Starting phenix.real_space_refine
on Sun Jul 27 21:15:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zk5_14755/07_2025/7zk5_14755.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zk5_14755/07_2025/7zk5_14755.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zk5_14755/07_2025/7zk5_14755.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zk5_14755/07_2025/7zk5_14755.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zk5_14755/07_2025/7zk5_14755.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zk5_14755/07_2025/7zk5_14755.cif"
  }
  resolution = 2.6
  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=   0.043
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       6      5.49       5
     Mg      2      5.21       5
     S      36      5.16       5
     C    6067      2.51       5
     N    1566      2.21       5
     O    1758      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9435
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1177, 9132
          Classifications: {'peptide': 1177}
          Link IDs: {'PTRANS': 29, 'TRANS': 1147}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 303
          Unusual residues: {' MG': 2, 'ATP': 2, 'JIZ': 1, 'Y01': 5}
          Classifications: {'undetermined': 10, 'water': 33}
          Link IDs: {None: 42}
  Time building chain proxies: 6.46, per 1000 atoms: 0.68
  Number of scatterers: 9435
  At special positions: 0
  Unit cell: (72.819, 84.537, 149.823, 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      36     16.00
     P       6     15.00
     Mg      2     11.99
     O    1758      8.00
     N    1566      7.00
     C    6067      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.66
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      70.3% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 38
      removed outlier: 3.714A  pdb=" N   THR A  37 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   MET A  38 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 34 through 38'
    Processing helix  chain 'A' and resid 42 through 71
      removed outlier: 3.940A  pdb=" N   ASP A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LEU A  64 " --> pdb=" O   HIS A  60 " (cutoff:3.500A)
      Proline residue:  A  65  - end of helix
      removed outlier: 3.602A  pdb=" N   MET A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 152
      removed outlier: 3.622A  pdb=" N   TRP A 132 " --> pdb=" O   GLN A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 162
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 180
      removed outlier: 5.013A  pdb=" N   VAL A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   SER A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 206
      removed outlier: 3.710A  pdb=" N   GLY A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 215
    Processing helix  chain 'A' and resid 216 through 256
      removed outlier: 4.559A  pdb=" N   VAL A 220 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 263
    Processing helix  chain 'A' and resid 265 through 319
      removed outlier: 3.716A  pdb=" N   ASN A 276 " --> pdb=" O   ARG A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 344
      removed outlier: 3.651A  pdb=" N   ILE A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLY A 337 " --> pdb=" O   SER A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 367
      removed outlier: 4.016A  pdb=" N   TYR A 359 " --> pdb=" O   ARG A 355 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   GLU A 360 " --> pdb=" O   GLY A 356 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   VAL A 361 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   PHE A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 437
    Processing helix  chain 'A' and resid 458 through 465
      removed outlier: 3.500A  pdb=" N   ILE A 465 " --> pdb=" O   TYR A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 486
    Processing helix  chain 'A' and resid 492 through 503
    Processing helix  chain 'A' and resid 505 through 512
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.982A  pdb=" N   THR A 518 " --> pdb=" O   GLN A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 525
    Processing helix  chain 'A' and resid 528 through 542
    Processing helix  chain 'A' and resid 558 through 571
    Processing helix  chain 'A' and resid 586 through 590
      removed outlier: 3.672A  pdb=" N   ASN A 590 " --> pdb=" O   THR A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 615
    Processing helix  chain 'A' and resid 616 through 624
    Processing helix  chain 'A' and resid 691 through 699
    Processing helix  chain 'A' and resid 703 through 737
      removed outlier: 3.597A  pdb=" N   PHE A 707 " --> pdb=" O   GLU A 703 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
      removed outlier: 4.701A  pdb=" N   SER A 725 " --> pdb=" O   GLN A 721 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL A 726 " --> pdb=" O   PRO A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 748
    Processing helix  chain 'A' and resid 749 through 795
    Processing helix  chain 'A' and resid 796 through 801
      removed outlier: 3.506A  pdb=" N   PHE A 800 " --> pdb=" O   ASP A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 823
