Starting phenix.real_space_refine
on Wed Sep 17 22:59:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oeb_12863/09_2025/7oeb_12863.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oeb_12863/09_2025/7oeb_12863.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2025/7oeb_12863.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2025/7oeb_12863.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2025/7oeb_12863.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2025/7oeb_12863.cif"
  }
  resolution = 3.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.020
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P       6      5.49       5
     Mg      2      5.21       5
     S      73      5.16       5
     C    7425      2.51       5
     N    1967      2.21       5
     O    2208      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11682
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "L"
      Number of atoms: 11549
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1434, 11539
          Classifications: {'peptide': 1434}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 46, 'TRANS': 1387}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 1434, 11539
          Classifications: {'peptide': 1434}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 46, 'TRANS': 1387}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 11745
    Chain: "E"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 129
          Classifications: {'RNA': 6}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3}
          Link IDs: {'rna2p': 3, 'rna3p': 2}
    Chain: "L"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 2, ' ZN': 1}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2483  SG  CYS L 321      38.338 100.395  64.570  1.00 54.49           S
  ATOM   2860  SG  CYS L 366      38.027  99.920  68.094  1.00 69.97           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS L1435 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS L1435 " occ=0.50
  Time building chain proxies: 4.90, per 1000 atoms: 0.42
  Number of scatterers: 11682
  At special positions: 0
  Unit cell: (118.261, 131.493, 101.721, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      73     16.00
     P       6     15.00
     Mg      2     11.99
     O    2208      8.00
     N    1967      7.00
     C    7425      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: 0.76
  Conformation dependent library (CDL) restraints added in 817.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN L2301 "
        pdb="ZN    ZN L2301 " - pdb=" SG  CYS L 321 "
        pdb="ZN    ZN L2301 " - pdb=" NE2 HIS L 364 "
        pdb="ZN    ZN L2301 " - pdb=" SG  CYS L 366 "


  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2754

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 10 sheets defined
      59.9% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'L' and resid 2 through 16
    Processing helix  chain 'L' and resid 19 through 32
      removed outlier: 4.550A  pdb=" N   ARG L  24 " --> pdb=" O   GLU L  20 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   GLN L  25 " --> pdb=" O   ARG L  21 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLN L  32 " --> pdb=" O   ALA L  28 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 34 through 58
    Processing helix  chain 'L' and resid 68 through 76
    Processing helix  chain 'L' and resid 108 through 131
    Processing helix  chain 'L' and resid 132 through 134
      No H-bonds generated for 'chain 'L' and resid 132 through 134'
    Processing helix  chain 'L' and resid 153 through 175
    Processing helix  chain 'L' and resid 179 through 191
    Processing helix  chain 'L' and resid 199 through 204
    Processing helix  chain 'L' and resid 211 through 223
      removed outlier: 3.731A  pdb=" N   GLU L 215 " --> pdb=" O   SER L 211 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 230 through 251
    Processing helix  chain 'L' and resid 262 through 272
    Processing helix  chain 'L' and resid 273 through 275
      No H-bonds generated for 'chain 'L' and resid 273 through 275'
    Processing helix  chain 'L' and resid 284 through 293
    Processing helix  chain 'L' and resid 296 through 303
    Processing helix  chain 'L' and resid 321 through 336
      removed outlier: 3.533A  pdb=" N   TYR L 325 " --> pdb=" O   CYS L 321 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER L 335 " --> pdb=" O   ASN L 331 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU L 336 " --> pdb=" O   LYS L 332 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 342 through 365
    Processing helix  chain 'L' and resid 385 through 404
    Processing helix  chain 'L' and resid 412 through 435
      removed outlier: 3.527A  pdb=" N   ASP L 434 " --> pdb=" O   ALA L 430 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL L 435 " --> pdb=" O   ALA L 431 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 438 through 442
    Processing helix  chain 'L' and resid 445 through 449
      removed outlier: 3.614A  pdb=" N   VAL L 448 " --> pdb=" O   ASN L 445 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 453 through 459
    Processing helix  chain 'L' and resid 491 through 507
    Processing helix  chain 'L' and resid 508 through 510
      No H-bonds generated for 'chain 'L' and resid 508 through 510'
    Processing helix  chain 'L' and resid 576 through 580
      removed outlier: 3.538A  pdb=" N   TYR L 580 " --> pdb=" O   PRO L 577 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 586 through 601
      removed outlier: 3.910A  pdb=" N   VAL L 601 " --> pdb=" O   MET L 597 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 604 through 608
    Processing helix  chain 'L' and resid 610 through 628
      removed outlier: 3.917A  pdb=" N   ILE L 614 " --> pdb=" O   GLN L 610 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 630 through 648
