Starting phenix.real_space_refine
on Wed Feb  4 08:27:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zk5_14755/02_2026/7zk5_14755.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zk5_14755/02_2026/7zk5_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zk5_14755/02_2026/7zk5_14755.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zk5_14755/02_2026/7zk5_14755.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zk5_14755/02_2026/7zk5_14755.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zk5_14755/02_2026/7zk5_14755.map"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.043
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 2.00, per 1000 atoms: 0.21
  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: 0.85
  Conformation dependent library (CDL) restraints added in 437.9 milliseconds
  

  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: 0.23
  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: 1.40

  Time building geometry restraints manager: 1.09 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:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.310
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.090
-------------------------------------------------------------------------------
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 : 8.96
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.24), 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
 ARG   0.009   0.001   ARG A 206 
 TYR   0.022   0.002   TYR A 322 
 PHE   0.027   0.002   PHE A 331 
 TRP   0.032   0.002   TRP A 208 
 HIS   0.006   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00970 ( 9590)
  covalent geometry    : angle       1.03038 (13009)
  hydrogen bonds       : bond        0.14927 (  624)
  hydrogen bonds       : angle       5.62694 ( 1830)
  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  : 0.259 
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: 0.6190
  time to fit residues: 134.8717
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  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0030
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0010
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.165167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.124918 restraints weight = 9960.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.75
r_work: 0.3294 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1595

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= 0.132
  Angle     :  0.534   7.171  13009  Z= 0.281
  Chirality :  0.039   0.154   1497
  Planarity :  0.004   0.059   1617
  Dihedral  :  9.137  72.297   1718
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.18 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.24), residues: 1173
  helix:  1.68 (0.18), residues: 796
  sheet:  0.69 (0.61), residues: 70
  loop : -0.07 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1164 
 TYR   0.013   0.001   TYR A 949 
 PHE   0.020   0.002   PHE A 940 
 TRP   0.017   0.001   TRP A 208 
 HIS   0.007   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9590)
  covalent geometry    : angle       0.53427 (13009)
  hydrogen bonds       : bond        0.05166 (  624)
  hydrogen bonds       : angle       4.31729 ( 1830)
  Misc. bond           : bond        0.00058 (    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
  162 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  332 PHE cc_start: 0.6677 (m-80) cc_final: 0.6320 (t80)
REVERT: A  482 GLU cc_start: 0.7508 (tp30) cc_final: 0.7172 (mm-30)
REVERT: A  703 GLU cc_start: 0.8276 (pm20) cc_final: 0.8050 (pm20)
REVERT: A  881 LYS cc_start: 0.7394 (tptm) cc_final: 0.6896 (tppt)
REVERT: A 1030 ASN cc_start: 0.7422 (m-40) cc_final: 0.7154 (m-40)
REVERT: A 1159 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6945 (t0)
REVERT: A 1219 GLU cc_start: 0.7268 (mp0) cc_final: 0.6723 (mp0)
  outliers start: 19
  outliers final: 3
  residues processed: 152
  average time/residue: 0.6339
  time to fit residues: 102.1601
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  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  872 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 25 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 93 optimal weight:    0.0770
   chunk 114 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   overall best weight:    1.5542

