Starting phenix.real_space_refine
on Wed Mar  4 08:06:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oea_12862/03_2026/7oea_12862.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oea_12862/03_2026/7oea_12862.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oea_12862/03_2026/7oea_12862.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oea_12862/03_2026/7oea_12862.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oea_12862/03_2026/7oea_12862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oea_12862/03_2026/7oea_12862.map"
  }
  resolution = 2.7
  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       7      5.49       5
     Mg      1      5.21       5
     S      71      5.16       5
     C    7426      2.51       5
     N    1968      2.21       5
     O    2229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 11703
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 11535
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1432, 11525
          Classifications: {'peptide': 1432}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 46, 'TRANS': 1385}
          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: 1432, 11525
          Classifications: {'peptide': 1432}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 46, 'TRANS': 1385}
          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: 11731
    Chain: "E"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 149
          Classifications: {'RNA': 7}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 3, 'rna3p': 3}
    Chain: "L"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2, 'water': 11}
          Link IDs: {None: 12}
    Chain: "E"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2475  SG  CYS L 321      37.569  99.999  65.452  1.00 57.95           S
  ATOM   2852  SG  CYS L 366      37.387  99.892  68.968  1.00 69.67           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: 4.97, per 1000 atoms: 0.42
  Number of scatterers: 11703
  At special positions: 0
  Unit cell: (117.434, 132.32, 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      71     16.00
     P       7     15.00
     Mg      1     11.99
     O    2229      8.00
     N    1968      7.00
     C    7426      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: 1.11
  Conformation dependent library (CDL) restraints added in 760.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN L2301 "
        pdb="ZN    ZN L2301 " - pdb=" SG  CYS L 366 "
        pdb="ZN    ZN L2301 " - pdb=" NE2 HIS L 364 "
        pdb="ZN    ZN L2301 " - pdb=" SG  CYS L 321 "


  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2750

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 10 sheets defined
      59.0% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'L' and resid 2 through 16
    Processing helix  chain 'L' and resid 19 through 32
      removed outlier: 4.060A  pdb=" N   ARG L  24 " --> pdb=" O   GLU L  20 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   GLN L  25 " --> pdb=" O   ARG L  21 " (cutoff:3.500A)
      removed outlier: 3.801A  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 200 through 206
      removed outlier: 3.720A  pdb=" N   LEU L 203 " --> pdb=" O   VAL L 200 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL L 205 " --> pdb=" O   SER L 202 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 211 through 223
      removed outlier: 3.777A  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 284 through 293
    Processing helix  chain 'L' and resid 296 through 303
    Processing helix  chain 'L' and resid 321 through 334
      removed outlier: 3.510A  pdb=" N   TYR L 325 " --> pdb=" O   CYS L 321 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 343 through 365
    Processing helix  chain 'L' and resid 385 through 404
    Processing helix  chain 'L' and resid 412 through 434
    Processing helix  chain 'L' and resid 438 through 443
    Processing helix  chain 'L' and resid 445 through 449
      removed outlier: 3.630A  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
    Processing helix  chain 'L' and resid 586 through 601
      removed outlier: 3.760A  pdb=" N   VAL L 601 " --> pdb=" O   MET L 597 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 608 through 610
      No H-bonds generated for 'chain 'L' and resid 608 through 610'
    Processing helix  chain 'L' and resid 611 through 628
    Processing helix  chain 'L' and resid 630 through 648
      removed outlier: 3.624A  pdb=" N   LEU L 640 " --> pdb=" O   LEU L 636 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ARG L 641 " --> pdb=" O   LEU L 637 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   TYR L 642 " --> pdb=" O   GLN L 638 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 655 through 660
    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 709
    Processing helix  chain 'L' and resid 715 through 735
      Proline residue:  L 730  - end of helix
    Processing helix  chain 'L' and resid 746 through 762