    Processing helix  chain 'A' and resid 826 through 850
      removed outlier: 3.806A  pdb=" N   ILE A 832 " --> pdb=" O   ARG A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 899
      removed outlier: 3.549A  pdb=" N   LEU A 857 " --> pdb=" O   LEU A 853 " (cutoff:3.500A)
      Proline residue:  A 862  - end of helix
      removed outlier: 4.160A  pdb=" N   ALA A 867 " --> pdb=" O   ILE A 863 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   GLY A 868 " --> pdb=" O   ILE A 864 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLY A 877 " --> pdb=" O   LYS A 873 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLN A 878 " --> pdb=" O   MET A 874 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A 880 " --> pdb=" O   SER A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 907
    Processing helix  chain 'A' and resid 908 through 920
    Processing helix  chain 'A' and resid 920 through 962
      removed outlier: 3.625A  pdb=" N   HIS A 932 " --> pdb=" O   MET A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 990
    Processing helix  chain 'A' and resid 990 through 1010
      removed outlier: 3.785A  pdb=" N   ARG A1006 " --> pdb=" O   SER A1002 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1080
      removed outlier: 3.664A  pdb=" N   VAL A1076 " --> pdb=" O   LYS A1072 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1108
      removed outlier: 3.530A  pdb=" N   GLN A1108 " --> pdb=" O   TRP A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1129
    Processing helix  chain 'A' and resid 1137 through 1148
    Processing helix  chain 'A' and resid 1150 through 1157
    Processing helix  chain 'A' and resid 1159 through 1163
    Processing helix  chain 'A' and resid 1166 through 1170
    Processing helix  chain 'A' and resid 1173 through 1188
      removed outlier: 4.129A  pdb=" N   ARG A1188 " --> pdb=" O   ARG A1184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1217
    Processing helix  chain 'A' and resid 1229 through 1234
    Processing helix  chain 'A' and resid 1252 through 1259
      removed outlier: 3.582A  pdb=" N   GLN A1259 " --> pdb=" O   GLN A1255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1261 through 1271
    Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413
      removed outlier: 6.887A  pdb=" N   LYS A 407 " --> pdb=" O   HIS A 394 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   HIS A 394 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   LEU A 409 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   PHE A 390 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   SER A 448 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   ASN A 392 " --> pdb=" O   MET A 446 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   MET A 446 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469
      removed outlier: 6.324A  pdb=" N   GLY A 467 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   ASP A 551 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   VAL A 469 " --> pdb=" O   ASP A 551 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   LEU A 548 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   ILE A 581 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LEU A 550 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   VAL A 419 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   GLU A 604 " --> pdb=" O   GLY A 596 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ASP A 598 " --> pdb=" O   ILE A 602 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   ILE A 602 " --> pdb=" O   ASP A 598 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1049 through 1056
      removed outlier: 6.946A  pdb=" N   GLN A1050 " --> pdb=" O   VAL A1037 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL A1037 " --> pdb=" O   GLN A1050 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   LEU A1052 " --> pdb=" O   GLY A1035 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   VAL A1036 " --> pdb=" O   ALA A1087 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA A1087 " --> pdb=" O   VAL A1036 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112
      removed outlier: 6.230A  pdb=" N   LEU A1193 " --> pdb=" O   ILE A1224 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   ILE A1226 " --> pdb=" O   LEU A1193 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU A1195 " --> pdb=" O   ILE A1226 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   LEU A1062 " --> pdb=" O   VAL A1225 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   THR A1061 " --> pdb=" O   LEU A1238 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   VAL A1240 " --> pdb=" O   THR A1061 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   ALA A1063 " --> pdb=" O   VAL A1240 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ILE A1242 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   VAL A1065 " --> pdb=" O   ILE A1242 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLU A1249 " --> pdb=" O   VAL A1241 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLN A1243 " --> pdb=" O   VAL A1247 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   VAL A1247 " --> pdb=" O   GLN A1243 " (cutoff:3.500A)

    624 hydrogen bonds defined for protein.
