Starting phenix.real_space_refine
on Tue Mar  3 15:19:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pdf_13336/03_2026/7pdf_13336.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pdf_13336/03_2026/7pdf_13336.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pdf_13336/03_2026/7pdf_13336.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pdf_13336/03_2026/7pdf_13336.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pdf_13336/03_2026/7pdf_13336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pdf_13336/03_2026/7pdf_13336.map"
  }
  resolution = 3.8
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 81 atoms to isotropic.
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       3      5.49       5
     Mg      1      5.21       5
     S      46      5.16       5
     C    4055      2.51       5
     N    1107      2.21       5
     O    1215      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6427
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3585
          Classifications: {'peptide': 453}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 9, 'TRANS': 443}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2809
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 13, 'TRANS': 327}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GSP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.55, per 1000 atoms: 0.24
  Number of scatterers: 6427
  At special positions: 0
  Unit cell: (109.35, 105.3, 102.06, 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      46     16.00
     P       3     15.00
     Mg      1     11.99
     O    1215      8.00
     N    1107      7.00
     C    4055      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 228.8 milliseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 5 sheets defined
      47.6% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 321 through 336
      removed outlier: 4.198A  pdb=" N   VAL A 325 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 346
    Processing helix  chain 'A' and resid 354 through 359
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 413 through 434
    Processing helix  chain 'A' and resid 457 through 478
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 4.120A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 1021 through 1037
      removed outlier: 4.073A  pdb=" N   MET A1025 " --> pdb=" O   LYS A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1048
      removed outlier: 3.758A  pdb=" N   LYS A1046 " --> pdb=" O   ALA A1042 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   VAL A1047 " --> pdb=" O   GLU A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1098
      removed outlier: 3.681A  pdb=" N   TYR A1083 " --> pdb=" O   GLY A1079 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASP A1092 " --> pdb=" O   GLU A1088 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE A1093 " --> pdb=" O   LEU A1089 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   SER A1098 " --> pdb=" O   ASP A1094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1133
      No H-bonds generated for 'chain 'A' and resid 1131 through 1133'
    Processing helix  chain 'A' and resid 1134 through 1156
    Processing helix  chain 'A' and resid 1190 through 1201
    Processing helix  chain 'A' and resid 1211 through 1219
      removed outlier: 4.089A  pdb=" N   LYS A1219 " --> pdb=" O   ARG A1215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 38
    Processing helix  chain 'B' and resid 52 through 65
    Processing helix  chain 'B' and resid 89 through 110
      removed outlier: 4.031A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 123
      No H-bonds generated for 'chain 'B' and resid 121 through 123'
    Processing helix  chain 'B' and resid 124 through 134
    Processing helix  chain 'B' and resid 143 through 156
      removed outlier: 3.677A  pdb=" N   ASP B 156 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 165
      removed outlier: 3.623A  pdb=" N   ARG B 165 " --> pdb=" O   ALA B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 184
      removed outlier: 3.650A  pdb=" N   ASP B 180 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   VAL B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 187
      No H-bonds generated for 'chain 'B' and resid 185 through 187'
    Processing helix  chain 'B' and resid 193 through 199
    Processing helix  chain 'B' and resid 233 through 237
    Processing helix  chain 'B' and resid 264 through 278
      removed outlier: 3.534A  pdb=" N   ASN B 278 " --> pdb=" O   LYS B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 304