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.158988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.118028 restraints weight = 10015.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 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: 3.82 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9591  Z= 0.185
  Angle     :  0.570  10.129  13009  Z= 0.296
  Chirality :  0.042   0.142   1497
  Planarity :  0.004   0.058   1617
  Dihedral  :  9.179  75.798   1718
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.24), residues: 1173
  helix:  1.73 (0.18), residues: 790
  sheet:  0.89 (0.60), residues: 70
  loop : -0.31 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 695 
 TYR   0.016   0.002   TYR A 949 
 PHE   0.027   0.002   PHE A 767 
 TRP   0.009   0.002   TRP A 208 
 HIS   0.009   0.002   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 9590)
  covalent geometry    : angle       0.57022 (13009)
  hydrogen bonds       : bond        0.05556 (  624)
  hydrogen bonds       : angle       4.17152 ( 1830)
  Misc. bond           : bond        0.00001 (    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
  144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  315 SER cc_start: 0.7905 (t) cc_final: 0.7298 (p)
REVERT: A  332 PHE cc_start: 0.6672 (m-80) cc_final: 0.6278 (t80)
REVERT: A  721 GLN cc_start: 0.8351 (tt0) cc_final: 0.8071 (tt0)
REVERT: A  874 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6512 (mtt)
REVERT: A  881 LYS cc_start: 0.7587 (tptm) cc_final: 0.7034 (tppt)
REVERT: A  925 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7219 (mtt90)
REVERT: A  982 MET cc_start: 0.7584 (mmt) cc_final: 0.7374 (mtt)
REVERT: A 1152 GLN cc_start: 0.7549 (mt0) cc_final: 0.6637 (mp-120)
REVERT: A 1159 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6983 (t0)
REVERT: A 1208 LYS cc_start: 0.6945 (ttpp) cc_final: 0.6682 (tttm)
  outliers start: 14
  outliers final: 3
  residues processed: 137
  average time/residue: 0.5124
  time to fit residues: 75.2001
Evaluate side-chains
  126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 121
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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 1159 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 116 optimal weight:    8.9990
   chunk 73 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.160363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.119255 restraints weight = 10055.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.77
r_work: 0.3252 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9591  Z= 0.134
  Angle     :  0.509   8.367  13009  Z= 0.265
  Chirality :  0.040   0.146   1497
  Planarity :  0.003   0.051   1617
  Dihedral  :  8.990  77.780   1718
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.77 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.24), residues: 1173
  helix:  1.88 (0.18), residues: 791
  sheet:  0.92 (0.59), residues: 70
  loop : -0.35 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  47 
 TYR   0.017   0.001   TYR A 949 
 PHE   0.023   0.002   PHE A 940 
 TRP   0.008   0.001   TRP A 208 
 HIS   0.006   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9590)
  covalent geometry    : angle       0.50872 (13009)
  hydrogen bonds       : bond        0.04974 (  624)
  hydrogen bonds       : angle       4.00063 ( 1830)
  Misc. bond           : bond        0.00037 (    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
  143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A  315 SER cc_start: 0.8124 (t) cc_final: 0.7525 (p)
REVERT: A  332 PHE cc_start: 0.6925 (m-80) cc_final: 0.6573 (t80)
REVERT: A  623 MET cc_start: 0.6508 (mmm) cc_final: 0.6130 (mpm)
REVERT: A  720 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7284 (mp)
REVERT: A  749 ASN cc_start: 0.7022 (m-40) cc_final: 0.6792 (m110)
REVERT: A  872 MET cc_start: 0.7721 (ttp) cc_final: 0.7452 (ptm)
REVERT: A  874 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6592 (mtt)
REVERT: A  881 LYS cc_start: 0.7654 (tptm) cc_final: 0.7119 (tppt)
REVERT: A  918 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8197 (tp40)
REVERT: A 1027 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7919 (tt)
REVERT: A 1152 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.6857 (mp-120)
REVERT: A 1159 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7111 (t0)
  outliers start: 18
  outliers final: 5
  residues processed: 134
  average time/residue: 0.5317
  time to fit residues: 76.1246
Evaluate side-chains
  130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  874 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 1152 GLN
Chi-restraints excluded: chain A residue 1159 ASP
Chi-restraints excluded: chain A residue 1233 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0870
   chunk 114 optimal weight:    6.9990
   chunk 70 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 90 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.6358