    1830 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: 3.25

  Time building geometry restraints manager: 3.10 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1519
        1.29 -     1.42: 2380
        1.42 -     1.55: 5596
        1.55 -     1.68: 31
        1.68 -     1.82: 64
  Bond restraints: 9590
  Sorted by residual:
  bond pdb=" C03 JIZ A2010 "
       pdb=" N02 JIZ A2010 "
    ideal  model  delta    sigma   weight residual
    1.367  1.639 -0.272 2.00e-02 2.50e+03 1.85e+02
  bond pdb=" C08 JIZ A2010 "
       pdb=" N04 JIZ A2010 "
    ideal  model  delta    sigma   weight residual
    1.366  1.617 -0.251 2.00e-02 2.50e+03 1.57e+02
  bond pdb=" C13 JIZ A2010 "
       pdb=" N06 JIZ A2010 "
    ideal  model  delta    sigma   weight residual
    1.366  1.616 -0.250 2.00e-02 2.50e+03 1.57e+02
  bond pdb=" C02 JIZ A2010 "
       pdb=" S01 JIZ A2010 "
    ideal  model  delta    sigma   weight residual
    1.728  1.546  0.182 2.00e-02 2.50e+03 8.28e+01
  bond pdb=" C03 JIZ A2010 "
       pdb=" C04 JIZ A2010 "
    ideal  model  delta    sigma   weight residual
    1.360  1.518 -0.158 2.00e-02 2.50e+03 6.27e+01
  ... (remaining 9585 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.53: 12778
        3.53 -     7.06: 210
        7.06 -    10.59: 17
       10.59 -    14.12: 1
       14.12 -    17.65: 3
  Bond angle restraints: 13009
  Sorted by residual:
  angle pdb=" N   ALA A  94 "
        pdb=" CA  ALA A  94 "
        pdb=" C   ALA A  94 "
      ideal   model   delta    sigma   weight residual
     112.72  102.26   10.46 1.28e+00 6.10e-01 6.68e+01
  angle pdb=" C   THR A 807 "
        pdb=" CA  THR A 807 "
        pdb=" CB  THR A 807 "
      ideal   model   delta    sigma   weight residual
     110.96  121.57  -10.61 1.54e+00 4.22e-01 4.75e+01
  angle pdb=" N   ASP A  95 "
        pdb=" CA  ASP A  95 "
        pdb=" C   ASP A  95 "
      ideal   model   delta    sigma   weight residual
     111.36  104.11    7.25 1.09e+00 8.42e-01 4.42e+01
  angle pdb=" C   ARG A 258 "
        pdb=" N   THR A 259 "
        pdb=" CA  THR A 259 "
      ideal   model   delta    sigma   weight residual
     120.44  128.56   -8.12 1.30e+00 5.92e-01 3.90e+01
  angle pdb=" C   VAL A1165 "
        pdb=" N   GLY A1166 "
        pdb=" CA  GLY A1166 "
      ideal   model   delta    sigma   weight residual
     122.83  115.41    7.42 1.21e+00 6.83e-01 3.76e+01
  ... (remaining 13004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 5432
       17.96 -    35.92: 439
       35.92 -    53.88: 94
       53.88 -    71.84: 21
       71.84 -    89.80: 10
  Dihedral angle restraints: 5996
    sinusoidal: 2625
      harmonic: 3371
  Sorted by residual:
  dihedral pdb=" C   ILE A 897 "
           pdb=" N   ILE A 897 "
           pdb=" CA  ILE A 897 "
           pdb=" CB  ILE A 897 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.83   14.83     0      2.50e+00 1.60e-01 3.52e+01
  dihedral pdb=" C   THR A 807 "
           pdb=" N   THR A 807 "
           pdb=" CA  THR A 807 "
           pdb=" CB  THR A 807 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.80   14.80     0      2.50e+00 1.60e-01 3.50e+01
  dihedral pdb=" C   PHE A 728 "
           pdb=" N   PHE A 728 "
           pdb=" CA  PHE A 728 "
           pdb=" CB  PHE A 728 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.87  -12.73     0      2.50e+00 1.60e-01 2.59e+01
  ... (remaining 5993 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 1355
       0.099 -    0.198: 111
       0.198 -    0.296: 20
       0.296 -    0.395: 8
       0.395 -    0.494: 3
  Chirality restraints: 1497
  Sorted by residual:
  chirality pdb=" CA  THR A 807 "
            pdb=" N   THR A 807 "
            pdb=" C   THR A 807 "
            pdb=" CB  THR A 807 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.03    0.49 2.00e-01 2.50e+01 6.10e+00
  chirality pdb=" CA  ILE A 897 "
            pdb=" N   ILE A 897 "
            pdb=" C   ILE A 897 "
            pdb=" CB  ILE A 897 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.01    0.42 2.00e-01 2.50e+01 4.45e+00
  chirality pdb=" CA  THR A 811 "
            pdb=" N   THR A 811 "
            pdb=" C   THR A 811 "
            pdb=" CB  THR A 811 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.12    0.41 2.00e-01 2.50e+01 4.11e+00
  ... (remaining 1494 not shown)

  Planarity restraints: 1617
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 320 "   -0.021 2.00e-02 2.50e+03   4.16e-02 1.73e+01
        pdb=" C   LYS A 320 "    0.072 2.00e-02 2.50e+03
        pdb=" O   LYS A 320 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   GLU A 321 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 314 "    0.020 2.00e-02 2.50e+03   4.03e-02 1.63e+01
        pdb=" C   THR A 314 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   THR A 314 "    0.026 2.00e-02 2.50e+03
        pdb=" N   SER A 315 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1118 "   -0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   LEU A1118 "    0.063 2.00e-02 2.50e+03