      removed outlier: 3.709A  pdb=" N   LEU L 640 " --> pdb=" O   LEU L 636 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ARG L 641 " --> pdb=" O   LEU L 637 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   TYR L 642 " --> pdb=" O   GLN L 638 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 655 through 661
      removed outlier: 3.570A  pdb=" N   ARG L 661 " --> pdb=" O   ILE L 657 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 666 through 684
    Processing helix  chain 'L' and resid 691 through 705
    Processing helix  chain 'L' and resid 706 through 708
      No H-bonds generated for 'chain 'L' and resid 706 through 708'
    Processing helix  chain 'L' and resid 715 through 735
      Proline residue:  L 730  - end of helix
    Processing helix  chain 'L' and resid 746 through 761
      removed outlier: 3.667A  pdb=" N   LEU L 761 " --> pdb=" O   ALA L 757 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 780 through 793
    Processing helix  chain 'L' and resid 1089 through 1096
    Processing helix  chain 'L' and resid 1137 through 1158
      removed outlier: 3.741A  pdb=" N   ILE L1147 " --> pdb=" O   PHE L1143 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU L1158 " --> pdb=" O   LEU L1154 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1165 through 1182
      removed outlier: 3.741A  pdb=" N   PHE L1169 " --> pdb=" O   ASN L1165 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1193 through 1198
    Processing helix  chain 'L' and resid 1199 through 1210
    Processing helix  chain 'L' and resid 1219 through 1236
    Processing helix  chain 'L' and resid 1242 through 1259
    Processing helix  chain 'L' and resid 1267 through 1278
    Processing helix  chain 'L' and resid 1297 through 1320
    Processing helix  chain 'L' and resid 1338 through 1348
    Processing helix  chain 'L' and resid 1348 through 1366
    Processing helix  chain 'L' and resid 1396 through 1407
    Processing helix  chain 'L' and resid 1412 through 1431
    Processing helix  chain 'L' and resid 1433 through 1451
    Processing helix  chain 'L' and resid 1465 through 1471
      removed outlier: 3.729A  pdb=" N   TRP L1469 " --> pdb=" O   ASP L1465 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1473 through 1486
    Processing helix  chain 'L' and resid 1486 through 1507
      removed outlier: 3.631A  pdb=" N   CYS L1490 " --> pdb=" O   ILE L1486 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLY L1491 " --> pdb=" O   PRO L1487 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   ARG L1492 " --> pdb=" O   ASP L1488 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE L1493 " --> pdb=" O   ALA L1489 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   THR L1506 " --> pdb=" O   ASN L1502 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY L1507 " --> pdb=" O   LYS L1503 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1524 through 1533
      removed outlier: 4.025A  pdb=" N   ASN L1528 " --> pdb=" O   SER L1524 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1541 through 1543
      No H-bonds generated for 'chain 'L' and resid 1541 through 1543'
    Processing helix  chain 'L' and resid 1579 through 1589
    Processing helix  chain 'L' and resid 1595 through 1608
      removed outlier: 4.101A  pdb=" N   ALA L1608 " --> pdb=" O   ILE L1604 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1612 through 1626
    Processing helix  chain 'L' and resid 1638 through 1649
      removed outlier: 3.791A  pdb=" N   ILE L1649 " --> pdb=" O   LEU L1645 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1674 through 1679
      removed outlier: 4.408A  pdb=" N   ILE L1678 " --> pdb=" O   ASN L1674 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   SER L1679 " --> pdb=" O   GLU L1675 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 1674 through 1679'
    Processing helix  chain 'L' and resid 1684 through 1700
    Processing helix  chain 'L' and resid 1701 through 1705
    Processing helix  chain 'L' and resid 1778 through 1790
      removed outlier: 4.045A  pdb=" N   LEU L1782 " --> pdb=" O   LYS L1778 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1795 through 1800
      removed outlier: 3.754A  pdb=" N   HIS L1798 " --> pdb=" O   LEU L1795 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ILE L1799 " --> pdb=" O   VAL L1796 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL L1800 " --> pdb=" O   SER L1797 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 1795 through 1800'
    Processing helix  chain 'L' and resid 1812 through 1817
    Processing sheet with id=AA1, first strand: chain 'L' and resid 61 through 62
      removed outlier: 6.465A  pdb=" N   LEU L  98 " --> pdb=" O   ILE L 138 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 103 through 105
    Processing sheet with id=AA3, first strand: chain 'L' and resid 207 through 208
      removed outlier: 6.367A  pdb=" N   LEU L 207 " --> pdb=" O   TYR L1107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'L' and resid 258 through 260
    Processing sheet with id=AA5, first strand: chain 'L' and resid 374 through 377
      removed outlier: 3.726A  pdb=" N   ARG L 381 " --> pdb=" O   SER L 377 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 738 through 739
      removed outlier: 7.073A  pdb=" N   PHE L1119 " --> pdb=" O   GLU L1240 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 1381 through 1383
    Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1656
      removed outlier: 8.925A  pdb=" N   GLN L1662 " --> pdb=" O   LEU L1548 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   LEU L1548 " --> pdb=" O   GLN L1662 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 1629 through 1630
    Processing sheet with id=AB1, first strand: chain 'L' and resid 1723 through 1726

    645 hydrogen bonds defined for protein.