      removed outlier: 3.627A  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 1090 through 1096
    Processing helix  chain 'L' and resid 1137 through 1158
      removed outlier: 4.015A  pdb=" N   ILE L1147 " --> pdb=" O   PHE L1143 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU L1158 " --> pdb=" O   LEU L1154 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1166 through 1182
    Processing helix  chain 'L' and resid 1193 through 1198
    Processing helix  chain 'L' and resid 1199 through 1210
      removed outlier: 3.521A  pdb=" N   ASN L1209 " --> pdb=" O   ALA L1205 " (cutoff:3.500A)
    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 1279
      removed outlier: 3.535A  pdb=" N   ILE L1279 " --> pdb=" O   SER L1275 " (cutoff:3.500A)
    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 1406
    Processing helix  chain 'L' and resid 1412 through 1431
    Processing helix  chain 'L' and resid 1433 through 1451
      removed outlier: 3.509A  pdb=" N   ALA L1451 " --> pdb=" O   LEU L1447 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1465 through 1471
      removed outlier: 3.697A  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 1490 through 1506
    Processing helix  chain 'L' and resid 1524 through 1533
      removed outlier: 3.650A  pdb=" N   ASN L1528 " --> pdb=" O   SER L1524 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1539 through 1544
      removed outlier: 3.645A  pdb=" N   GLU L1544 " --> pdb=" O   GLU L1540 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1579 through 1589
    Processing helix  chain 'L' and resid 1595 through 1608
      removed outlier: 3.576A  pdb=" N   LYS L1606 " --> pdb=" O   GLU L1602 " (cutoff:3.500A)
      removed outlier: 3.949A  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: 3.647A  pdb=" N   ILE L1649 " --> pdb=" O   LEU L1645 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1674 through 1679
      removed outlier: 4.051A  pdb=" N   ILE L1678 " --> pdb=" O   ASN L1674 " (cutoff:3.500A)
      removed outlier: 3.757A  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 1788
      removed outlier: 3.952A  pdb=" N   LEU L1782 " --> pdb=" O   LYS L1778 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1796 through 1800
      removed outlier: 4.012A  pdb=" N   ILE L1799 " --> pdb=" O   VAL L1796 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   VAL L1800 " --> pdb=" O   SER L1797 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 1796 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: 6.881A  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
      removed outlier: 6.674A  pdb=" N   PHE L 104 " --> pdb=" O   ARG L 144 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'L' and resid 207 through 208
      removed outlier: 6.555A  pdb=" N   LEU L 207 " --> pdb=" O   TYR L1107 " (cutoff:3.500A)
    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 376
    Processing sheet with id=AA6, first strand: chain 'L' and resid 738 through 739
      removed outlier: 7.090A  pdb=" N   PHE L1119 " --> pdb=" O   GLU L1240 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLY L1129 " --> pdb=" O   GLN L1126 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 1380 through 1382
    Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1656
      removed outlier: 8.927A  pdb=" N   GLN L1662 " --> pdb=" O   LEU L1548 " (cutoff:3.500A)
      removed outlier: 5.537A  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

    641 hydrogen bonds defined for protein.
    1845 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: 2.18

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3566
        1.34 -     1.45: 1695
        1.45 -     1.57: 6540
        1.57 -     1.69: 14
        1.69 -     1.81: 105
  Bond restraints: 11920
  Sorted by residual:
  bond pdb=" N   PRO L1487 "
       pdb=" CA  PRO L1487 "
    ideal  model  delta    sigma   weight residual
    1.469  1.699 -0.230 1.28e-02 6.10e+03 3.23e+02
  bond pdb=" C   ILE L1486 "
       pdb=" N   PRO L1487 "
    ideal  model  delta    sigma   weight residual
    1.334  1.451 -0.117 2.34e-02 1.83e+03 2.52e+01
  bond pdb=" N   PRO L 582 "
       pdb=" CD  PRO L 582 "
    ideal  model  delta    sigma   weight residual
    1.473  1.538 -0.065 1.40e-02 5.10e+03 2.15e+01
  bond pdb=" N   ILE L1408 "
       pdb=" CA  ILE L1408 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.22e-02 6.72e+03 7.93e+00
  bond pdb=" N   VAL L1401 "
       pdb=" CA  VAL L1401 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.83e+00
  ... (remaining 11915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.22: 16113
       10.22 -    20.44: 1
       20.44 -    30.65: 2
       30.65 -    40.87: 1
       40.87 -    51.09: 1
  Bond angle restraints: 16118
  Sorted by residual:
  angle pdb=" C   LEU L1713 "
        pdb=" CA  LEU L1713 "
        pdb=" CB  LEU L1713 "
      ideal   model   delta    sigma   weight residual
     110.42  161.51  -51.09 1.99e+00 2.53e-01 6.59e+02