        pdb=" O   LEU A1118 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   PHE A1119 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1614 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 104
        2.63 -     3.20: 8844
        3.20 -     3.76: 15414
        3.76 -     4.33: 21981
        4.33 -     4.90: 34638
  Nonbonded interactions: 80981
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1073 "
            pdb="MG    MG A2004 "
     model   vdw
     2.061 2.170
  nonbonded pdb="MG    MG A2004 "
            pdb=" O   HOH A2104 "
     model   vdw
     2.078 2.170
  nonbonded pdb="MG    MG A2004 "
            pdb=" O   HOH A2109 "
     model   vdw
     2.079 2.170
  nonbonded pdb="MG    MG A2002 "
            pdb=" O   HOH A2107 "
     model   vdw
     2.079 2.170
  nonbonded pdb="MG    MG A2002 "
            pdb=" O   HOH A2111 "
     model   vdw
     2.088 2.170
  ... (remaining 80976 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.260
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
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      :  0.010   0.272   9591  Z= 0.596
  Angle     :  1.030  17.652  13009  Z= 0.673
  Chirality :  0.065   0.494   1497
  Planarity :  0.006   0.068   1617
  Dihedral  : 14.219  89.804   3836
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.13 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.76 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.56 %
  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:  1.16 (0.24), residues: 1173
  helix:  1.23 (0.18), residues: 787
  sheet:  0.75 (0.62), residues: 70
  loop : -0.21 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 208 
 HIS   0.006   0.001   HIS A1003 
 PHE   0.027   0.002   PHE A 331 
 TYR   0.022   0.002   TYR A 322 
 ARG   0.009   0.001   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14927 (  624)
  hydrogen bonds       : angle       5.62694 ( 1830)
  covalent geometry    : bond        0.00970 ( 9590)
  covalent geometry    : angle       1.03038 (13009)
  Misc. bond           : bond        0.03176 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 1.057 
Fit side-chains
REVERT: A 1219 GLU cc_start: 0.7100 (mp0) cc_final: 0.6866 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 206
  average time/residue: 1.4122
  time to fit residues: 308.5912
Evaluate side-chains
  135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 91 optimal weight:    0.4980
   chunk 35 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 68 optimal weight:    0.5980
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN
A 749 ASN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 969 ASN
A1050 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.164515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.124113 restraints weight = 9907.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.75
r_work: 0.3318 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9591  Z= 0.136
  Angle     :  0.540   7.434  13009  Z= 0.284
  Chirality :  0.040   0.149   1497
  Planarity :  0.004   0.059   1617
  Dihedral  :  9.137  72.499   1718
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.18 %
    Favored  : 86.96 %
  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:  1.69 (0.24), residues: 1173
  helix:  1.70 (0.18), residues: 790
  sheet:  0.71 (0.61), residues: 70
  loop : -0.19 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 208 
 HIS   0.007   0.001   HIS A1003 
 PHE   0.020   0.002   PHE A 508 
 TYR   0.013   0.001   TYR A 949 
 ARG   0.005   0.001   ARG A1164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05210 (  624)
  hydrogen bonds       : angle       4.31552 ( 1830)
  covalent geometry    : bond        0.00279 ( 9590)
  covalent geometry    : angle       0.54025 (13009)
  Misc. bond           : bond        0.00061 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A  332 PHE cc_start: 0.6732 (m-80) cc_final: 0.6397 (t80)
REVERT: A  703 GLU cc_start: 0.8295 (pm20) cc_final: 0.8068 (pm20)
REVERT: A  721 GLN cc_start: 0.8190 (tt0) cc_final: 0.7895 (tt0)
REVERT: A  728 PHE cc_start: 0.8130 (t80) cc_final: 0.7891 (t80)
REVERT: A  881 LYS cc_start: 0.7467 (tptm) cc_final: 0.6966 (tppt)
REVERT: A  982 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.7059 (mmt)
REVERT: A 1030 ASN cc_start: 0.7478 (m-40) cc_final: 0.7213 (m-40)
REVERT: A 1159 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6981 (t0)
REVERT: A 1219 GLU cc_start: 0.7285 (mp0) cc_final: 0.6747 (mp0)
  outliers start: 18
  outliers final: 3
  residues processed: 151
  average time/residue: 1.4159
  time to fit residues: 227.8255
Evaluate side-chains
  125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  982 MET
Chi-restraints excluded: chain A residue 1089 SER
Chi-restraints excluded: chain A residue 1137 SER
Chi-restraints excluded: chain A residue 1159 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 18 optimal weight:    0.4980
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 458 ASN
A 749 ASN
A 820 GLN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.163438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.122956 restraints weight = 9987.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.74
