PHE   0.017   0.002   PHE A1348 
 TYR   0.012   0.001   TYR A 978 
 ARG   0.007   0.001   ARG A1484 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14855 (  587)
  hydrogen bonds       : angle       5.71783 ( 1609)
  covalent geometry    : bond        0.00575 (13622)
  covalent geometry    : angle       0.69548 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.162 
Fit side-chains
REVERT: A  175 ASP cc_start: 0.8219 (m-30) cc_final: 0.7758 (m-30)
REVERT: A  960 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7769 (mtt180)
REVERT: A  969 TYR cc_start: 0.7806 (p90) cc_final: 0.7560 (p90)
REVERT: A  972 MET cc_start: 0.8216 (mmp) cc_final: 0.7344 (mmm)
REVERT: A 1006 MET cc_start: 0.7636 (ttp) cc_final: 0.7225 (ttp)
REVERT: A 1061 ARG cc_start: 0.8530 (mtp180) cc_final: 0.7931 (mtp180)
REVERT: A 1170 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8236 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.3744
  time to fit residues: 43.0230
Evaluate side-chains
  65 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 111 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9990
   chunk 128 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1301 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.114441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.082567 restraints weight = 28305.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.68
r_work: 0.3102 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.0937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13622  Z= 0.154
  Angle     :  0.559   8.455  19105  Z= 0.301
  Chirality :  0.036   0.311   2173
  Planarity :  0.004   0.046   1929
  Dihedral  : 20.057 175.032   3463
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.55 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  5.69 %
    Favored  : 93.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.24), residues: 1262
  helix:  1.65 (0.21), residues: 647
  sheet: -0.03 (0.47), residues: 119
  loop : -1.32 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 177 
 HIS   0.010   0.001   HIS A 770 
 PHE   0.015   0.001   PHE A1348 
 TYR   0.011   0.001   TYR A 978 
 ARG   0.006   0.000   ARG A1484 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05027 (  587)
  hydrogen bonds       : angle       4.24253 ( 1609)
  covalent geometry    : bond        0.00333 (13622)
  covalent geometry    : angle       0.55868 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 ASP cc_start: 0.8276 (m-30) cc_final: 0.7932 (m-30)
REVERT: A  177 TRP cc_start: 0.8524 (m100) cc_final: 0.7970 (m-10)
REVERT: A  969 TYR cc_start: 0.7903 (p90) cc_final: 0.7616 (p90)
REVERT: A  972 MET cc_start: 0.8281 (mmp) cc_final: 0.7747 (mmm)
REVERT: A 1006 MET cc_start: 0.7836 (ttp) cc_final: 0.7352 (ttp)
REVERT: A 1061 ARG cc_start: 0.8563 (mtp180) cc_final: 0.8061 (mtp180)
REVERT: A 1064 MET cc_start: 0.8671 (mtt) cc_final: 0.8423 (ptp)
REVERT: A 1282 MET cc_start: 0.6255 (pmm) cc_final: 0.5690 (pmm)
REVERT: A 1483 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7155 (tt)
  outliers start: 8
  outliers final: 6
  residues processed: 78
  average time/residue: 0.3917
  time to fit residues: 41.3616
Evaluate side-chains
  73 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain A residue 1029 ASN
Chi-restraints excluded: chain A residue 1304 GLN
Chi-restraints excluded: chain A residue 1361 LEU
Chi-restraints excluded: chain A residue 1483 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 66 optimal weight:    0.0970
   chunk 62 optimal weight:    5.9990
   chunk 122 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 80 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    2.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 312 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.112432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.080346 restraints weight = 28692.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.69
r_work: 0.3059 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13622  Z= 0.231
  Angle     :  0.590   8.454  19105  Z= 0.317
  Chirality :  0.038   0.336   2173
  Planarity :  0.005   0.047   1929
  Dihedral  : 20.114 173.864   3463
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.07 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  9.85 %
    Favored  : 89.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.24), residues: 1262
  helix:  1.60 (0.20), residues: 649
  sheet: -0.11 (0.46), residues: 124
  loop : -1.38 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 177 
 HIS   0.010   0.001   HIS A 770 
 PHE   0.013   0.002   PHE A 712 
 TYR   0.012   0.001   TYR A 978 
 ARG   0.006   0.000   ARG A1313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05634 (  587)
  hydrogen bonds       : angle       4.24152 ( 1609)
  covalent geometry    : bond        0.00518 (13622)
  covalent geometry    : angle       0.58997 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 1.430 
Fit side-chains
REVERT: A  175 ASP cc_start: 0.8334 (m-30) cc_final: 0.8018 (m-30)
REVERT: A  969 TYR cc_start: 0.7885 (p90) cc_final: 0.7615 (p90)
REVERT: A  972 MET cc_start: 0.8269 (mmp) cc_final: 0.7846 (mmm)
REVERT: A 1006 MET cc_start: 0.7792 (ttp) cc_final: 0.7335 (ttp)