      removed outlier: 3.563A  pdb=" N   LEU B 297 " --> pdb=" O   LYS B 293 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY B 304 " --> pdb=" O   LYS B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 312
    Processing helix  chain 'B' and resid 313 through 316
      removed outlier: 3.549A  pdb=" N   ALA B 316 " --> pdb=" O   PRO B 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 313 through 316'
    Processing helix  chain 'B' and resid 331 through 347
    Processing helix  chain 'B' and resid 368 through 388
      removed outlier: 3.854A  pdb=" N   LEU B 388 " --> pdb=" O   GLN B 384 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 439
      removed outlier: 7.265A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 7.265A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   GLN A 389 " --> pdb=" O   CYS A 497 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   GLU A 391 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL A 495 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   HIS A 530 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   VAL A 488 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1106 through 1109
      removed outlier: 7.214A  pdb=" N   MET A1116 " --> pdb=" O   ILE A1108 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   HIS A1170 " --> pdb=" O   SER A1210 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   THR A1240 " --> pdb=" O   GLY A1228 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   GLY A1228 " --> pdb=" O   THR A1240 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 213
      removed outlier: 5.891A  pdb=" N   HIS B  41 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   PHE B 222 " --> pdb=" O   HIS B  41 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   LEU B  43 " --> pdb=" O   PHE B 222 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ALA B 243 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ARG B  42 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ILE B 245 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   LEU B  44 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    891 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: 1.05

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1988
        1.33 -     1.45: 969
        1.45 -     1.57: 3514
        1.57 -     1.69: 5
        1.69 -     1.81: 72
  Bond restraints: 6548
  Sorted by residual:
  bond pdb=" CB  GLU A1088 "
       pdb=" CG  GLU A1088 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.53e+00
  bond pdb=" CB  GLN B  59 "
       pdb=" CG  GLN B  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.41e+00
  bond pdb=" CB  TRP A 510 "
       pdb=" CG  TRP A 510 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.05e+00
  bond pdb=" CG1 ILE B 288 "
       pdb=" CD1 ILE B 288 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 2.02e+00
  bond pdb=" CB  TRP A1188 "
       pdb=" CG  TRP A1188 "
    ideal  model  delta    sigma   weight residual
    1.498  1.457  0.041 3.10e-02 1.04e+03 1.77e+00
  ... (remaining 6543 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 8631
        2.38 -     4.77: 180
        4.77 -     7.15: 16
        7.15 -     9.53: 2
        9.53 -    11.91: 1
  Bond angle restraints: 8830
  Sorted by residual:
  angle pdb=" C   LYS A 437 "
        pdb=" N   ILE A 438 "
        pdb=" CA  ILE A 438 "
      ideal   model   delta    sigma   weight residual
     123.16  118.62    4.54 1.06e+00 8.90e-01 1.83e+01
  angle pdb=" C   TYR A 445 "
        pdb=" N   TYR A 446 "
        pdb=" CA  TYR A 446 "
      ideal   model   delta    sigma   weight residual
     121.75  115.52    6.23 1.73e+00 3.34e-01 1.30e+01
  angle pdb=" N   ILE A1178 "
        pdb=" CA  ILE A1178 "
        pdb=" C   ILE A1178 "
      ideal   model   delta    sigma   weight residual
     110.74  113.98   -3.24 9.10e-01 1.21e+00 1.27e+01
  angle pdb=" CA  LEU A 496 "
        pdb=" CB  LEU A 496 "
        pdb=" CG  LEU A 496 "
      ideal   model   delta    sigma   weight residual
     116.30  128.21  -11.91 3.50e+00 8.16e-02 1.16e+01
  angle pdb=" C1' GSP B 501 "
        pdb=" C2' GSP B 501 "
        pdb=" C3' GSP B 501 "
      ideal   model   delta    sigma   weight residual
     111.00  102.48    8.52 3.00e+00 1.11e-01 8.07e+00
  ... (remaining 8825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 3469
       17.01 -    34.02: 398
       34.02 -    51.03: 75
       51.03 -    68.05: 10
       68.05 -    85.06: 5