r_work: 0.3276 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9591  Z= 0.128
  Angle     :  0.501   7.245  13009  Z= 0.262
  Chirality :  0.039   0.142   1497
  Planarity :  0.004   0.055   1617
  Dihedral  :  8.915  75.771   1718
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.53 %
    Favored  : 85.92 %
  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:  1.94 (0.24), residues: 1173
  helix:  1.95 (0.18), residues: 790
  sheet:  0.78 (0.60), residues: 70
  loop : -0.24 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 208 
 HIS   0.006   0.001   HIS A1003 
 PHE   0.017   0.002   PHE A 940 
 TYR   0.018   0.001   TYR A 949 
 ARG   0.003   0.000   ARG A1229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04901 (  624)
  hydrogen bonds       : angle       4.03847 ( 1830)
  covalent geometry    : bond        0.00270 ( 9590)
  covalent geometry    : angle       0.50132 (13009)
  Misc. bond           : bond        0.00045 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 SER cc_start: 0.7970 (t) cc_final: 0.7338 (p)
REVERT: A  332 PHE cc_start: 0.6649 (m-80) cc_final: 0.6302 (t80)
REVERT: A  720 LEU cc_start: 0.7661 (tt) cc_final: 0.7147 (mp)
REVERT: A  874 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6482 (mtt)
REVERT: A  881 LYS cc_start: 0.7402 (tptm) cc_final: 0.6890 (tppt)
REVERT: A  928 MET cc_start: 0.8702 (mmp) cc_final: 0.8424 (mmp)
REVERT: A 1152 GLN cc_start: 0.7531 (mt0) cc_final: 0.6625 (mp-120)
  outliers start: 15
  outliers final: 4
  residues processed: 129
  average time/residue: 1.3327
  time to fit residues: 184.1984
Evaluate side-chains
  119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  874 MET
Chi-restraints excluded: chain A residue 1089 SER
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1137 SER
Chi-restraints excluded: chain A residue 1167 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS
A 749 ASN
A 820 GLN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.160801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.120032 restraints weight = 9906.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.74
r_work: 0.3263 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9591  Z= 0.143
  Angle     :  0.518   8.337  13009  Z= 0.270
  Chirality :  0.040   0.153   1497
  Planarity :  0.003   0.051   1617
  Dihedral  :  8.922  77.618   1718
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.66 %
    Favored  : 85.20 %
  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:  1.92 (0.24), residues: 1173
  helix:  1.94 (0.18), residues: 791
  sheet:  0.91 (0.59), residues: 70
  loop : -0.33 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 208 
 HIS   0.006   0.001   HIS A1003 
 PHE   0.022   0.002   PHE A 940 
 TYR   0.017   0.001   TYR A 949 
 ARG   0.003   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04999 (  624)
  hydrogen bonds       : angle       3.96414 ( 1830)
  covalent geometry    : bond        0.00319 ( 9590)
  covalent geometry    : angle       0.51753 (13009)
  Misc. bond           : bond        0.00042 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A  315 SER cc_start: 0.7957 (t) cc_final: 0.7249 (p)
REVERT: A  332 PHE cc_start: 0.6736 (m-80) cc_final: 0.6340 (t80)
REVERT: A  482 GLU cc_start: 0.7761 (tp30) cc_final: 0.7068 (tt0)
REVERT: A  720 LEU cc_start: 0.7760 (tt) cc_final: 0.7256 (mp)
REVERT: A  872 MET cc_start: 0.7594 (ttp) cc_final: 0.7351 (ptm)
REVERT: A  881 LYS cc_start: 0.7469 (tptm) cc_final: 0.6936 (tppt)
REVERT: A  918 GLN cc_start: 0.8351 (tp-100) cc_final: 0.8041 (tp40)
REVERT: A  982 MET cc_start: 0.7658 (mtt) cc_final: 0.7453 (mtt)
REVERT: A 1027 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7900 (tt)
REVERT: A 1152 GLN cc_start: 0.7586 (mt0) cc_final: 0.6648 (mp-120)
  outliers start: 11
  outliers final: 3
  residues processed: 138
  average time/residue: 1.3018
  time to fit residues: 192.3387
Evaluate side-chains
  125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1089 SER
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1137 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 113 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   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 168 ASN
A 749 ASN
A 820 GLN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.158168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.117022 restraints weight = 9986.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.75
r_work: 0.3224 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9591  Z= 0.175
  Angle     :  0.546   9.558  13009  Z= 0.284
  Chirality :  0.042   0.148   1497
  Planarity :  0.004   0.048   1617
  Dihedral  :  9.116  78.096   1718
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.29 %
    Favored  : 84.06 %
  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:  1.80 (0.24), residues: 1173
  helix:  1.83 (0.18), residues: 790
  sheet:  1.00 (0.58), residues: 70
  loop : -0.35 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 158 
 HIS   0.007   0.001   HIS A  60 
 PHE   0.022   0.002   PHE A 767 
 TYR   0.017   0.002   TYR A 949 