REVERT: A 1061 ARG cc_start: 0.8445 (mtp180) cc_final: 0.7988 (mtp180)
REVERT: A 1170 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8274 (mm-30)
REVERT: A 1291 THR cc_start: 0.7740 (m) cc_final: 0.7530 (p)
REVERT: A 1304 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6741 (pm20)
  outliers start: 9
  outliers final: 5
  residues processed: 76
  average time/residue: 0.5197
  time to fit residues: 54.6915
Evaluate side-chains
  72 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue 1029 ASN
Chi-restraints excluded: chain A residue 1304 GLN
Chi-restraints excluded: chain A residue 1361 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 105 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 38 optimal weight:    9.9990
   chunk 113 optimal weight:    8.9990
   chunk 117 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9990
   chunk 114 optimal weight:    8.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1221 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.114797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.083156 restraints weight = 28094.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.65
r_work: 0.3111 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13622  Z= 0.138
  Angle     :  0.510   8.564  19105  Z= 0.274
  Chirality :  0.034   0.296   2173
  Planarity :  0.004   0.044   1929
  Dihedral  : 20.041 176.553   3463
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.91 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.37 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.24), residues: 1262
  helix:  1.97 (0.21), residues: 643
  sheet:  0.02 (0.47), residues: 119
  loop : -1.18 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 177 
 HIS   0.008   0.001   HIS A 770 
 PHE   0.010   0.001   PHE A 712 
 TYR   0.009   0.001   TYR A 978 
 ARG   0.006   0.000   ARG A1313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  587)
  hydrogen bonds       : angle       3.87850 ( 1609)
  covalent geometry    : bond        0.00302 (13622)
  covalent geometry    : angle       0.50963 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 1.228 
Fit side-chains
REVERT: A  175 ASP cc_start: 0.8281 (m-30) cc_final: 0.7955 (m-30)
REVERT: A  969 TYR cc_start: 0.7843 (p90) cc_final: 0.7561 (p90)
REVERT: A  972 MET cc_start: 0.8263 (mmp) cc_final: 0.7916 (mmm)
REVERT: A 1006 MET cc_start: 0.7689 (ttp) cc_final: 0.7217 (ttp)
REVERT: A 1027 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6562 (tp)
REVERT: A 1061 ARG cc_start: 0.8366 (mtp180) cc_final: 0.7907 (mtp180)
REVERT: A 1069 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7528 (mp0)
REVERT: A 1285 GLN cc_start: 0.8347 (tt0) cc_final: 0.8090 (tt0)
REVERT: A 1304 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6727 (pm20)
  outliers start: 12
  outliers final: 6
  residues processed: 87
  average time/residue: 0.3613
  time to fit residues: 42.5138
Evaluate side-chains
  76 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain A residue  966 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1069 GLU
Chi-restraints excluded: chain A residue 1221 ASN
Chi-restraints excluded: chain A residue 1304 GLN
Chi-restraints excluded: chain A residue 1361 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 139 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 30 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 312 HIS
A1221 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.113079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.081172 restraints weight = 28563.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.67
r_work: 0.3071 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13622  Z= 0.194
  Angle     :  0.555   8.634  19105  Z= 0.296
  Chirality :  0.036   0.326   2173
  Planarity :  0.004   0.051   1929
  Dihedral  : 20.107 175.438   3463
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.91 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 11.98 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.24), residues: 1262
  helix:  1.86 (0.21), residues: 645
  sheet:  0.01 (0.47), residues: 119
  loop : -1.27 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 177 
 HIS   0.009   0.001   HIS A 770 
 PHE   0.013   0.001   PHE A 712 
 TYR   0.010   0.001   TYR A 978 
 ARG   0.005   0.000   ARG A 960 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05095 (  587)
  hydrogen bonds       : angle       4.01981 ( 1609)
  covalent geometry    : bond        0.00433 (13622)
  covalent geometry    : angle       0.55483 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 1.312 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ASP cc_start: 0.8301 (m-30) cc_final: 0.7984 (m-30)
REVERT: A  969 TYR cc_start: 0.7868 (p90) cc_final: 0.7595 (p90)
REVERT: A  972 MET cc_start: 0.8287 (mmp) cc_final: 0.7905 (mmm)
REVERT: A 1006 MET cc_start: 0.7703 (ttp) cc_final: 0.7302 (ttp)
REVERT: A 1027 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6661 (tp)
REVERT: A 1061 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7847 (mtp180)
REVERT: A 1069 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7452 (mp0)
REVERT: A 1239 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6948 (tt)