    1851 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: 2.46

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3356
        1.33 -     1.45: 1834
        1.45 -     1.57: 6604
        1.57 -     1.69: 11
        1.69 -     1.81: 107
  Bond restraints: 11912
  Sorted by residual:
  bond pdb=" N   ILE L 348 "
       pdb=" CA  ILE L 348 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 8.10e+00
  bond pdb=" N   VAL L1712 "
       pdb=" CA  VAL L1712 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.76e+00
  bond pdb=" N   GLN L1333 "
       pdb=" CA  GLN L1333 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.18e-02 7.18e+03 7.60e+00
  bond pdb=" N   ASP L1332 "
       pdb=" CA  ASP L1332 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.27e-02 6.20e+03 6.84e+00
  bond pdb=" N   ASP L 350 "
       pdb=" CA  ASP L 350 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.20e-02 6.94e+03 6.24e+00
  ... (remaining 11907 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 15592
        1.38 -     2.75: 419
        2.75 -     4.13: 75
        4.13 -     5.50: 14
        5.50 -     6.88: 2
  Bond angle restraints: 16102
  Sorted by residual:
  angle pdb=" N   LYS L 602 "
        pdb=" CA  LYS L 602 "
        pdb=" C   LYS L 602 "
      ideal   model   delta    sigma   weight residual
     114.62  110.76    3.86 1.14e+00 7.69e-01 1.15e+01
  angle pdb=" CA  ASP L1332 "
        pdb=" C   ASP L1332 "
        pdb=" O   ASP L1332 "
      ideal   model   delta    sigma   weight residual
     121.56  117.92    3.64 1.09e+00 8.42e-01 1.12e+01
  angle pdb=" N   ASP L1331 "
        pdb=" CA  ASP L1331 "
        pdb=" C   ASP L1331 "
      ideal   model   delta    sigma   weight residual
     114.04  109.94    4.10 1.24e+00 6.50e-01 1.09e+01
  angle pdb=" O   ILE L 348 "
        pdb=" C   ILE L 348 "
        pdb=" N   PHE L 349 "
      ideal   model   delta    sigma   weight residual
     121.91  124.65   -2.74 9.80e-01 1.04e+00 7.80e+00
  angle pdb=" CA  ILE L 348 "
        pdb=" C   ILE L 348 "
        pdb=" O   ILE L 348 "
      ideal   model   delta    sigma   weight residual
     121.17  118.23    2.94 1.06e+00 8.90e-01 7.68e+00
  ... (remaining 16097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.21: 6575
       18.21 -    36.43: 538
       36.43 -    54.64: 105
       54.64 -    72.85: 33
       72.85 -    91.07: 17
  Dihedral angle restraints: 7268
    sinusoidal: 3038
      harmonic: 4230
  Sorted by residual:
  dihedral pdb=" CA  ILE L1670 "
           pdb=" C   ILE L1670 "
           pdb=" N   ARG L1671 "
           pdb=" CA  ARG L1671 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.63   20.37     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  VAL L 275 "
           pdb=" C   VAL L 275 "
           pdb=" N   ASP L 276 "
           pdb=" CA  ASP L 276 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.07   18.93     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  MET L1198 "
           pdb=" C   MET L1198 "
           pdb=" N   CYS L1199 "
           pdb=" CA  CYS L1199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.44  -18.56     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 7265 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1217
       0.036 -    0.071: 452
       0.071 -    0.107: 123
       0.107 -    0.143: 34
       0.143 -    0.179: 9
  Chirality restraints: 1835
  Sorted by residual:
  chirality pdb=" CB  ILE L 138 "
            pdb=" CA  ILE L 138 "
            pdb=" CG1 ILE L 138 "
            pdb=" CG2 ILE L 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.98e-01
  chirality pdb=" CA  VAL L1712 "
            pdb=" N   VAL L1712 "
            pdb=" C   VAL L1712 "
            pdb=" CB  VAL L1712 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.33e-01
  chirality pdb=" CA  ILE L1376 "
            pdb=" N   ILE L1376 "
            pdb=" C   ILE L1376 "
            pdb=" CB  ILE L1376 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.09e-01
  ... (remaining 1832 not shown)

  Planarity restraints: 2015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L1666 "   -0.051 5.00e-02 4.00e+02   7.67e-02 9.41e+00
        pdb=" N   PRO L1667 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO L1667 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO L1667 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE L1486 "   -0.044 5.00e-02 4.00e+02   6.75e-02 7.29e+00
        pdb=" N   PRO L1487 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO L1487 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO L1487 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E  12 "   -0.028 2.00e-02 2.50e+03   1.16e-02 4.06e+00
        pdb=" N9    G E  12 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    G E  12 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G E  12 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G E  12 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    G E  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6    G E  12 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    G E  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G E  12 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G E  12 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G E  12 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G E  12 "    0.003 2.00e-02 2.50e+03