 ARG   0.003   0.000   ARG A 695 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05310 (  624)
  hydrogen bonds       : angle       4.03233 ( 1830)
  covalent geometry    : bond        0.00407 ( 9590)
  covalent geometry    : angle       0.54597 (13009)
  Misc. bond           : bond        0.00025 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7144 (tm-30)
REVERT: A  315 SER cc_start: 0.7967 (t) cc_final: 0.7312 (p)
REVERT: A  332 PHE cc_start: 0.6874 (m-80) cc_final: 0.6491 (t80)
REVERT: A  623 MET cc_start: 0.6445 (mmm) cc_final: 0.6052 (mpm)
REVERT: A  720 LEU cc_start: 0.7869 (tt) cc_final: 0.7651 (mt)
REVERT: A  749 ASN cc_start: 0.6903 (m-40) cc_final: 0.6671 (m110)
REVERT: A  872 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7421 (ptm)
REVERT: A  881 LYS cc_start: 0.7544 (tptm) cc_final: 0.6985 (tppt)
REVERT: A  918 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8100 (tp40)
REVERT: A 1027 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7905 (tt)
REVERT: A 1152 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.6712 (mp-120)
REVERT: A 1157 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7808 (tp)
REVERT: A 1246 LYS cc_start: 0.7538 (mmmt) cc_final: 0.7330 (mmmm)
  outliers start: 16
  outliers final: 6
  residues processed: 134
  average time/residue: 1.3352
  time to fit residues: 191.2781
Evaluate side-chains
  129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  558 ASP
Chi-restraints excluded: chain A residue  746 GLN
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1089 SER
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1137 SER
Chi-restraints excluded: chain A residue 1152 GLN
Chi-restraints excluded: chain A residue 1157 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 56 optimal weight:    0.1980
   chunk 105 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 424 ASN
A 820 GLN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.159987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.119097 restraints weight = 9972.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.76
r_work: 0.3240 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9591  Z= 0.126
  Angle     :  0.498   8.012  13009  Z= 0.259
  Chirality :  0.039   0.157   1497
  Planarity :  0.003   0.043   1617
  Dihedral  :  8.933  79.559   1718
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.80 %
    Favored  : 83.13 %
  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:  1.92 (0.24), residues: 1173
  helix:  1.95 (0.18), residues: 794
  sheet:  1.01 (0.59), residues: 70
  loop : -0.41 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 208 
 HIS   0.005   0.001   HIS A1003 
 PHE   0.023   0.001   PHE A 940 
 TYR   0.019   0.001   TYR A 949 
 ARG   0.004   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04803 (  624)
  hydrogen bonds       : angle       3.91229 ( 1830)
  covalent geometry    : bond        0.00269 ( 9590)
  covalent geometry    : angle       0.49780 (13009)
  Misc. bond           : bond        0.00030 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.965 
Fit side-chains
REVERT: A  217 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.6184 (mp)
REVERT: A  332 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6589 (t80)
REVERT: A  623 MET cc_start: 0.6507 (mmm) cc_final: 0.6216 (mpm)
REVERT: A  720 LEU cc_start: 0.7865 (tt) cc_final: 0.7641 (mt)
REVERT: A  749 ASN cc_start: 0.6986 (m-40) cc_final: 0.6742 (m110)
REVERT: A  881 LYS cc_start: 0.7466 (tptm) cc_final: 0.6921 (tppt)
REVERT: A  918 GLN cc_start: 0.8409 (tp-100) cc_final: 0.8130 (tp40)
REVERT: A  925 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7369 (mtt90)
REVERT: A 1027 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7904 (tt)
REVERT: A 1152 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6767 (mp-120)
REVERT: A 1157 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7824 (tp)
REVERT: A 1246 LYS cc_start: 0.7539 (mmmt) cc_final: 0.7327 (mmmm)
  outliers start: 20
  outliers final: 5
  residues processed: 134
  average time/residue: 1.3545
  time to fit residues: 193.3107
Evaluate side-chains
  128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1089 SER
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1152 GLN
Chi-restraints excluded: chain A residue 1157 LEU
Chi-restraints excluded: chain A residue 1233 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 112 optimal weight:    0.2980
   chunk 54 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 452 GLN
A 820 GLN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 GLN
A 986 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.158507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.117350 restraints weight = 10118.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.77
r_work: 0.3217 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9591  Z= 0.156
  Angle     :  0.523   9.185  13009  Z= 0.272
  Chirality :  0.041   0.175   1497
  Planarity :  0.003   0.042   1617
  Dihedral  :  9.043  79.425   1718
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.11 %
    Favored  : 82.82 %