  Dihedral angle restraints: 3957
    sinusoidal: 1643
      harmonic: 2314
  Sorted by residual:
  dihedral pdb=" CA  VAL B 114 "
           pdb=" C   VAL B 114 "
           pdb=" N   PRO B 115 "
           pdb=" CA  PRO B 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.19   29.81     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  SER A 511 "
           pdb=" C   SER A 511 "
           pdb=" N   ASN A 512 "
           pdb=" CA  ASN A 512 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.98   25.02     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  VAL A1177 "
           pdb=" C   VAL A1177 "
           pdb=" N   ILE A1178 "
           pdb=" CA  ILE A1178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.22  -23.78     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 3954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 540
       0.037 -    0.073: 293
       0.073 -    0.110: 102
       0.110 -    0.146: 21
       0.146 -    0.183: 3
  Chirality restraints: 959
  Sorted by residual:
  chirality pdb=" C2' GSP B 501 "
            pdb=" C1' GSP B 501 "
            pdb=" C3' GSP B 501 "
            pdb=" O2' GSP B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.65    0.18 2.00e-01 2.50e+01 8.37e-01
  chirality pdb=" C3' GSP B 501 "
            pdb=" C2' GSP B 501 "
            pdb=" C4' GSP B 501 "
            pdb=" O3' GSP B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.65    0.18 2.00e-01 2.50e+01 8.28e-01
  chirality pdb=" CB  ILE B 235 "
            pdb=" CA  ILE B 235 "
            pdb=" CG1 ILE B 235 "
            pdb=" CG2 ILE B 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.39e-01
  ... (remaining 956 not shown)

  Planarity restraints: 1140
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1037 "   -0.031 5.00e-02 4.00e+02   4.68e-02 3.51e+00
        pdb=" N   PRO A1038 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A1038 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A1038 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 385 "   -0.006 2.00e-02 2.50e+03   1.19e-02 2.48e+00
        pdb=" CG  PHE A 385 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 385 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 385 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 385 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 385 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 385 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 114 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO B 115 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 115 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 115 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1137 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 71
        2.49 -     3.09: 5038
        3.09 -     3.69: 10076
        3.69 -     4.30: 14353
        4.30 -     4.90: 23454
  Nonbonded interactions: 52992
  Sorted by model distance:
  nonbonded pdb=" O2G GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     1.885 2.170
  nonbonded pdb=" O2B GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     1.916 2.170
  nonbonded pdb=" O   ALA A 412 "
            pdb=" OG  SER A1052 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" OE2 GLU A1211 "
            pdb=" NH2 ARG A1215 "
     model   vdw
     2.142 3.120
  nonbonded pdb=" O1B GSP B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     2.151 2.170
  ... (remaining 52987 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.140
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
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      :  0.008   0.055   6548  Z= 0.368
  Angle     :  0.829  11.913   8830  Z= 0.465
  Chirality :  0.048   0.183    959
  Planarity :  0.004   0.047   1140
  Dihedral  : 14.632  85.056   2463
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 12.36 %
    Favored  : 87.36 %
  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: -4.24 (0.24), residues: 782
  helix: -2.27 (0.21), residues: 368
  sheet: -2.71 (0.40), residues: 121
  loop : -3.38 (0.29), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1026 
 TYR   0.020   0.002   TYR A1083 
 PHE   0.025   0.002   PHE A 385 
 TRP   0.010   0.002   TRP B 277 
 HIS   0.010   0.002   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00819 ( 6548)
  covalent geometry    : angle       0.82899 ( 8830)
  hydrogen bonds       : bond        0.13693 (  294)
  hydrogen bonds       : angle       7.17844 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.8712 (tpp) cc_final: 0.8231 (mmt)