REVERT: A 1304 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6724 (pm20)
REVERT: A 1439 MET cc_start: 0.6663 (ptp) cc_final: 0.6156 (ptt)
  outliers start: 19
  outliers final: 8
  residues processed: 83
  average time/residue: 0.3586
  time to fit residues: 41.8038
Evaluate side-chains
  77 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1058 GLU
Chi-restraints excluded: chain A residue 1069 GLU
Chi-restraints excluded: chain A residue 1221 ASN
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1304 GLN
Chi-restraints excluded: chain A residue 1361 LEU
Chi-restraints excluded: chain A residue 1405 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 110 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 312 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.113651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.081809 restraints weight = 28763.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.68
r_work: 0.3084 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13622  Z= 0.171
  Angle     :  0.535   8.796  19105  Z= 0.287
  Chirality :  0.035   0.320   2173
  Planarity :  0.004   0.053   1929
  Dihedral  : 20.108 175.637   3463
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.31 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.59 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.24), residues: 1262
  helix:  1.88 (0.21), residues: 645
  sheet:  0.05 (0.47), residues: 119
  loop : -1.25 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 177 
 HIS   0.008   0.001   HIS A 770 
 PHE   0.012   0.001   PHE A 772 
 TYR   0.009   0.001   TYR A 978 
 ARG   0.003   0.000   ARG A 960 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04888 (  587)
  hydrogen bonds       : angle       3.95108 ( 1609)
  covalent geometry    : bond        0.00380 (13622)
  covalent geometry    : angle       0.53544 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 1.193 
Fit side-chains
REVERT: A  175 ASP cc_start: 0.8279 (m-30) cc_final: 0.7966 (m-30)
REVERT: A  866 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8526 (tt0)
REVERT: A  969 TYR cc_start: 0.7862 (p90) cc_final: 0.7612 (p90)
REVERT: A  972 MET cc_start: 0.8303 (mmp) cc_final: 0.7722 (mmm)
REVERT: A 1006 MET cc_start: 0.7852 (ttp) cc_final: 0.7466 (ttp)
REVERT: A 1027 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6639 (tp)
REVERT: A 1061 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7829 (mtp180)
REVERT: A 1069 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7480 (mp0)
REVERT: A 1239 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6664 (tt)
REVERT: A 1439 MET cc_start: 0.6628 (ptp) cc_final: 0.6102 (ptt)
  outliers start: 17
  outliers final: 8
  residues processed: 82
  average time/residue: 0.4094
  time to fit residues: 47.6544
Evaluate side-chains
  76 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 2.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1069 GLU
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1361 LEU
Chi-restraints excluded: chain A residue 1405 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 133 optimal weight:    7.9990
   chunk 100 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 111 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0270
   chunk 136 optimal weight:    8.9990
   overall best weight:    4.2046

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 312 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.110400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.078378 restraints weight = 28754.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.70
r_work: 0.3019 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046  13622  Z= 0.325
  Angle     :  0.666   8.418  19105  Z= 0.354
  Chirality :  0.041   0.367   2173
  Planarity :  0.005   0.061   1929
  Dihedral  : 20.273 172.804   3463
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.10 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.99 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.24), residues: 1262
  helix:  1.37 (0.20), residues: 650
  sheet: -0.07 (0.47), residues: 121
  loop : -1.40 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 177 
 HIS   0.009   0.001   HIS A 770 
 PHE   0.019   0.002   PHE A 712 
 TYR   0.013   0.002   TYR A 978 
 ARG   0.006   0.001   ARG A1283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06412 (  587)
  hydrogen bonds       : angle       4.42026 ( 1609)
  covalent geometry    : bond        0.00733 (13622)
  covalent geometry    : angle       0.66573 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 1.287 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.7816 (mmt-90) cc_final: 0.7387 (mtt-85)
REVERT: A  175 ASP cc_start: 0.8339 (m-30) cc_final: 0.7944 (m-30)
REVERT: A  866 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8583 (tt0)
REVERT: A  972 MET cc_start: 0.8295 (mmp) cc_final: 0.7661 (mmm)
REVERT: A 1006 MET cc_start: 0.7794 (ttp) cc_final: 0.7358 (ttp)
REVERT: A 1061 ARG cc_start: 0.8365 (mtp180) cc_final: 0.7923 (mtp180)
REVERT: A 1239 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6787 (tt)
REVERT: A 1283 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6684 (mtt180)