  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:  1.85 (0.24), residues: 1173
  helix:  1.88 (0.18), residues: 794
  sheet:  1.03 (0.59), residues: 70
  loop : -0.38 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 132 
 HIS   0.006   0.001   HIS A  60 
 PHE   0.019   0.002   PHE A 508 
 TYR   0.022   0.002   TYR A 949 
 ARG   0.005   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05064 (  624)
  hydrogen bonds       : angle       3.94599 ( 1830)
  covalent geometry    : bond        0.00354 ( 9590)
  covalent geometry    : angle       0.52326 (13009)
  Misc. bond           : bond        0.00029 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 1.480 
Fit side-chains
REVERT: A  332 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6616 (t80)
REVERT: A  623 MET cc_start: 0.6538 (mmm) cc_final: 0.6181 (mpm)
REVERT: A  720 LEU cc_start: 0.7921 (tt) cc_final: 0.7700 (mt)
REVERT: A  749 ASN cc_start: 0.6962 (m-40) cc_final: 0.6735 (m110)
REVERT: A  881 LYS cc_start: 0.7592 (tptm) cc_final: 0.7029 (tppt)
REVERT: A  918 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8201 (tp40)
REVERT: A  925 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7418 (mtt90)
REVERT: A 1027 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7945 (tt)
REVERT: A 1152 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6755 (mp-120)
REVERT: A 1157 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7868 (tp)
  outliers start: 20
  outliers final: 7
  residues processed: 136
  average time/residue: 1.6434
  time to fit residues: 239.5619
Evaluate side-chains
  126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 2.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1089 SER
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1152 GLN
Chi-restraints excluded: chain A residue 1157 LEU
Chi-restraints excluded: chain A residue 1233 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 94 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 64 optimal weight:   10.0000
   chunk 113 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.4782

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 452 GLN
A 820 GLN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 GLN
A 986 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.158267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.116490 restraints weight = 10140.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.77
r_work: 0.3223 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9591  Z= 0.173
  Angle     :  0.547   9.644  13009  Z= 0.283
  Chirality :  0.042   0.191   1497
  Planarity :  0.003   0.042   1617
  Dihedral  :  9.198  78.763   1718
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.73 %
    Favored  : 82.61 %
  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:  1.72 (0.24), residues: 1173
  helix:  1.76 (0.18), residues: 797
  sheet:  1.05 (0.59), residues: 70
  loop : -0.40 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 158 
 HIS   0.006   0.001   HIS A  60 
 PHE   0.026   0.002   PHE A 940 
 TYR   0.022   0.002   TYR A 949 
 ARG   0.005   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05254 (  624)
  hydrogen bonds       : angle       4.00385 ( 1830)
  covalent geometry    : bond        0.00402 ( 9590)
  covalent geometry    : angle       0.54677 (13009)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 1.188 
Fit side-chains
REVERT: A  315 SER cc_start: 0.7951 (t) cc_final: 0.7318 (p)
REVERT: A  332 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6594 (t80)
REVERT: A  623 MET cc_start: 0.6564 (mmm) cc_final: 0.6173 (mpm)
REVERT: A  749 ASN cc_start: 0.6884 (m-40) cc_final: 0.6680 (m110)
REVERT: A  881 LYS cc_start: 0.7607 (tptm) cc_final: 0.7004 (tppt)
REVERT: A  918 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8196 (tp40)
REVERT: A  925 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7331 (mtt90)
REVERT: A 1027 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7864 (tt)
REVERT: A 1152 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6703 (mp-120)
REVERT: A 1157 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7865 (tp)
  outliers start: 16
  outliers final: 6
  residues processed: 133
  average time/residue: 1.3587
  time to fit residues: 193.9043
Evaluate side-chains
  127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1089 SER
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1152 GLN
Chi-restraints excluded: chain A residue 1157 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 452 GLN
A 820 GLN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 GLN
A 986 GLN
A1039 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.160629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.119353 restraints weight = 9992.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.78
r_work: 0.3258 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9591  Z= 0.125
  Angle     :  0.507   9.322  13009  Z= 0.262
  Chirality :  0.040   0.211   1497
  Planarity :  0.003   0.039   1617
  Dihedral  :  8.997  79.855   1718
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.42 %
    Favored  : 82.82 %