REVERT: A  413 HIS cc_start: 0.8169 (t70) cc_final: 0.7754 (t-90)
REVERT: A 1094 ASP cc_start: 0.8101 (m-30) cc_final: 0.7700 (m-30)
REVERT: A 1106 GLU cc_start: 0.8256 (mp0) cc_final: 0.7772 (mp0)
REVERT: A 1136 LEU cc_start: 0.9520 (mt) cc_final: 0.9213 (mt)
REVERT: A 1157 MET cc_start: 0.8314 (tpp) cc_final: 0.7724 (tpp)
REVERT: B  151 LYS cc_start: 0.7686 (mmpt) cc_final: 0.7471 (mmtt)
  outliers start: 2
  outliers final: 2
  residues processed: 125
  average time/residue: 0.1009
  time to fit residues: 16.0501
Evaluate side-chains
  90 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0370
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 420 ASN
A 458 HIS
A1040 HIS
A1044 GLN
B  41 HIS
B  98 ASN
B 124 ASN
B 136 ASN
B 267 GLN
B 271 ASN
B 294 GLN
B 362 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.118237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.093360 restraints weight = 14217.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.096178 restraints weight = 7739.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.098124 restraints weight = 5327.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.099333 restraints weight = 4206.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.099995 restraints weight = 3631.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6548  Z= 0.131
  Angle     :  0.610   8.116   8830  Z= 0.317
  Chirality :  0.043   0.154    959
  Planarity :  0.004   0.055   1140
  Dihedral  :  5.385  49.458    884
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.37 %
    Favored  : 83.48 %
  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: -2.38 (0.28), residues: 782
  helix: -0.43 (0.26), residues: 377
  sheet: -2.36 (0.41), residues: 123
  loop : -2.69 (0.32), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 389 
 TYR   0.014   0.002   TYR B 163 
 PHE   0.013   0.001   PHE A1142 
 TRP   0.012   0.001   TRP A1159 
 HIS   0.004   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6548)
  covalent geometry    : angle       0.60996 ( 8830)
  hydrogen bonds       : bond        0.04273 (  294)
  hydrogen bonds       : angle       5.21330 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  326 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7242 (tp30)
REVERT: A  333 MET cc_start: 0.8724 (tpp) cc_final: 0.8223 (mmt)
REVERT: A  413 HIS cc_start: 0.8080 (t70) cc_final: 0.7654 (t-90)
REVERT: A  464 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: A 1094 ASP cc_start: 0.8151 (m-30) cc_final: 0.7787 (m-30)
REVERT: A 1136 LEU cc_start: 0.9200 (mt) cc_final: 0.8954 (mt)
REVERT: A 1157 MET cc_start: 0.7965 (tpp) cc_final: 0.7200 (tpp)
REVERT: B   59 GLN cc_start: 0.8372 (tp-100) cc_final: 0.7975 (tp40)
REVERT: B  125 GLN cc_start: 0.8139 (tp40) cc_final: 0.7707 (tp-100)
REVERT: B  198 LEU cc_start: 0.9191 (mt) cc_final: 0.8651 (mt)
  outliers start: 15
  outliers final: 6
  residues processed: 139
  average time/residue: 0.0756
  time to fit residues: 14.3595
Evaluate side-chains
  110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1027 ASP
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  379 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0970
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 5 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.118066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.093428 restraints weight = 14260.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.096240 restraints weight = 7793.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.098085 restraints weight = 5380.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.099291 restraints weight = 4271.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.099838 restraints weight = 3701.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6548  Z= 0.143
  Angle     :  0.602   9.104   8830  Z= 0.310
  Chirality :  0.043   0.152    959
  Planarity :  0.003   0.052   1140
  Dihedral  :  5.078  46.705    882
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.97 %
    Favored  : 78.02 %
  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 (0.29), residues: 782
  helix:  0.13 (0.26), residues: 376
  sheet: -2.09 (0.40), residues: 134
  loop : -2.34 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 389 
 TYR   0.016   0.002   TYR B 130 
 PHE   0.015   0.001   PHE B 140 
 TRP   0.008   0.001   TRP A1159 
 HIS   0.003   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6548)
  covalent geometry    : angle       0.60206 ( 8830)
  hydrogen bonds       : bond        0.04147 (  294)