  angle pdb=" N   GLU L1714 "
        pdb=" CA  GLU L1714 "
        pdb=" CB  GLU L1714 "
      ideal   model   delta    sigma   weight residual
     110.49  140.03  -29.54 1.69e+00 3.50e-01 3.05e+02
  angle pdb=" C   ILE L1486 "
        pdb=" N   PRO L1487 "
        pdb=" CA  PRO L1487 "
      ideal   model   delta    sigma   weight residual
     119.84  140.61  -20.77 1.25e+00 6.40e-01 2.76e+02
  angle pdb=" N   LEU L1713 "
        pdb=" CA  LEU L1713 "
        pdb=" C   LEU L1713 "
      ideal   model   delta    sigma   weight residual
     110.80   76.13   34.67 2.13e+00 2.20e-01 2.65e+02
  angle pdb=" CA  PRO L1487 "
        pdb=" N   PRO L1487 "
        pdb=" CD  PRO L1487 "
      ideal   model   delta    sigma   weight residual
     112.00   98.11   13.89 1.40e+00 5.10e-01 9.85e+01
  ... (remaining 16113 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 6689
       17.85 -    35.70: 461
       35.70 -    53.54: 88
       53.54 -    71.39: 25
       71.39 -    89.24: 11
  Dihedral angle restraints: 7274
    sinusoidal: 3050
      harmonic: 4224
  Sorted by residual:
  dihedral pdb=" C   LEU L1713 "
           pdb=" N   LEU L1713 "
           pdb=" CA  LEU L1713 "
           pdb=" CB  LEU L1713 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -162.16   39.56     0      2.50e+00 1.60e-01 2.50e+02
  dihedral pdb=" N   GLU L1714 "
           pdb=" C   GLU L1714 "
           pdb=" CA  GLU L1714 "
           pdb=" CB  GLU L1714 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  153.98  -31.18     0      2.50e+00 1.60e-01 1.56e+02
  dihedral pdb=" C   GLU L1714 "
           pdb=" N   GLU L1714 "
           pdb=" CA  GLU L1714 "
           pdb=" CB  GLU L1714 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.06   17.46     0      2.50e+00 1.60e-01 4.88e+01
  ... (remaining 7271 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.311: 1836
       0.311 -    0.622: 0
       0.622 -    0.934: 0
       0.934 -    1.245: 1
       1.245 -    1.556: 1
  Chirality restraints: 1838
  Sorted by residual:
  chirality pdb=" CA  LEU L1713 "
            pdb=" N   LEU L1713 "
            pdb=" C   LEU L1713 "
            pdb=" CB  LEU L1713 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.95    1.56 2.00e-01 2.50e+01 6.05e+01
  chirality pdb=" CA  GLU L1714 "
            pdb=" N   GLU L1714 "
            pdb=" C   GLU L1714 "
            pdb=" CB  GLU L1714 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.39    1.12 2.00e-01 2.50e+01 3.16e+01
  chirality pdb=" CA  ILE L1408 "
            pdb=" N   ILE L1408 "
            pdb=" C   ILE L1408 "
            pdb=" CB  ILE L1408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1835 not shown)

  Planarity restraints: 2014
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS L 450 "    0.063 5.00e-02 4.00e+02   9.37e-02 1.41e+01
        pdb=" N   PRO L 451 "   -0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO L 451 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO L 451 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L1666 "   -0.044 5.00e-02 4.00e+02   6.63e-02 7.02e+00
        pdb=" N   PRO L1667 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO L1667 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO L1667 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E  12 "   -0.027 2.00e-02 2.50e+03   1.20e-02 4.28e+00
        pdb=" N9    G E  12 "    0.029 2.00e-02 2.50e+03
        pdb=" C8    G E  12 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G E  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    G E  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    G E  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6    G E  12 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G E  12 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    G E  12 "    0.002 2.00e-02 2.50e+03
        pdb=" N2    G E  12 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G E  12 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G E  12 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2011 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 118
        2.63 -     3.20: 10364
        3.20 -     3.76: 18448
        3.76 -     4.33: 25693
        4.33 -     4.90: 41967
  Nonbonded interactions: 96590
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP L1332 "
            pdb="MG    MG L2302 "
     model   vdw
     2.061 2.170
  nonbonded pdb=" OG  SER L 498 "
            pdb=" O   ILE L 584 "
     model   vdw
     2.073 3.040
  nonbonded pdb="MG    MG L2302 "
            pdb=" O   HOH L2404 "
     model   vdw
     2.092 2.170
  nonbonded pdb=" O   ASN L1586 "
            pdb=" OG  SER L1590 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OG  SER L1626 "
            pdb=" O2'   U E  11 "
     model   vdw
     2.195 3.040
  ... (remaining 96585 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:             2.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     16.190