  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:  1.92 (0.24), residues: 1173
  helix:  1.94 (0.18), residues: 793
  sheet:  1.05 (0.60), residues: 70
  loop : -0.38 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  44 
 HIS   0.006   0.001   HIS A1003 
 PHE   0.017   0.001   PHE A 508 
 TYR   0.027   0.001   TYR A 949 
 ARG   0.006   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04738 (  624)
  hydrogen bonds       : angle       3.89738 ( 1830)
  covalent geometry    : bond        0.00268 ( 9590)
  covalent geometry    : angle       0.50749 (13009)
  Misc. bond           : bond        0.00028 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A  881 LYS cc_start: 0.7520 (tptm) cc_final: 0.6945 (tppt)
REVERT: A  918 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8220 (tp40)
REVERT: A  925 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7382 (mtt90)
REVERT: A 1027 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7892 (tt)
REVERT: A 1152 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.6769 (mp-120)
REVERT: A 1157 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7837 (tp)
  outliers start: 17
  outliers final: 6
  residues processed: 130
  average time/residue: 1.5503
  time to fit residues: 214.3318
Evaluate side-chains
  128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 1.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1089 SER
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1152 GLN
Chi-restraints excluded: chain A residue 1157 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 92 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 452 GLN
A 721 GLN
A 749 ASN
A 820 GLN
A 835 ASN
A 878 GLN
A 986 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.160642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.119454 restraints weight = 10109.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.76
r_work: 0.3261 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9591  Z= 0.126
  Angle     :  0.519  13.153  13009  Z= 0.265
  Chirality :  0.040   0.210   1497
  Planarity :  0.003   0.040   1617
  Dihedral  :  8.968  80.461   1718
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 16.05 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.95 (0.24), residues: 1173
  helix:  1.96 (0.18), residues: 793
  sheet:  1.10 (0.60), residues: 70
  loop : -0.37 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 208 
 HIS   0.005   0.001   HIS A1003 
 PHE   0.021   0.001   PHE A 940 
 TYR   0.025   0.001   TYR A 949 
 ARG   0.005   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04681 (  624)
  hydrogen bonds       : angle       3.88243 ( 1830)
  covalent geometry    : bond        0.00271 ( 9590)
  covalent geometry    : angle       0.51858 (13009)
  Misc. bond           : bond        0.00026 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
REVERT: A  482 GLU cc_start: 0.7735 (tp30) cc_final: 0.7026 (tt0)
REVERT: A  881 LYS cc_start: 0.7401 (tptm) cc_final: 0.6821 (tppt)
REVERT: A  918 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8136 (tp40)
REVERT: A  925 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7261 (mtt90)
REVERT: A 1027 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7881 (tt)
REVERT: A 1152 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6637 (mp-120)
REVERT: A 1157 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7773 (tp)
  outliers start: 14
  outliers final: 6
  residues processed: 130
  average time/residue: 1.3799
  time to fit residues: 191.0329
Evaluate side-chains
  125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1089 SER
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1152 GLN
Chi-restraints excluded: chain A residue 1157 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 110 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 452 GLN
A 721 GLN
A 878 GLN
A 986 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.159308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.117674 restraints weight = 10013.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.79
r_work: 0.3238 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9591  Z= 0.150
  Angle     :  0.541  11.270  13009  Z= 0.277
  Chirality :  0.041   0.204   1497
  Planarity :  0.003   0.040   1617
  Dihedral  :  9.083  79.595   1718
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 16.25 %
    Favored  : 82.30 %
  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:  1.86 (0.24), residues: 1173
  helix:  1.87 (0.18), residues: 794
  sheet:  1.13 (0.60), residues: 70
  loop : -0.39 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1104 
 HIS   0.005   0.001   HIS A  60 
 PHE   0.021   0.002   PHE A 508 
 TYR   0.029   0.002   TYR A 949 
 ARG   0.005   0.000   ARG A  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04958 (  624)
  hydrogen bonds       : angle       3.93747 ( 1830)
  covalent geometry    : bond        0.00339 ( 9590)
  covalent geometry    : angle       0.54129 (13009)
  Misc. bond           : bond        0.00008 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7985.15 seconds
wall clock time: 138 minutes 24.16 seconds (8304.16 seconds total)