  ... (remaining 2012 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 181
        2.68 -     3.23: 11139
        3.23 -     3.79: 18525
        3.79 -     4.34: 25058
        4.34 -     4.90: 41163
  Nonbonded interactions: 96066
  Sorted by model distance:
  nonbonded pdb=" OG  SER L 498 "
            pdb=" O   ILE L 584 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" O   ASN L1586 "
            pdb=" OG  SER L1590 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" NH2 ARG L1452 "
            pdb=" OP1   U E  13 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" OD2 ASP L1332 "
            pdb=" N   LYS L1384 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OG  SER L1626 "
            pdb=" O2'   U E  11 "
     model   vdw
     2.225 3.040
  ... (remaining 96061 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.060
  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:             0.020
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.180
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
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      :  0.004   0.041  11915  Z= 0.184
  Angle     :  0.557   6.880  16102  Z= 0.313
  Chirality :  0.042   0.179   1835
  Planarity :  0.004   0.077   2015
  Dihedral  : 14.775  91.066   4514
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.04 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  0.30 %
    Favored  : 99.16 %
  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 aren not related in a simple way.
  whole:  0.94 (0.23), residues: 1413
  helix:  1.77 (0.18), residues: 797
  sheet: -0.13 (0.51), residues: 101
  loop : -1.06 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L1347 
 TYR   0.013   0.001   TYR L1187 
 PHE   0.015   0.002   PHE L 539 
 TRP   0.013   0.002   TRP L1547 
 HIS   0.004   0.001   HIS L1522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11912)
  covalent geometry    : angle       0.55750 (16102)
  hydrogen bonds       : bond        0.13112 (  645)
  hydrogen bonds       : angle       5.25496 ( 1851)
  metal coordination   : bond        0.00147 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 167
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  165 PHE cc_start: 0.7704 (t80) cc_final: 0.7197 (t80)
  outliers start: 7
  outliers final: 1
  residues processed: 172
  average time/residue: 0.1611
  time to fit residues: 36.4934
Evaluate side-chains
  89 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  341 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0770
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.9142

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

Flipped N/Q/H residues before XYZ refinement:
L 175 ASN
L 359 HIS
L 506 ASN
L 720 GLN
L1105 GLN
L1171 ASN
L1346 GLN
L1481 GLN
L1516 ASN
L1789 ASN
L1798 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.073823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.056587 restraints weight = 60580.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 3.61
r_work: 0.2929 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11915  Z= 0.130
  Angle     :  0.551   9.415  16102  Z= 0.284
  Chirality :  0.040   0.153   1835
  Planarity :  0.004   0.064   2015
  Dihedral  :  7.555  73.375   1646
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.98 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.09 %
    Favored  : 94.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.23), residues: 1413
  helix:  2.01 (0.18), residues: 807
  sheet:  0.17 (0.54), residues: 89
  loop : -0.97 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L 398 
 TYR   0.018   0.001   TYR L  15 
 PHE   0.018   0.001   PHE L1716 
 TRP   0.014   0.001   TRP L1194 
 HIS   0.008   0.001   HIS L1798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (11912)
  covalent geometry    : angle       0.55117 (16102)
  hydrogen bonds       : bond        0.03980 (  645)
  hydrogen bonds       : angle       4.13217 ( 1851)
  metal coordination   : bond        0.00099 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8087 (mp0)
REVERT: L  363 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8436 (ttp80)
REVERT: L  365 LYS cc_start: 0.8537 (mmtm) cc_final: 0.8307 (mmmt)
  outliers start: 8
  outliers final: 5
  residues processed: 96
  average time/residue: 0.1191
  time to fit residues: 15.8947
Evaluate side-chains
  87 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  100 LEU
Chi-restraints excluded: chain L residue  134 ASP
Chi-restraints excluded: chain L residue  138 ILE
Chi-restraints excluded: chain L residue  341 THR
Chi-restraints excluded: chain L residue 1817 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 135 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 136 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 138 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