  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:7.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
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   0.230  11923  Z= 0.228
  Angle     :  0.772  51.090  16118  Z= 0.433
  Chirality :  0.059   1.556   1838
  Planarity :  0.004   0.094   2014
  Dihedral  : 13.353  89.240   4524
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.47 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.30 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.15 %
  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:  0.83 (0.23), residues: 1411
  helix:  1.60 (0.19), residues: 811
  sheet:  1.10 (0.57), residues: 82
  loop : -1.27 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L1347 
 TYR   0.034   0.001   TYR L1187 
 PHE   0.014   0.001   PHE L1277 
 TRP   0.018   0.001   TRP L 395 
 HIS   0.006   0.001   HIS L1298 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (11920)
  covalent geometry    : angle       0.77199 (16118)
  hydrogen bonds       : bond        0.12313 (  641)
  hydrogen bonds       : angle       5.15943 ( 1845)
  metal coordination   : bond        0.00154 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   40 MET cc_start: 0.7956 (tpp) cc_final: 0.7356 (tpp)
REVERT: L   50 ILE cc_start: 0.8833 (mp) cc_final: 0.8597 (mm)
REVERT: L  120 PHE cc_start: 0.8964 (t80) cc_final: 0.8633 (t80)
REVERT: L  124 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8663 (mm-30)
REVERT: L  137 LEU cc_start: 0.6459 (tp) cc_final: 0.5389 (mp)
REVERT: L  188 GLU cc_start: 0.8711 (tt0) cc_final: 0.8463 (tp30)
REVERT: L 1257 GLN cc_start: 0.7901 (pp30) cc_final: 0.7611 (pp30)
  outliers start: 1
  outliers final: 1
  residues processed: 164
  average time/residue: 0.8486
  time to fit residues: 147.1856
Evaluate side-chains
  89 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1407 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
L  19 ASN
L 111 ASN
L 287 HIS
** L 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1105 GLN
L1184 HIS
L1298 HIS
L1481 GLN
L1597 GLN
L1798 HIS
L1823 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.074524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.050579 restraints weight = 56950.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 3.18
r_work: 0.2826 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11923  Z= 0.134
  Angle     :  0.605   9.060  16118  Z= 0.312
  Chirality :  0.040   0.159   1838
  Planarity :  0.004   0.065   2014
  Dihedral  :  8.162  73.459   1661
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.91 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.53 %
    Favored  : 91.48 %
  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:  1.06 (0.23), residues: 1411
  helix:  1.81 (0.18), residues: 822
  sheet:  0.78 (0.55), residues: 82
  loop : -1.21 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L 343 
 TYR   0.023   0.001   TYR L1187 
 PHE   0.014   0.001   PHE L 783 
 TRP   0.014   0.001   TRP L 395 
 HIS   0.009   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (11920)
  covalent geometry    : angle       0.60494 (16118)
  hydrogen bonds       : bond        0.03999 (  641)
  hydrogen bonds       : angle       4.16840 ( 1845)
  metal coordination   : bond        0.00164 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   19 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7564 (p0)
REVERT: L   40 MET cc_start: 0.7637 (tpp) cc_final: 0.7219 (tpp)
REVERT: L  120 PHE cc_start: 0.9075 (t80) cc_final: 0.8795 (t80)
REVERT: L  137 LEU cc_start: 0.7027 (tp) cc_final: 0.5797 (mp)
REVERT: L  188 GLU cc_start: 0.8965 (tt0) cc_final: 0.8668 (tp30)
REVERT: L  716 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.8100 (tpp-160)
REVERT: L 1257 GLN cc_start: 0.8296 (pp30) cc_final: 0.7995 (pp30)
REVERT: L 1509 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8882 (tm)
REVERT: L 1599 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8083 (pt)
  outliers start: 13
  outliers final: 4
  residues processed: 105
  average time/residue: 0.7569
  time to fit residues: 84.9017
Evaluate side-chains
  87 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue 1346 GLN
Chi-restraints excluded: chain L residue 1407 ASN
Chi-restraints excluded: chain L residue 1509 LEU
Chi-restraints excluded: chain L residue 1599 LEU
Chi-restraints excluded: chain L residue 1780 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 118 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 139 optimal weight:    0.9990
   chunk 140 optimal weight:    0.1980
   chunk 12 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0670
   chunk 108 optimal weight:    0.9980
   chunk 104 optimal weight:    4.9990
   overall best weight:    0.8522

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

Flipped N/Q/H residues before XYZ refinement:
L 379 ASN
** L 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1313 ASN
L1798 HIS