  hydrogen bonds       : angle       4.94288 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 GLU cc_start: 0.8046 (pp20) cc_final: 0.7315 (tm-30)
REVERT: A  326 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7370 (tp30)
REVERT: A  333 MET cc_start: 0.8724 (tpp) cc_final: 0.8315 (mmt)
REVERT: A  413 HIS cc_start: 0.8118 (t70) cc_final: 0.7709 (t-90)
REVERT: A  464 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7743 (mt-10)
REVERT: A 1094 ASP cc_start: 0.8141 (m-30) cc_final: 0.7845 (m-30)
REVERT: A 1136 LEU cc_start: 0.9214 (mt) cc_final: 0.8975 (mt)
REVERT: A 1157 MET cc_start: 0.7888 (tpp) cc_final: 0.7369 (tpp)
REVERT: B  110 MET cc_start: 0.8620 (mtp) cc_final: 0.8296 (mtt)
REVERT: B  125 GLN cc_start: 0.7976 (tp40) cc_final: 0.7510 (tp-100)
  outliers start: 14
  outliers final: 7
  residues processed: 127
  average time/residue: 0.0728
  time to fit residues: 12.8998
Evaluate side-chains
  108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1138 ILE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  379 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0670
   chunk 38 optimal weight:    0.0970
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
A 491 HIS
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.120266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.095739 restraints weight = 14161.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.098604 restraints weight = 7688.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.100460 restraints weight = 5291.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.101680 restraints weight = 4231.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.102258 restraints weight = 3661.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6548  Z= 0.116
  Angle     :  0.581  10.062   8830  Z= 0.296
  Chirality :  0.042   0.139    959
  Planarity :  0.003   0.052   1140
  Dihedral  :  4.843  46.912    882
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 20.98 %
    Favored  : 77.16 %
  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: -1.25 (0.29), residues: 782
  helix:  0.54 (0.27), residues: 372
  sheet: -2.00 (0.39), residues: 139
  loop : -2.01 (0.34), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 389 
 TYR   0.012   0.001   TYR A1214 
 PHE   0.011   0.001   PHE A1142 
 TRP   0.008   0.001   TRP A1159 
 HIS   0.011   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6548)
  covalent geometry    : angle       0.58073 ( 8830)
  hydrogen bonds       : bond        0.03926 (  294)
  hydrogen bonds       : angle       4.72567 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 GLU cc_start: 0.7969 (pp20) cc_final: 0.7299 (tm-30)
REVERT: A  413 HIS cc_start: 0.8071 (t70) cc_final: 0.7652 (t-90)
REVERT: A  464 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7804 (mt-10)
REVERT: A 1094 ASP cc_start: 0.8141 (m-30) cc_final: 0.7892 (m-30)
REVERT: A 1157 MET cc_start: 0.7625 (tpp) cc_final: 0.6949 (tpp)
REVERT: B   37 TYR cc_start: 0.8259 (t80) cc_final: 0.8047 (t80)
REVERT: B  110 MET cc_start: 0.8558 (mtp) cc_final: 0.8272 (mtt)
REVERT: B  125 GLN cc_start: 0.7851 (tp40) cc_final: 0.7406 (pt0)
  outliers start: 13
  outliers final: 5
  residues processed: 123
  average time/residue: 0.0754
  time to fit residues: 12.6508
Evaluate side-chains
  109 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 68 optimal weight:    0.0980
   chunk 7 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0370
   chunk 32 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
A1075 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.121041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.096463 restraints weight = 14294.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.099381 restraints weight = 7782.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.101308 restraints weight = 5343.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.102544 restraints weight = 4233.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.102931 restraints weight = 3663.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6548  Z= 0.115
  Angle     :  0.580  10.480   8830  Z= 0.296
  Chirality :  0.042   0.136    959
  Planarity :  0.003   0.052   1140
  Dihedral  :  4.732  47.031    882
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 22.13 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.29), residues: 782
  helix:  0.68 (0.27), residues: 372
  sheet: -1.84 (0.39), residues: 139
  loop : -1.80 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1026 
 TYR   0.017   0.001   TYR A1214 