  outliers start: 21
  outliers final: 15
  residues processed: 85
  average time/residue: 0.2970
  time to fit residues: 36.2525
Evaluate side-chains
  79 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  384 SER
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  787 ILE
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1283 ARG
Chi-restraints excluded: chain A residue 1311 THR
Chi-restraints excluded: chain A residue 1361 LEU
Chi-restraints excluded: chain A residue 1405 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 121 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 1 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 672 GLN
A1221 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.113318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.081502 restraints weight = 28665.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.68
r_work: 0.3079 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13622  Z= 0.158
  Angle     :  0.552  10.938  19105  Z= 0.296
  Chirality :  0.036   0.315   2173
  Planarity :  0.004   0.058   1929
  Dihedral  : 20.129 174.991   3463
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.75 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.21 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.24), residues: 1262
  helix:  1.77 (0.21), residues: 641
  sheet: -0.04 (0.46), residues: 124
  loop : -1.24 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 177 
 HIS   0.008   0.001   HIS A 770 
 PHE   0.011   0.001   PHE A 772 
 TYR   0.012   0.001   TYR A 969 
 ARG   0.003   0.000   ARG A 960 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  587)
  hydrogen bonds       : angle       4.09516 ( 1609)
  covalent geometry    : bond        0.00347 (13622)
  covalent geometry    : angle       0.55212 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 1.226 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.7657 (mmt-90) cc_final: 0.7152 (mtt-85)
REVERT: A  175 ASP cc_start: 0.8283 (m-30) cc_final: 0.7956 (m-30)
REVERT: A  972 MET cc_start: 0.8327 (mmp) cc_final: 0.7761 (mmm)
REVERT: A 1006 MET cc_start: 0.7838 (ttp) cc_final: 0.7464 (ttp)
REVERT: A 1061 ARG cc_start: 0.8324 (mtp180) cc_final: 0.7918 (mtp180)
REVERT: A 1069 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7466 (mp0)
REVERT: A 1239 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6615 (tt)
REVERT: A 1282 MET cc_start: 0.6600 (pmm) cc_final: 0.6130 (pmm)
REVERT: A 1283 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6342 (mtt180)
  outliers start: 17
  outliers final: 13
  residues processed: 81
  average time/residue: 0.3267
  time to fit residues: 37.1951
Evaluate side-chains
  78 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  787 ILE
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue 1069 GLU
Chi-restraints excluded: chain A residue 1221 ASN
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1283 ARG
Chi-restraints excluded: chain A residue 1311 THR
Chi-restraints excluded: chain A residue 1361 LEU
Chi-restraints excluded: chain A residue 1405 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 135 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 119 optimal weight:    4.9990
   chunk 87 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 140 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   chunk 123 optimal weight:    0.8980
   chunk 122 optimal weight:    5.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 672 GLN
A1221 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.113875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.082085 restraints weight = 28482.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.67
r_work: 0.3088 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13622  Z= 0.146
  Angle     :  0.536   9.073  19105  Z= 0.287
  Chirality :  0.035   0.310   2173
  Planarity :  0.004   0.059   1929
  Dihedral  : 20.098 176.301   3463
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.99 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.11 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.24), residues: 1262
  helix:  1.89 (0.21), residues: 642
  sheet:  0.07 (0.47), residues: 119
  loop : -1.16 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 177 
 HIS   0.007   0.001   HIS A 770 
 PHE   0.009   0.001   PHE A1161 
 TYR   0.018   0.001   TYR A 969 
 ARG   0.003   0.000   ARG A 960 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04677 (  587)
  hydrogen bonds       : angle       3.99365 ( 1609)
  covalent geometry    : bond        0.00321 (13622)
  covalent geometry    : angle       0.53573 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 1.486 
Fit side-chains
REVERT: A  175 ASP cc_start: 0.8247 (m-30) cc_final: 0.7916 (m-30)
REVERT: A  972 MET cc_start: 0.8251 (mmp) cc_final: 0.7746 (mmm)
REVERT: A 1006 MET cc_start: 0.7924 (ttp) cc_final: 0.7541 (ttp)
REVERT: A 1061 ARG cc_start: 0.8298 (mtp180) cc_final: 0.7897 (mtp180)
REVERT: A 1069 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7428 (mp0)
REVERT: A 1239 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6453 (tt)
REVERT: A 1282 MET cc_start: 0.6535 (pmm) cc_final: 0.5944 (pmm)