L1823 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.073968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.050213 restraints weight = 61209.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 3.29
r_work: 0.2816 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8873
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11923  Z= 0.127
  Angle     :  0.562   9.425  16118  Z= 0.288
  Chirality :  0.039   0.201   1838
  Planarity :  0.004   0.062   2014
  Dihedral  :  8.086  73.404   1661
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.05 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.91 %
    Favored  : 91.10 %
  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:  1.12 (0.23), residues: 1411
  helix:  1.88 (0.18), residues: 822
  sheet:  0.57 (0.54), residues: 87
  loop : -1.19 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L 716 
 TYR   0.020   0.001   TYR L1187 
 PHE   0.014   0.001   PHE L 783 
 TRP   0.011   0.001   TRP L 395 
 HIS   0.012   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (11920)
  covalent geometry    : angle       0.56181 (16118)
  hydrogen bonds       : bond        0.03751 (  641)
  hydrogen bonds       : angle       4.00569 ( 1845)
  metal coordination   : bond        0.00141 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   40 MET cc_start: 0.7695 (tpp) cc_final: 0.7285 (tpp)
REVERT: L  137 LEU cc_start: 0.6944 (tp) cc_final: 0.5725 (mp)
REVERT: L  188 GLU cc_start: 0.8946 (tt0) cc_final: 0.8658 (tp30)
REVERT: L  716 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.8116 (tpp-160)
REVERT: L 1257 GLN cc_start: 0.8370 (pp30) cc_final: 0.8019 (pp30)
REVERT: L 1509 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8843 (tm)
REVERT: L 1599 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8172 (pp)
REVERT: L 1675 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8134 (mp0)
  outliers start: 13
  outliers final: 3
  residues processed: 96
  average time/residue: 0.7243
  time to fit residues: 74.5621
Evaluate side-chains
  86 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue 1346 GLN
Chi-restraints excluded: chain L residue 1407 ASN
Chi-restraints excluded: chain L residue 1509 LEU
Chi-restraints excluded: chain L residue 1599 LEU
Chi-restraints excluded: chain L residue 1675 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 27 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 119 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 115 optimal weight:    0.0670
   chunk 89 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    0.8920

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

Flipped N/Q/H residues before XYZ refinement:
L  19 ASN
L 415 GLN
L 720 GLN
L1798 HIS
L1823 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.073658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.050186 restraints weight = 53920.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 3.07
r_work: 0.2822 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11923  Z= 0.123
  Angle     :  0.541   8.657  16118  Z= 0.277
  Chirality :  0.039   0.180   1838
  Planarity :  0.004   0.058   2014
  Dihedral  :  8.018  73.412   1661
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.69 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  9.36 %
    Favored  : 89.88 %
  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:  1.19 (0.23), residues: 1411
  helix:  1.95 (0.18), residues: 824
  sheet:  0.43 (0.55), residues: 87
  loop : -1.15 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L1557 
 TYR   0.018   0.001   TYR L1187 
 PHE   0.013   0.001   PHE L 783 
 TRP   0.011   0.001   TRP L 395 
 HIS   0.011   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11920)
  covalent geometry    : angle       0.54114 (16118)
  hydrogen bonds       : bond        0.03612 (  641)
  hydrogen bonds       : angle       3.90063 ( 1845)
  metal coordination   : bond        0.00137 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   40 MET cc_start: 0.7722 (tpp) cc_final: 0.7301 (tpp)
REVERT: L  137 LEU cc_start: 0.6960 (tp) cc_final: 0.5702 (mt)
REVERT: L  188 GLU cc_start: 0.8932 (tt0) cc_final: 0.8659 (tp30)
REVERT: L 1509 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8852 (tm)
  outliers start: 10
  outliers final: 4
  residues processed: 93
  average time/residue: 0.7221
  time to fit residues: 71.8113
Evaluate side-chains
  81 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue 1298 HIS
Chi-restraints excluded: chain L residue 1346 GLN
Chi-restraints excluded: chain L residue 1407 ASN
Chi-restraints excluded: chain L residue 1509 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 86 optimal weight:    0.0070
   chunk 107 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 129 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 2 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 108 optimal weight:    0.7980
   overall best weight:    1.1002

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

Flipped N/Q/H residues before XYZ refinement:
L1278 GLN
L1798 HIS