 PHE   0.010   0.001   PHE B 212 
 TRP   0.006   0.001   TRP A1159 
 HIS   0.010   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6548)
  covalent geometry    : angle       0.58038 ( 8830)
  hydrogen bonds       : bond        0.03939 (  294)
  hydrogen bonds       : angle       4.64036 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 GLU cc_start: 0.7937 (pp20) cc_final: 0.7374 (tm-30)
REVERT: A  413 HIS cc_start: 0.8101 (t70) cc_final: 0.7637 (t-90)
REVERT: A 1094 ASP cc_start: 0.8147 (m-30) cc_final: 0.7865 (m-30)
REVERT: A 1157 MET cc_start: 0.7562 (tpp) cc_final: 0.6968 (tpp)
REVERT: B  110 MET cc_start: 0.8498 (mtp) cc_final: 0.8237 (mtt)
REVERT: B  125 GLN cc_start: 0.7774 (tp40) cc_final: 0.7421 (pt0)
REVERT: B  135 MET cc_start: 0.8297 (ppp) cc_final: 0.8035 (ppp)
REVERT: B  376 PHE cc_start: 0.8155 (t80) cc_final: 0.7936 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 130
  average time/residue: 0.0743
  time to fit residues: 13.2351
Evaluate side-chains
  114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 72 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0030
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
A1055 HIS
B  93 GLN
B  98 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.120392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.095973 restraints weight = 14291.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.098822 restraints weight = 7982.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.100722 restraints weight = 5538.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.101966 restraints weight = 4402.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.102490 restraints weight = 3807.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6548  Z= 0.133
  Angle     :  0.617  11.324   8830  Z= 0.311
  Chirality :  0.044   0.281    959
  Planarity :  0.003   0.050   1140
  Dihedral  :  4.756  47.222    882
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 23.13 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.29), residues: 782
  helix:  0.69 (0.27), residues: 373
  sheet: -1.98 (0.38), residues: 138
  loop : -1.50 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1084 
 TYR   0.018   0.001   TYR A1214 
 PHE   0.014   0.001   PHE B 376 
 TRP   0.006   0.001   TRP A1031 
 HIS   0.009   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6548)
  covalent geometry    : angle       0.61706 ( 8830)
  hydrogen bonds       : bond        0.03940 (  294)
  hydrogen bonds       : angle       4.67834 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7362 (p0) cc_final: 0.6134 (p0)
REVERT: A  324 GLU cc_start: 0.7963 (pp20) cc_final: 0.7457 (tm-30)
REVERT: A  413 HIS cc_start: 0.8164 (t70) cc_final: 0.7665 (t-90)
REVERT: A 1094 ASP cc_start: 0.8151 (m-30) cc_final: 0.7893 (m-30)
REVERT: A 1136 LEU cc_start: 0.9192 (mt) cc_final: 0.8927 (mt)
REVERT: B  110 MET cc_start: 0.8547 (mtp) cc_final: 0.8292 (mtt)
REVERT: B  125 GLN cc_start: 0.7758 (tp40) cc_final: 0.7394 (pt0)
REVERT: B  135 MET cc_start: 0.8403 (ppp) cc_final: 0.8117 (ppp)
  outliers start: 16
  outliers final: 7
  residues processed: 123
  average time/residue: 0.0697
  time to fit residues: 11.9989
Evaluate side-chains
  107 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 16 optimal weight:    0.1980
   chunk 5 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 76 optimal weight:    0.2980
   chunk 75 optimal weight:    0.0670
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
B 267 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.121761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.097127 restraints weight = 14135.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.100056 restraints weight = 7640.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.101978 restraints weight = 5242.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.103057 restraints weight = 4152.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.103976 restraints weight = 3631.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6548  Z= 0.117
  Angle     :  0.598  11.738   8830  Z= 0.301
  Chirality :  0.043   0.199    959
  Planarity :  0.003   0.047   1140
  Dihedral  :  4.655  47.407    882
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 24.28 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.30), residues: 782
  helix:  0.92 (0.27), residues: 365
  sheet: -1.94 (0.37), residues: 149
  loop : -1.21 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 487 
 TYR   0.021   0.001   TYR A1241 
 PHE   0.008   0.001   PHE B 212 