L 125 GLN
L 175 ASN
L1522 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.072973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.055870 restraints weight = 62074.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 3.61
r_work: 0.2910 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2912
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2912
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11915  Z= 0.132
  Angle     :  0.517   9.452  16102  Z= 0.265
  Chirality :  0.039   0.160   1835
  Planarity :  0.004   0.058   2015
  Dihedral  :  7.453  73.372   1646
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.76 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  6.16 %
    Favored  : 93.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.23), residues: 1413
  helix:  2.17 (0.18), residues: 806
  sheet:  0.04 (0.52), residues: 92
  loop : -0.92 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 398 
 TYR   0.020   0.001   TYR L  15 
 PHE   0.012   0.001   PHE L1592 
 TRP   0.012   0.001   TRP L1194 
 HIS   0.003   0.001   HIS L 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11912)
  covalent geometry    : angle       0.51668 (16102)
  hydrogen bonds       : bond        0.03747 (  645)
  hydrogen bonds       : angle       4.00365 ( 1851)
  metal coordination   : bond        0.00119 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8054 (mp0)
REVERT: L  363 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8350 (ttp80)
REVERT: L  368 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8657 (mtmt)
REVERT: L  415 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8633 (mp10)
  outliers start: 10
  outliers final: 7
  residues processed: 99
  average time/residue: 0.1417
  time to fit residues: 19.1276
Evaluate side-chains
  87 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  100 LEU
Chi-restraints excluded: chain L residue  123 LEU
Chi-restraints excluded: chain L residue  125 GLN
Chi-restraints excluded: chain L residue  134 ASP
Chi-restraints excluded: chain L residue  138 ILE
Chi-restraints excluded: chain L residue  388 THR
Chi-restraints excluded: chain L residue 1817 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 128 optimal weight:    4.9990
   chunk 140 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.071769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.055495 restraints weight = 41976.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.91
r_work: 0.2924 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2926
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2926
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11915  Z= 0.174
  Angle     :  0.531   9.364  16102  Z= 0.272
  Chirality :  0.041   0.186   1835
  Planarity :  0.004   0.054   2015
  Dihedral  :  7.481  73.299   1645
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.83 %
    Favored  : 91.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.23), residues: 1413
  helix:  2.09 (0.18), residues: 808
  sheet: -0.29 (0.51), residues: 98
  loop : -1.00 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 398 
 TYR   0.017   0.001   TYR L  15 
 PHE   0.017   0.001   PHE L 539 
 TRP   0.008   0.001   TRP L1547 
 HIS   0.003   0.001   HIS L 653 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (11912)
  covalent geometry    : angle       0.53097 (16102)
  hydrogen bonds       : bond        0.03874 (  645)
  hydrogen bonds       : angle       4.06500 ( 1851)
  metal coordination   : bond        0.00154 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7991 (mp0)
REVERT: L  415 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8611 (mp10)
REVERT: L  483 MET cc_start: 0.8389 (mmt) cc_final: 0.8051 (mmt)
  outliers start: 9
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1403
  time to fit residues: 16.8951
Evaluate side-chains
  88 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  100 LEU
Chi-restraints excluded: chain L residue  123 LEU
Chi-restraints excluded: chain L residue  134 ASP
Chi-restraints excluded: chain L residue  138 ILE
Chi-restraints excluded: chain L residue  388 THR
Chi-restraints excluded: chain L residue  463 SER
Chi-restraints excluded: chain L residue 1298 HIS
Chi-restraints excluded: chain L residue 1780 LEU
Chi-restraints excluded: chain L residue 1817 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 110 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 120 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
L 175 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.072391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.055320 restraints weight = 62329.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 3.61
r_work: 0.2900 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11915  Z= 0.125
  Angle     :  0.490   9.915  16102  Z= 0.250
  Chirality :  0.039   0.170   1835
  Planarity :  0.004   0.051   2015
  Dihedral  :  7.374  73.430   1645