L1823 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.073206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.050088 restraints weight = 41993.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.70
r_work: 0.2830 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11923  Z= 0.133
  Angle     :  0.543   7.939  16118  Z= 0.280
  Chirality :  0.039   0.157   1838
  Planarity :  0.004   0.055   2014
  Dihedral  :  8.010  73.410   1661
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.12 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.20 %
    Favored  : 89.04 %
  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 (0.23), residues: 1411
  helix:  2.00 (0.18), residues: 821
  sheet:  0.45 (0.55), residues: 87
  loop : -1.14 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L 716 
 TYR   0.017   0.001   TYR L1187 
 PHE   0.016   0.001   PHE L 120 
 TRP   0.010   0.001   TRP L 395 
 HIS   0.011   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11920)
  covalent geometry    : angle       0.54279 (16118)
  hydrogen bonds       : bond        0.03647 (  641)
  hydrogen bonds       : angle       3.89070 ( 1845)
  metal coordination   : bond        0.00172 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   40 MET cc_start: 0.7682 (tpp) cc_final: 0.7262 (tpp)
REVERT: L  137 LEU cc_start: 0.6973 (tp) cc_final: 0.5735 (mt)
REVERT: L  188 GLU cc_start: 0.8887 (tt0) cc_final: 0.8640 (tp30)
REVERT: L  446 MET cc_start: 0.9237 (tpp) cc_final: 0.9012 (tpt)
REVERT: L  716 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.8165 (tpp-160)
  outliers start: 10
  outliers final: 6
  residues processed: 87
  average time/residue: 0.7054
  time to fit residues: 65.9346
Evaluate side-chains
  81 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue  116 TYR
Chi-restraints excluded: chain L residue  489 LEU
Chi-restraints excluded: chain L residue 1346 GLN
Chi-restraints excluded: chain L residue 1407 ASN
Chi-restraints excluded: chain L residue 1509 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 118 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** L1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L1798 HIS
L1823 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.072518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.049387 restraints weight = 41881.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 2.69
r_work: 0.2808 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11923  Z= 0.160
  Angle     :  0.567  10.086  16118  Z= 0.289
  Chirality :  0.041   0.327   1838
  Planarity :  0.004   0.053   2014
  Dihedral  :  8.030  73.462   1661
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.05 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 10.88 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.23), residues: 1411
  helix:  1.95 (0.18), residues: 821
  sheet:  0.49 (0.55), residues: 87
  loop : -1.14 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG L 716 
 TYR   0.017   0.001   TYR L1187 
 PHE   0.015   0.001   PHE L 783 
 TRP   0.008   0.001   TRP L 155 
 HIS   0.011   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (11920)
  covalent geometry    : angle       0.56660 (16118)
  hydrogen bonds       : bond        0.03756 (  641)
  hydrogen bonds       : angle       3.95434 ( 1845)
  metal coordination   : bond        0.00250 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   40 MET cc_start: 0.7749 (tpp) cc_final: 0.7342 (tpp)
REVERT: L  137 LEU cc_start: 0.7099 (tp) cc_final: 0.5872 (mt)
REVERT: L  188 GLU cc_start: 0.9010 (tt0) cc_final: 0.8713 (tp30)
REVERT: L  446 MET cc_start: 0.9232 (tpp) cc_final: 0.9007 (tpt)
REVERT: L  716 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.8180 (tpp-160)
  outliers start: 8
  outliers final: 4
  residues processed: 89
  average time/residue: 0.7452
  time to fit residues: 70.9796
Evaluate side-chains
  81 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue  489 LEU
Chi-restraints excluded: chain L residue 1346 GLN
Chi-restraints excluded: chain L residue 1407 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 130 optimal weight:    0.0170
   chunk 64 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 118 optimal weight:   10.0000
   chunk 35 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 121 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
L1597 GLN
L1798 HIS
L1823 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.073640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.050508 restraints weight = 50714.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.97
r_work: 0.2834 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11923  Z= 0.109
  Angle     :  0.568  11.639  16118  Z= 0.283
  Chirality :  0.039   0.296   1838
  Planarity :  0.004   0.052   2014
  Dihedral  :  7.956  73.451   1661
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.05 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 11.04 %
    Favored  : 88.36 %
  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:  1.29 (0.23), residues: 1411