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.161418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.120708 restraints weight = 10053.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.75
r_work: 0.3239 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9591  Z= 0.117
  Angle     :  0.489   7.825  13009  Z= 0.254
  Chirality :  0.039   0.146   1497
  Planarity :  0.003   0.046   1617
  Dihedral  :  8.839  79.572   1718
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.98 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.24), residues: 1173
  helix:  2.00 (0.18), residues: 796
  sheet:  0.91 (0.59), residues: 70
  loop : -0.36 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  47 
 TYR   0.018   0.001   TYR A 949 
 PHE   0.017   0.001   PHE A 508 
 TRP   0.007   0.001   TRP A 208 
 HIS   0.006   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9590)
  covalent geometry    : angle       0.48850 (13009)
  hydrogen bonds       : bond        0.04684 (  624)
  hydrogen bonds       : angle       3.88252 ( 1830)
  Misc. bond           : bond        0.00037 (    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
  148 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  217 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.6081 (mp)
REVERT: A  332 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6430 (t80)
REVERT: A  482 GLU cc_start: 0.7725 (tp30) cc_final: 0.6992 (tt0)
REVERT: A  623 MET cc_start: 0.6528 (mmm) cc_final: 0.6136 (mpm)
REVERT: A  720 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6947 (mp)
REVERT: A  749 ASN cc_start: 0.6840 (m-40) cc_final: 0.6601 (m110)
REVERT: A  872 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7373 (ptm)
REVERT: A  881 LYS cc_start: 0.7265 (tptm) cc_final: 0.6704 (tppt)
REVERT: A  918 GLN cc_start: 0.8267 (tp-100) cc_final: 0.7958 (tp40)
REVERT: A 1027 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7810 (tt)
REVERT: A 1152 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6524 (mp-120)
REVERT: A 1159 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.7020 (t0)
REVERT: A 1203 ASP cc_start: 0.7001 (t0) cc_final: 0.6719 (p0)
  outliers start: 18
  outliers final: 5
  residues processed: 139
  average time/residue: 0.6268
  time to fit residues: 92.5466
Evaluate side-chains
  129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
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  720 LEU
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 1152 GLN
Chi-restraints excluded: chain A residue 1159 ASP
Chi-restraints excluded: chain A residue 1233 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0470
   chunk 69 optimal weight:    0.7980
   chunk 115 optimal weight:    9.9990
   chunk 86 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7680

-------------------------------------------------------------------------------
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 452 GLN
A 820 GLN
** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.161014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.120250 restraints weight = 10016.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.75
r_work: 0.3233 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9591  Z= 0.123
  Angle     :  0.490   7.598  13009  Z= 0.255
  Chirality :  0.039   0.143   1497
  Planarity :  0.003   0.043   1617
  Dihedral  :  8.824  79.935   1718
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.18 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.24), residues: 1173
  helix:  2.03 (0.18), residues: 796
  sheet:  0.93 (0.59), residues: 70
  loop : -0.35 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  47 
 TYR   0.019   0.001   TYR A 949 
 PHE   0.029   0.001   PHE A 940 
 TRP   0.006   0.001   TRP A 208 
 HIS   0.005   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9590)
  covalent geometry    : angle       0.49033 (13009)
  hydrogen bonds       : bond        0.04685 (  624)
  hydrogen bonds       : angle       3.85121 ( 1830)
  Misc. bond           : bond        0.00041 (    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: 21
    poor density    : 122
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7065 (tm-30)
REVERT: A  332 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6461 (t80)
REVERT: A  482 GLU cc_start: 0.7768 (tp30) cc_final: 0.7045 (tt0)
REVERT: A  720 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6996 (mp)
REVERT: A  749 ASN cc_start: 0.6880 (m-40) cc_final: 0.6651 (m110)
REVERT: A  881 LYS cc_start: 0.7312 (tptm) cc_final: 0.6756 (tppt)
REVERT: A  918 GLN cc_start: 0.8312 (tp-100) cc_final: 0.8019 (tp40)
REVERT: A 1027 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7847 (tt)
REVERT: A 1152 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6593 (mp-120)
  outliers start: 21
  outliers final: 7
  residues processed: 133
  average time/residue: 0.6496
  time to fit residues: 91.9038
Evaluate side-chains
  130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
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  720 LEU
Chi-restraints excluded: chain A residue  928 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 1152 GLN
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 17 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0980
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.160940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.119909 restraints weight = 10072.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.77
r_work: 0.3253 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2534