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  8.59 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.23), residues: 1413
  helix:  2.23 (0.18), residues: 806
  sheet: -0.31 (0.52), residues: 92
  loop : -0.96 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 398 
 TYR   0.018   0.001   TYR L  15 
 PHE   0.015   0.001   PHE L 539 
 TRP   0.006   0.001   TRP L1547 
 HIS   0.002   0.000   HIS L1359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (11912)
  covalent geometry    : angle       0.48984 (16102)
  hydrogen bonds       : bond        0.03512 (  645)
  hydrogen bonds       : angle       3.93580 ( 1851)
  metal coordination   : bond        0.00117 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8033 (mp0)
REVERT: L  363 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8300 (ttp80)
REVERT: L  415 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8665 (mp10)
REVERT: L  691 MET cc_start: 0.8910 (mtp) cc_final: 0.8648 (mtm)
REVERT: L 1345 MET cc_start: 0.8907 (ttp) cc_final: 0.8618 (ttm)
  outliers start: 10
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1462
  time to fit residues: 19.2522
Evaluate side-chains
  91 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  100 LEU
Chi-restraints excluded: chain L residue  123 LEU
Chi-restraints excluded: chain L residue  134 ASP
Chi-restraints excluded: chain L residue  138 ILE
Chi-restraints excluded: chain L residue  388 THR
Chi-restraints excluded: chain L residue  463 SER
Chi-restraints excluded: chain L residue 1298 HIS
Chi-restraints excluded: chain L residue 1817 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 129 optimal weight:    0.0870
   chunk 134 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 97 optimal weight:    0.2980
   chunk 100 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.0760

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

Flipped N/Q/H residues before XYZ refinement:
L1171 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.071992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.054647 restraints weight = 71414.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 3.87
r_work: 0.2882 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11915  Z= 0.124
  Angle     :  0.488  10.185  16102  Z= 0.250
  Chirality :  0.038   0.167   1835
  Planarity :  0.004   0.049   2015
  Dihedral  :  7.340  73.391   1645
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  8.89 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.23), residues: 1413
  helix:  2.27 (0.18), residues: 808
  sheet: -0.30 (0.52), residues: 92
  loop : -0.95 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  24 
 TYR   0.018   0.001   TYR L  15 
 PHE   0.015   0.001   PHE L 539 
 TRP   0.011   0.001   TRP L1194 
 HIS   0.002   0.001   HIS L 653 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11912)
  covalent geometry    : angle       0.48811 (16102)
  hydrogen bonds       : bond        0.03466 (  645)
  hydrogen bonds       : angle       3.91160 ( 1851)
  metal coordination   : bond        0.00106 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7982 (mp0)
REVERT: L  363 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8280 (ttp80)
REVERT: L  415 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8687 (mp10)
REVERT: L  473 ARG cc_start: 0.5689 (tpp-160) cc_final: 0.5364 (tpp-160)
REVERT: L  691 MET cc_start: 0.8919 (mtp) cc_final: 0.8661 (mtm)
REVERT: L 1345 MET cc_start: 0.8919 (ttp) cc_final: 0.8633 (ttm)
  outliers start: 10
  outliers final: 8
  residues processed: 92
  average time/residue: 0.1526
  time to fit residues: 19.1656
Evaluate side-chains
  91 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  100 LEU
Chi-restraints excluded: chain L residue  123 LEU
Chi-restraints excluded: chain L residue  134 ASP
Chi-restraints excluded: chain L residue  138 ILE
Chi-restraints excluded: chain L residue  388 THR
Chi-restraints excluded: chain L residue  463 SER
Chi-restraints excluded: chain L residue 1298 HIS
Chi-restraints excluded: chain L residue 1817 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 102 optimal weight:    0.4980
   chunk 76 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 104 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
L  62 HIS
** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.070754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.053752 restraints weight = 66696.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 3.68
r_work: 0.2861 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11915  Z= 0.168
  Angle     :  0.516  10.133  16102  Z= 0.264
  Chirality :  0.040   0.179   1835
  Planarity :  0.004   0.049   2015
  Dihedral  :  7.427  73.321   1645
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.89 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.23), residues: 1413
  helix:  2.20 (0.18), residues: 808
  sheet: -0.39 (0.51), residues: 98
  loop : -1.02 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  24 
 TYR   0.017   0.001   TYR L  15 
 PHE   0.015   0.001   PHE L 539 
 TRP   0.009   0.001   TRP L1194 