  helix:  2.02 (0.18), residues: 822
  sheet:  0.45 (0.56), residues: 87
  loop : -1.09 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L 716 
 TYR   0.012   0.001   TYR L 183 
 PHE   0.015   0.001   PHE L 120 
 TRP   0.012   0.001   TRP L 395 
 HIS   0.011   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (11920)
  covalent geometry    : angle       0.56846 (16118)
  hydrogen bonds       : bond        0.03327 (  641)
  hydrogen bonds       : angle       3.83165 ( 1845)
  metal coordination   : bond        0.00076 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  137 LEU cc_start: 0.7015 (tp) cc_final: 0.5776 (mt)
REVERT: L  184 SER cc_start: 0.9475 (t) cc_final: 0.9184 (p)
REVERT: L  188 GLU cc_start: 0.8973 (tt0) cc_final: 0.8676 (tp30)
REVERT: L  446 MET cc_start: 0.9261 (tpp) cc_final: 0.9007 (tpt)
REVERT: L  716 ARG cc_start: 0.8474 (mtp-110) cc_final: 0.8235 (tpp-160)
REVERT: L 1598 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8087 (pptt)
REVERT: L 1599 LEU cc_start: 0.8292 (pp) cc_final: 0.7997 (pp)
  outliers start: 8
  outliers final: 2
  residues processed: 89
  average time/residue: 0.7129
  time to fit residues: 68.2527
Evaluate side-chains
  80 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue 1346 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 98 optimal weight:    4.9990
   chunk 79 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 140 optimal weight:    9.9990
   chunk 82 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 119 optimal weight:    3.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** L1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L1278 GLN
L1823 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.072360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.048280 restraints weight = 70564.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 3.53
r_work: 0.2754 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8934
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11923  Z= 0.159
  Angle     :  0.569   9.803  16118  Z= 0.291
  Chirality :  0.040   0.152   1838
  Planarity :  0.004   0.050   2014
  Dihedral  :  7.903  73.503   1659
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.26 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 11.34 %
    Favored  : 87.98 %
  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:  1.29 (0.23), residues: 1411
  helix:  2.06 (0.19), residues: 815
  sheet:  0.31 (0.57), residues: 89
  loop : -1.09 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG L 716 
 TYR   0.016   0.001   TYR L1226 
 PHE   0.015   0.001   PHE L 783 
 TRP   0.009   0.001   TRP L 155 
 HIS   0.010   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (11920)
  covalent geometry    : angle       0.56857 (16118)
  hydrogen bonds       : bond        0.03764 (  641)
  hydrogen bonds       : angle       3.93312 ( 1845)
  metal coordination   : bond        0.00249 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  137 LEU cc_start: 0.7066 (tp) cc_final: 0.5807 (mt)
REVERT: L  184 SER cc_start: 0.9477 (t) cc_final: 0.9202 (p)
REVERT: L  188 GLU cc_start: 0.9050 (tt0) cc_final: 0.8769 (tp30)
REVERT: L  446 MET cc_start: 0.9273 (tpp) cc_final: 0.9041 (tpt)
REVERT: L  716 ARG cc_start: 0.8542 (mtp-110) cc_final: 0.8296 (tpp-160)
REVERT: L 1407 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8722 (t0)
  outliers start: 9
  outliers final: 3
  residues processed: 86
  average time/residue: 0.7093
  time to fit residues: 65.4220
Evaluate side-chains
  82 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue 1346 GLN
Chi-restraints excluded: chain L residue 1407 ASN
Chi-restraints excluded: chain L residue 1823 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 135 optimal weight:    0.1980
   chunk 81 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 102 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 43 optimal weight:    6.9990
   chunk 123 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
L1278 GLN
L1798 HIS
L1823 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.073245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.049754 restraints weight = 57797.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 3.18
r_work: 0.2808 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11923  Z= 0.113
  Angle     :  0.594  14.177  16118  Z= 0.291
  Chirality :  0.040   0.379   1838
  Planarity :  0.004   0.050   2014
  Dihedral  :  7.886  73.435   1659
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.84 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 11.87 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.28 (0.23), residues: 1411
  helix:  2.01 (0.18), residues: 821
  sheet:  0.33 (0.56), residues: 89
  loop : -1.06 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 716 
 TYR   0.016   0.001   TYR L1226 
 PHE   0.014   0.001   PHE L 120 
 TRP   0.010   0.001   TRP L 395 
 HIS   0.017   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (11920)