 TRP   0.007   0.001   TRP A1159 
 HIS   0.008   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6548)
  covalent geometry    : angle       0.59815 ( 8830)
  hydrogen bonds       : bond        0.03871 (  294)
  hydrogen bonds       : angle       4.56897 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7218 (p0) cc_final: 0.6090 (p0)
REVERT: A  347 MET cc_start: 0.6879 (mmm) cc_final: 0.6676 (mmp)
REVERT: A  413 HIS cc_start: 0.8079 (t70) cc_final: 0.7546 (t-90)
REVERT: A  486 MET cc_start: 0.8635 (tpp) cc_final: 0.8338 (mmm)
REVERT: A 1094 ASP cc_start: 0.8125 (m-30) cc_final: 0.7834 (m-30)
REVERT: A 1157 MET cc_start: 0.7246 (tpp) cc_final: 0.6869 (ttm)
REVERT: B  110 MET cc_start: 0.8449 (mtp) cc_final: 0.8229 (mtt)
REVERT: B  125 GLN cc_start: 0.7671 (tp40) cc_final: 0.7434 (pt0)
REVERT: B  135 MET cc_start: 0.8411 (ppp) cc_final: 0.8148 (ppp)
REVERT: B  360 TYR cc_start: 0.7976 (m-80) cc_final: 0.7480 (m-10)
  outliers start: 11
  outliers final: 9
  residues processed: 128
  average time/residue: 0.0689
  time to fit residues: 12.2029
Evaluate side-chains
  113 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1095 GLU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 40 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0040
   overall best weight:    0.7794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.120439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.095860 restraints weight = 14250.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.098691 restraints weight = 7868.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.100562 restraints weight = 5450.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.101743 restraints weight = 4347.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.102389 restraints weight = 3775.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6548  Z= 0.138
  Angle     :  0.629  12.693   8830  Z= 0.315
  Chirality :  0.044   0.266    959
  Planarity :  0.003   0.045   1140
  Dihedral  :  4.678  45.202    882
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 23.85 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.30), residues: 782
  helix:  0.86 (0.27), residues: 369
  sheet: -1.73 (0.38), residues: 154
  loop : -1.40 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1084 
 TYR   0.019   0.001   TYR A1241 
 PHE   0.021   0.001   PHE B 178 
 TRP   0.006   0.001   TRP A1159 
 HIS   0.007   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6548)
  covalent geometry    : angle       0.62877 ( 8830)
  hydrogen bonds       : bond        0.03905 (  294)
  hydrogen bonds       : angle       4.65090 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7198 (p0) cc_final: 0.5979 (p0)
REVERT: A  324 GLU cc_start: 0.7677 (pp20) cc_final: 0.6797 (pp20)
REVERT: A  413 HIS cc_start: 0.8040 (t70) cc_final: 0.7488 (t-90)
REVERT: A 1094 ASP cc_start: 0.8131 (m-30) cc_final: 0.7856 (m-30)
REVERT: A 1157 MET cc_start: 0.7289 (tpp) cc_final: 0.6815 (ttm)
REVERT: B  125 GLN cc_start: 0.7640 (tp40) cc_final: 0.7422 (pt0)
REVERT: B  360 TYR cc_start: 0.8045 (m-80) cc_final: 0.7549 (m-10)
  outliers start: 12
  outliers final: 9
  residues processed: 120
  average time/residue: 0.0605
  time to fit residues: 10.4607
Evaluate side-chains
  117 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue 1050 THR
Chi-restraints excluded: chain A residue 1095 GLU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 70 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 491 HIS
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.121767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.097050 restraints weight = 14267.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.099977 restraints weight = 7758.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.101876 restraints weight = 5308.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.103109 restraints weight = 4207.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.103516 restraints weight = 3634.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6548  Z= 0.122
  Angle     :  0.621  12.790   8830  Z= 0.311
  Chirality :  0.044   0.322    959
  Planarity :  0.003   0.046   1140
  Dihedral  :  4.626  46.723    882
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 25.43 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.30), residues: 782
  helix:  1.08 (0.28), residues: 362
  sheet: -1.55 (0.39), residues: 147
  loop : -1.24 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1215 
 TYR   0.021   0.001   TYR A1214 
 PHE   0.026   0.001   PHE B 178 