 HIS   0.003   0.001   HIS L 653 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (11912)
  covalent geometry    : angle       0.51647 (16102)
  hydrogen bonds       : bond        0.03774 (  645)
  hydrogen bonds       : angle       4.00108 ( 1851)
  metal coordination   : bond        0.00175 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: L  165 PHE cc_start: 0.9249 (t80) cc_final: 0.8319 (t80)
REVERT: L  169 ARG cc_start: 0.8790 (mtm180) cc_final: 0.8200 (mtm110)
REVERT: L  363 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8269 (ttp80)
REVERT: L  415 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8685 (mp10)
REVERT: L  473 ARG cc_start: 0.5742 (tpp-160) cc_final: 0.5407 (tpp-160)
REVERT: L  691 MET cc_start: 0.8922 (mtp) cc_final: 0.8649 (mtm)
REVERT: L 1672 ASP cc_start: 0.8629 (m-30) cc_final: 0.8423 (t70)
  outliers start: 8
  outliers final: 7
  residues processed: 93
  average time/residue: 0.1386
  time to fit residues: 17.6331
Evaluate side-chains
  90 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  100 LEU
Chi-restraints excluded: chain L residue  123 LEU
Chi-restraints excluded: chain L residue  138 ILE
Chi-restraints excluded: chain L residue  388 THR
Chi-restraints excluded: chain L residue  463 SER
Chi-restraints excluded: chain L residue 1298 HIS
Chi-restraints excluded: chain L residue 1817 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 117 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 120 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
L 175 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.071401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.054262 restraints weight = 70935.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 3.82
r_work: 0.2872 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11915  Z= 0.131
  Angle     :  0.502  10.094  16102  Z= 0.256
  Chirality :  0.039   0.198   1835
  Planarity :  0.004   0.048   2015
  Dihedral  :  7.370  73.403   1645
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  9.12 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.23), residues: 1413
  helix:  2.23 (0.18), residues: 808
  sheet:  0.01 (0.56), residues: 86
  loop : -1.02 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  24 
 TYR   0.015   0.001   TYR L  15 
 PHE   0.015   0.001   PHE L 539 
 TRP   0.010   0.001   TRP L1194 
 HIS   0.002   0.001   HIS L 653 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11912)
  covalent geometry    : angle       0.50173 (16102)
  hydrogen bonds       : bond        0.03536 (  645)
  hydrogen bonds       : angle       3.93146 ( 1851)
  metal coordination   : bond        0.00118 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: L  169 ARG cc_start: 0.8784 (mtm180) cc_final: 0.8243 (mtm110)
REVERT: L  363 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8270 (ttp80)
REVERT: L  415 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8676 (mp10)
REVERT: L  691 MET cc_start: 0.8908 (mtp) cc_final: 0.8637 (mtm)
REVERT: L 1345 MET cc_start: 0.8927 (ttp) cc_final: 0.8645 (ttm)
REVERT: L 1672 ASP cc_start: 0.8655 (m-30) cc_final: 0.8449 (t70)
  outliers start: 10
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1415
  time to fit residues: 18.6476
Evaluate side-chains
  90 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  100 LEU
Chi-restraints excluded: chain L residue  123 LEU
Chi-restraints excluded: chain L residue  138 ILE
Chi-restraints excluded: chain L residue  388 THR
Chi-restraints excluded: chain L residue  463 SER
Chi-restraints excluded: chain L residue 1298 HIS
Chi-restraints excluded: chain L residue 1817 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
L 324 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.071350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.055700 restraints weight = 36021.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 2.63
r_work: 0.2941 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11915  Z= 0.131
  Angle     :  0.501  10.204  16102  Z= 0.256
  Chirality :  0.039   0.190   1835
  Planarity :  0.004   0.047   2015
  Dihedral  :  7.344  73.388   1645
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  9.35 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.23), residues: 1413
  helix:  2.24 (0.18), residues: 808
  sheet: -0.35 (0.52), residues: 98
  loop : -1.00 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  24 
 TYR   0.015   0.001   TYR L  15 
 PHE   0.014   0.001   PHE L 539 
 TRP   0.010   0.001   TRP L1194 
 HIS   0.002   0.001   HIS L 653 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11912)
  covalent geometry    : angle       0.50092 (16102)
  hydrogen bonds       : bond        0.03510 (  645)
  hydrogen bonds       : angle       3.91363 ( 1851)
  metal coordination   : bond        0.00118 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: L  165 PHE cc_start: 0.9237 (t80) cc_final: 0.8383 (t80)
REVERT: L  169 ARG cc_start: 0.8749 (mtm180) cc_final: 0.8191 (mtm180)
REVERT: L  363 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8251 (ttp80)