  covalent geometry    : angle       0.59399 (16118)
  hydrogen bonds       : bond        0.03410 (  641)
  hydrogen bonds       : angle       3.87046 ( 1845)
  metal coordination   : bond        0.00082 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  137 LEU cc_start: 0.7059 (tp) cc_final: 0.5844 (mt)
REVERT: L  184 SER cc_start: 0.9463 (t) cc_final: 0.9195 (p)
REVERT: L  188 GLU cc_start: 0.8985 (tt0) cc_final: 0.8737 (tp30)
REVERT: L  446 MET cc_start: 0.9234 (tpp) cc_final: 0.8978 (tpt)
REVERT: L  716 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.8288 (tpp-160)
REVERT: L 1598 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8050 (pptt)
REVERT: L 1599 LEU cc_start: 0.8306 (pp) cc_final: 0.8028 (pt)
  outliers start: 4
  outliers final: 1
  residues processed: 82
  average time/residue: 0.6392
  time to fit residues: 56.3893
Evaluate side-chains
  80 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1346 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0470
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 89 optimal weight:    0.2980
   chunk 55 optimal weight:    0.0270
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
L1278 GLN
L1798 HIS
L1823 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.073532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.050096 restraints weight = 60651.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 3.27
r_work: 0.2816 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8881
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  11923  Z= 0.105
  Angle     :  0.574  13.650  16118  Z= 0.282
  Chirality :  0.039   0.228   1838
  Planarity :  0.003   0.049   2014
  Dihedral  :  7.811  73.443   1659
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.98 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 11.80 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.39 (0.23), residues: 1411
  helix:  2.08 (0.18), residues: 824
  sheet:  0.55 (0.56), residues: 87
  loop : -1.02 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 716 
 TYR   0.021   0.001   TYR L  15 
 PHE   0.012   0.001   PHE L 539 
 TRP   0.009   0.001   TRP L 395 
 HIS   0.009   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (11920)
  covalent geometry    : angle       0.57374 (16118)
  hydrogen bonds       : bond        0.03288 (  641)
  hydrogen bonds       : angle       3.80518 ( 1845)
  metal coordination   : bond        0.00084 (    3)

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

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

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2822 Ramachandran restraints generated.
    1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  137 LEU cc_start: 0.7106 (tp) cc_final: 0.5887 (mt)
REVERT: L  184 SER cc_start: 0.9461 (t) cc_final: 0.9197 (p)
REVERT: L  188 GLU cc_start: 0.9046 (tt0) cc_final: 0.8778 (tp30)
REVERT: L  716 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.8291 (tpp-160)
REVERT: L 1407 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8712 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 86
  average time/residue: 0.6686
  time to fit residues: 61.8621
Evaluate side-chains
  79 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1298 HIS
Chi-restraints excluded: chain L residue 1346 GLN
Chi-restraints excluded: chain L residue 1407 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 138 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 134 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 39 optimal weight:    0.3980
   chunk 123 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
L1798 HIS
L1823 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.073139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.049089 restraints weight = 88539.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 3.94
r_work: 0.2769 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2774
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11923  Z= 0.117
  Angle     :  0.567  12.322  16118  Z= 0.283
  Chirality :  0.039   0.153   1838
  Planarity :  0.004   0.049   2014
  Dihedral  :  7.801  73.426   1659
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.91 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 11.72 %
    Favored  : 87.98 %
  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:  1.38 (0.23), residues: 1411
  helix:  2.08 (0.19), residues: 822
  sheet:  0.60 (0.59), residues: 82
  loop : -1.04 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 716 
 TYR   0.027   0.001   TYR L  15 
 PHE   0.014   0.001   PHE L 120 
 TRP   0.009   0.001   TRP L 395 
 HIS   0.009   0.001   HIS L1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (11920)
  covalent geometry    : angle       0.56727 (16118)
  hydrogen bonds       : bond        0.03376 (  641)
  hydrogen bonds       : angle       3.84305 ( 1845)
  metal coordination   : bond        0.00124 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4449.55 seconds
wall clock time: 76 minutes 28.06 seconds (4588.06 seconds total)