 TRP   0.006   0.001   TRP A1159 
 HIS   0.008   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6548)
  covalent geometry    : angle       0.62073 ( 8830)
  hydrogen bonds       : bond        0.03865 (  294)
  hydrogen bonds       : angle       4.61353 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7133 (p0) cc_final: 0.5983 (p0)
REVERT: A  413 HIS cc_start: 0.8064 (t70) cc_final: 0.7469 (t-90)
REVERT: A 1094 ASP cc_start: 0.8129 (m-30) cc_final: 0.7832 (m-30)
REVERT: A 1157 MET cc_start: 0.7199 (tpp) cc_final: 0.6834 (ttm)
REVERT: B  360 TYR cc_start: 0.7978 (m-80) cc_final: 0.7493 (m-10)
  outliers start: 9
  outliers final: 8
  residues processed: 125
  average time/residue: 0.0655
  time to fit residues: 11.5232
Evaluate side-chains
  116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1095 GLU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 33 optimal weight:    0.0980
   chunk 36 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   chunk 24 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0470
   chunk 47 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    0.2678

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.122613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.098610 restraints weight = 14116.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.101329 restraints weight = 8082.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.103023 restraints weight = 5699.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.104265 restraints weight = 4645.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.104843 restraints weight = 4009.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   6548  Z= 0.120
  Angle     :  0.671  13.394   8830  Z= 0.337
  Chirality :  0.045   0.312    959
  Planarity :  0.003   0.047   1140
  Dihedral  :  4.666  45.743    882
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 26.01 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.30), residues: 782
  helix:  0.90 (0.27), residues: 372
  sheet: -1.53 (0.38), residues: 151
  loop : -1.19 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 374 
 TYR   0.025   0.001   TYR A1214 
 PHE   0.022   0.001   PHE B 178 
 TRP   0.007   0.001   TRP A1159 
 HIS   0.008   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6548)
  covalent geometry    : angle       0.67106 ( 8830)
  hydrogen bonds       : bond        0.03911 (  294)
  hydrogen bonds       : angle       4.57474 (  891)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ASP cc_start: 0.7129 (p0) cc_final: 0.6060 (p0)
REVERT: A  413 HIS cc_start: 0.8051 (t70) cc_final: 0.7450 (t-90)
REVERT: A 1094 ASP cc_start: 0.8092 (m-30) cc_final: 0.7825 (m-30)
REVERT: A 1157 MET cc_start: 0.7045 (tpp) cc_final: 0.6824 (ttm)
REVERT: B  360 TYR cc_start: 0.7919 (m-80) cc_final: 0.7446 (m-10)
  outliers start: 9
  outliers final: 8
  residues processed: 121
  average time/residue: 0.0655
  time to fit residues: 11.3154
Evaluate side-chains
  112 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1095 GLU
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 377 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.120298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.095975 restraints weight = 14372.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.098647 restraints weight = 8329.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.100453 restraints weight = 5895.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.101593 restraints weight = 4736.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.102142 restraints weight = 4144.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   6548  Z= 0.154
  Angle     :  0.679  13.406   8830  Z= 0.344
  Chirality :  0.044   0.196    959
  Planarity :  0.003   0.046   1140
  Dihedral  :  4.842  45.924    882
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 25.72 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.30), residues: 782
  helix:  0.81 (0.27), residues: 375
  sheet: -1.47 (0.40), residues: 146
  loop : -1.29 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 374 
 TYR   0.019   0.001   TYR A1214 
 PHE   0.020   0.002   PHE B 178 
 TRP   0.009   0.001   TRP A 510 
 HIS   0.008   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6548)
  covalent geometry    : angle       0.67861 ( 8830)
  hydrogen bonds       : bond        0.04027 (  294)
  hydrogen bonds       : angle       4.71835 (  891)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1258.68 seconds
wall clock time: 22 minutes 26.89 seconds (1346.89 seconds total)