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= 0.121
  Angle     :  0.493   7.533  13009  Z= 0.255
  Chirality :  0.039   0.179   1497
  Planarity :  0.003   0.041   1617
  Dihedral  :  8.801  80.034   1718
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.60 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.24), residues: 1173
  helix:  2.01 (0.18), residues: 798
  sheet:  0.95 (0.59), residues: 70
  loop : -0.35 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  47 
 TYR   0.021   0.001   TYR A 949 
 PHE   0.017   0.001   PHE A 508 
 TRP   0.006   0.001   TRP A 208 
 HIS   0.005   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9590)
  covalent geometry    : angle       0.49307 (13009)
  hydrogen bonds       : bond        0.04632 (  624)
  hydrogen bonds       : angle       3.82790 ( 1830)
  Misc. bond           : bond        0.00026 (    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
  144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7073 (tm-30)
REVERT: A  332 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6488 (t80)
REVERT: A  482 GLU cc_start: 0.7778 (tp30) cc_final: 0.7014 (tt0)
REVERT: A  720 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6944 (mp)
REVERT: A  749 ASN cc_start: 0.6874 (m-40) cc_final: 0.6649 (m110)
REVERT: A  881 LYS cc_start: 0.7309 (tptm) cc_final: 0.6755 (tppt)
REVERT: A  918 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8045 (tp40)
REVERT: A  925 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7226 (mtt90)
REVERT: A 1027 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7821 (tt)
REVERT: A 1152 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6626 (mp-120)
  outliers start: 19
  outliers final: 8
  residues processed: 137
  average time/residue: 0.6710
  time to fit residues: 98.1453
Evaluate side-chains
  130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
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  720 LEU
Chi-restraints excluded: chain A residue  928 MET
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1054 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 1233 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 107 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   overall best weight:    1.9584

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.157208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.115412 restraints weight = 9990.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.77
r_work: 0.3188 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9591  Z= 0.212
  Angle     :  0.589  11.318  13009  Z= 0.304
  Chirality :  0.044   0.192   1497
  Planarity :  0.004   0.045   1617
  Dihedral  :  9.309  80.727   1718
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.24), residues: 1173
  helix:  1.71 (0.18), residues: 794
  sheet:  1.09 (0.59), residues: 70
  loop : -0.37 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  47 
 TYR   0.021   0.002   TYR A 949 
 PHE   0.029   0.002   PHE A 940 
 TRP   0.007   0.002   TRP A 158 
 HIS   0.006   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9590)
  covalent geometry    : angle       0.58896 (13009)
  hydrogen bonds       : bond        0.05621 (  624)
  hydrogen bonds       : angle       4.06454 ( 1830)
  Misc. bond           : bond        0.00000 (    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  : 0.355 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7142 (tm-30)
REVERT: A  315 SER cc_start: 0.7960 (t) cc_final: 0.7342 (p)
REVERT: A  623 MET cc_start: 0.6381 (mmm) cc_final: 0.6029 (mpm)
REVERT: A  720 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7071 (mp)
REVERT: A  749 ASN cc_start: 0.6849 (m-40) cc_final: 0.6648 (m110)
REVERT: A  881 LYS cc_start: 0.7602 (tptm) cc_final: 0.6992 (tppt)
REVERT: A  918 GLN cc_start: 0.8413 (tp-100) cc_final: 0.8130 (tp40)
REVERT: A  925 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7295 (mtt90)
REVERT: A 1027 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7868 (tt)
REVERT: A 1152 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6642 (mp-120)
  outliers start: 16
  outliers final: 5
  residues processed: 131
  average time/residue: 0.7050
  time to fit residues: 98.1341
Evaluate side-chains
  125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  720 LEU
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 36 optimal weight:    0.1980
   chunk 94 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 GLN
A 986 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.119119 restraints weight = 9940.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.77
r_work: 0.3221 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2678