REVERT: A 1283 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.6245 (mtt180)
  outliers start: 18
  outliers final: 12
  residues processed: 85
  average time/residue: 0.3780
  time to fit residues: 46.0589
Evaluate side-chains
  77 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 1.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  384 SER
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  787 ILE
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue 1069 GLU
Chi-restraints excluded: chain A residue 1221 ASN
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1283 ARG
Chi-restraints excluded: chain A residue 1361 LEU
Chi-restraints excluded: chain A residue 1405 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 81 optimal weight:   20.0000
   chunk 2 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 130 optimal weight:   10.0000
   chunk 138 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1221 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.113088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.081214 restraints weight = 28494.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.68
r_work: 0.3074 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13622  Z= 0.181
  Angle     :  0.550   8.662  19105  Z= 0.295
  Chirality :  0.036   0.323   2173
  Planarity :  0.004   0.060   1929
  Dihedral  : 20.098 175.953   3463
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.07 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.62 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.24), residues: 1262
  helix:  1.85 (0.21), residues: 644
  sheet:  0.04 (0.47), residues: 119
  loop : -1.25 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 177 
 HIS   0.006   0.001   HIS A 770 
 PHE   0.011   0.001   PHE A 712 
 TYR   0.019   0.001   TYR A 969 
 ARG   0.003   0.000   ARG A1313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04959 (  587)
  hydrogen bonds       : angle       4.02531 ( 1609)
  covalent geometry    : bond        0.00403 (13622)
  covalent geometry    : angle       0.54986 (19105)

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

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

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2524 Ramachandran restraints generated.
    1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 1.257 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.7682 (mmt-90) cc_final: 0.7165 (mtt-85)
REVERT: A  175 ASP cc_start: 0.8270 (m-30) cc_final: 0.7943 (m-30)
REVERT: A  972 MET cc_start: 0.8299 (mmp) cc_final: 0.7737 (mmm)
REVERT: A 1006 MET cc_start: 0.7926 (ttp) cc_final: 0.7534 (ttp)
REVERT: A 1061 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7899 (mtp180)
REVERT: A 1069 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7470 (mp0)
REVERT: A 1239 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6455 (tt)
REVERT: A 1283 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6410 (mtt180)
  outliers start: 16
  outliers final: 13
  residues processed: 79
  average time/residue: 0.3643
  time to fit residues: 41.3113
Evaluate side-chains
  78 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  384 SER
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  787 ILE
Chi-restraints excluded: chain A residue  946 ARG
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue 1069 GLU
Chi-restraints excluded: chain A residue 1221 ASN
Chi-restraints excluded: chain A residue 1239 LEU
Chi-restraints excluded: chain A residue 1283 ARG
Chi-restraints excluded: chain A residue 1361 LEU
Chi-restraints excluded: chain A residue 1405 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0970
   chunk 58 optimal weight:    0.8980
   chunk 133 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 109 optimal weight:    0.0370
   chunk 115 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.9458

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 614 GLN
A 672 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.115297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.083662 restraints weight = 28717.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.68
r_work: 0.3116 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  13622  Z= 0.116
  Angle     :  0.509   8.901  19105  Z= 0.274
  Chirality :  0.034   0.287   2173
  Planarity :  0.004   0.058   1929
  Dihedral  : 20.011 177.694   3463
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.07 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.43 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.24), residues: 1262
  helix:  2.01 (0.21), residues: 650
  sheet:  0.14 (0.47), residues: 119
  loop : -1.15 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1102 
 HIS   0.006   0.001   HIS A 770 
 PHE   0.008   0.001   PHE A 772 
 TYR   0.016   0.001   TYR A 969 
 ARG   0.005   0.000   ARG A1392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04089 (  587)
  hydrogen bonds       : angle       3.81652 ( 1609)
  covalent geometry    : bond        0.00247 (13622)
  covalent geometry    : angle       0.50936 (19105)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6989.15 seconds
wall clock time: 125 minutes 23.11 seconds (7523.11 seconds total)