REVERT: L  415 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8623 (mp10)
REVERT: L  691 MET cc_start: 0.8836 (mtp) cc_final: 0.8582 (mtm)
REVERT: L 1345 MET cc_start: 0.8907 (ttp) cc_final: 0.8620 (ttm)
  outliers start: 7
  outliers final: 7
  residues processed: 90
  average time/residue: 0.1429
  time to fit residues: 17.6830
Evaluate side-chains
  90 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  100 LEU
Chi-restraints excluded: chain L residue  123 LEU
Chi-restraints excluded: chain L residue  138 ILE
Chi-restraints excluded: chain L residue  388 THR
Chi-restraints excluded: chain L residue  463 SER
Chi-restraints excluded: chain L residue 1298 HIS
Chi-restraints excluded: chain L residue 1817 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 104 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 141 optimal weight:    0.0050
   chunk 75 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0870
   chunk 10 optimal weight:    5.9990
   chunk 125 optimal weight:    7.9990
   overall best weight:    0.7174

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.072165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.055494 restraints weight = 57878.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 3.41
r_work: 0.2915 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11915  Z= 0.105
  Angle     :  0.488  10.444  16102  Z= 0.249
  Chirality :  0.038   0.189   1835
  Planarity :  0.004   0.047   2015
  Dihedral  :  7.278  73.443   1645
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  9.57 %
    Favored  : 89.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.23), residues: 1413
  helix:  2.30 (0.18), residues: 808
  sheet: -0.02 (0.58), residues: 82
  loop : -0.98 (0.27), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  24 
 TYR   0.015   0.001   TYR L  15 
 PHE   0.015   0.001   PHE L 539 
 TRP   0.011   0.001   TRP L1194 
 HIS   0.002   0.000   HIS L1359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (11912)
  covalent geometry    : angle       0.48822 (16102)
  hydrogen bonds       : bond        0.03280 (  645)
  hydrogen bonds       : angle       3.83159 ( 1851)
  metal coordination   : bond        0.00103 (    3)

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

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

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2826 Ramachandran restraints generated.
    1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
REVERT: L    1 MET cc_start: 0.6098 (tmm) cc_final: 0.5875 (tmm)
REVERT: L   40 MET cc_start: 0.7830 (tpt) cc_final: 0.7552 (tpt)
REVERT: L  165 PHE cc_start: 0.9201 (t80) cc_final: 0.8656 (t80)
REVERT: L  169 ARG cc_start: 0.8751 (mtm180) cc_final: 0.8144 (mtm180)
REVERT: L  363 ARG cc_start: 0.8519 (ttp80) cc_final: 0.8260 (ttp80)
REVERT: L  415 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8668 (mp10)
REVERT: L  691 MET cc_start: 0.8915 (mtp) cc_final: 0.8646 (mtm)
REVERT: L 1345 MET cc_start: 0.8881 (ttp) cc_final: 0.8611 (ttm)
  outliers start: 6
  outliers final: 6
  residues processed: 90
  average time/residue: 0.1355
  time to fit residues: 16.7730
Evaluate side-chains
  91 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  100 LEU
Chi-restraints excluded: chain L residue  123 LEU
Chi-restraints excluded: chain L residue  138 ILE
Chi-restraints excluded: chain L residue  388 THR
Chi-restraints excluded: chain L residue 1298 HIS
Chi-restraints excluded: chain L residue 1817 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 135 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 131 optimal weight:    7.9990
   chunk 98 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0470
   chunk 129 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6878

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.072185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.056366 restraints weight = 41124.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.82
r_work: 0.2961 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11915  Z= 0.103
  Angle     :  0.482  10.375  16102  Z= 0.245
  Chirality :  0.038   0.189   1835
  Planarity :  0.004   0.047   2015
  Dihedral  :  7.238  73.431   1645
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  9.50 %
    Favored  : 89.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.23), residues: 1413
  helix:  2.32 (0.18), residues: 810
  sheet: -0.07 (0.58), residues: 82
  loop : -0.95 (0.27), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  24 
 TYR   0.015   0.001   TYR L  15 
 PHE   0.014   0.001   PHE L 539 
 TRP   0.010   0.001   TRP L1194 
 HIS   0.003   0.000   HIS L  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (11912)
  covalent geometry    : angle       0.48162 (16102)
  hydrogen bonds       : bond        0.03232 (  645)
  hydrogen bonds       : angle       3.79760 ( 1851)
  metal coordination   : bond        0.00089 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3227.01 seconds
wall clock time: 56 minutes 8.59 seconds (3368.59 seconds total)