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= 0.129
  Angle     :  0.514   9.565  13009  Z= 0.265
  Chirality :  0.040   0.204   1497
  Planarity :  0.003   0.040   1617
  Dihedral  :  9.029  79.233   1718
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.32 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.24), residues: 1173
  helix:  1.87 (0.18), residues: 797
  sheet:  1.09 (0.59), residues: 70
  loop : -0.39 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  47 
 TYR   0.023   0.001   TYR A 949 
 PHE   0.018   0.001   PHE A 508 
 TRP   0.007   0.001   TRP A  44 
 HIS   0.005   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9590)
  covalent geometry    : angle       0.51406 (13009)
  hydrogen bonds       : bond        0.04813 (  624)
  hydrogen bonds       : angle       3.91403 ( 1830)
  Misc. bond           : bond        0.00031 (    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
  132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7091 (tm-30)
REVERT: A  623 MET cc_start: 0.6400 (mmm) cc_final: 0.6034 (mpm)
REVERT: A  720 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7047 (mp)
REVERT: A  881 LYS cc_start: 0.7515 (tptm) cc_final: 0.6921 (tppt)
REVERT: A  918 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8126 (tp40)
REVERT: A  925 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7278 (mtt90)
REVERT: A 1027 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7831 (tt)
REVERT: A 1152 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6629 (mp-120)
  outliers start: 14
  outliers final: 5
  residues processed: 127
  average time/residue: 0.6146
  time to fit residues: 82.7442
Evaluate side-chains
  123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  720 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 48 optimal weight:    0.2980
   chunk 87 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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 749 ASN
A 820 GLN
A 835 ASN
A 878 GLN
A 986 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.159615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.118079 restraints weight = 10009.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.78
r_work: 0.3243 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2711

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= 0.141
  Angle     :  0.537  14.260  13009  Z= 0.274
  Chirality :  0.040   0.198   1497
  Planarity :  0.003   0.041   1617
  Dihedral  :  9.056  79.880   1718
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.15 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.24), residues: 1173
  helix:  1.85 (0.18), residues: 797
  sheet:  1.08 (0.60), residues: 70
  loop : -0.39 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  47 
 TYR   0.026   0.001   TYR A 949 
 PHE   0.024   0.002   PHE A 940 
 TRP   0.006   0.001   TRP A1104 
 HIS   0.005   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9590)
  covalent geometry    : angle       0.53712 (13009)
  hydrogen bonds       : bond        0.04894 (  624)
  hydrogen bonds       : angle       3.91913 ( 1830)
  Misc. bond           : bond        0.00018 (    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
  127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  623 MET cc_start: 0.6408 (mmm) cc_final: 0.6066 (mpm)
REVERT: A  720 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7092 (mp)
REVERT: A  881 LYS cc_start: 0.7585 (tptm) cc_final: 0.6992 (tppt)
REVERT: A  918 GLN cc_start: 0.8473 (tp-100) cc_final: 0.8211 (tp40)
REVERT: A  925 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7365 (mtt90)
REVERT: A 1027 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7916 (tt)
REVERT: A 1152 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6728 (mp-120)
REVERT: A 1243 GLN cc_start: 0.6537 (pt0) cc_final: 0.5669 (mt0)
  outliers start: 11
  outliers final: 5
  residues processed: 123
  average time/residue: 0.6242
  time to fit residues: 81.3459
Evaluate side-chains
  124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  720 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 96 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.160446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.119370 restraints weight = 9945.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.75
r_work: 0.3247 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2742

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= 0.128
  Angle     :  0.513  11.920  13009  Z= 0.264
  Chirality :  0.040   0.187   1497
  Planarity :  0.003   0.040   1617
  Dihedral  :  8.966  80.065   1718
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.24), residues: 1173
  helix:  1.93 (0.18), residues: 793
  sheet:  1.10 (0.60), residues: 70
  loop : -0.41 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  47 
 TYR   0.025   0.001   TYR A 949 
 PHE   0.019   0.001   PHE A 508 
 TRP   0.006   0.001   TRP A  44 
 HIS   0.005   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9590)
  covalent geometry    : angle       0.51328 (13009)
  hydrogen bonds       : bond        0.04709 (  624)
  hydrogen bonds       : angle       3.87517 ( 1830)
  Misc. bond           : bond        0.00022 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3541.05 seconds
wall clock time: 61 minutes 1.94 seconds (3661.94 seconds total)