Starting phenix.real_space_refine
on Wed Jul 30 05:00:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oeb_12863/07_2025/7oeb_12863.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oeb_12863/07_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_12863/07_2025/7oeb_12863.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oeb_12863/07_2025/7oeb_12863.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oeb_12863/07_2025/7oeb_12863.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oeb_12863/07_2025/7oeb_12863.cif"
  }
  resolution = 3.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 13.24, per 1000 atoms: 1.13
  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: 3.03
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  
  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: 2.01
  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: 5.20

  Time building geometry restraints manager: 3.60 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:             1.820
  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:          0.560
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     43.510
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.100
  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:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.560
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.013   0.002   TRP L1547 
 HIS   0.004   0.001   HIS L1522 
 PHE   0.015   0.002   PHE L 539 
 TYR   0.013   0.001   TYR L1187 
 ARG   0.007   0.000   ARG L1347 

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

*********************** 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  : 1.495 
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: 0.3661
  time to fit residues: 84.1935
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  : 1.289 
-------------------------------------------------------------------------------
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 120 optimal weight:    0.9990
   chunk 108 optimal weight:    0.0060
   chunk 60 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 112 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 129 optimal weight:    3.9990
   overall best weight:    0.7598

-------------------------------------------------------------------------------
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
** L1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L1346 GLN
L1481 GLN
L1516 ASN
L1554 HIS
L1789 ASN
L1798 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.074107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.056487 restraints weight = 73233.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 4.00
r_work: 0.2917 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
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 = 0.50   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: 0.8709
moved from start:          0.1691

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= 0.123
  Angle     :  0.547   9.431  16102  Z= 0.281
  Chirality :  0.039   0.153   1835
  Planarity :  0.004   0.064   2015
  Dihedral  :  7.530  73.404   1646
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.05 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  5.09 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.23), residues: 1413
  helix:  2.03 (0.18), residues: 807
  sheet:  0.21 (0.54), residues: 89
  loop : -0.96 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L1194 
 HIS   0.007   0.001   HIS L1798 
 PHE   0.017   0.001   PHE L1716 
 TYR   0.014   0.001   TYR L1450 
 ARG   0.010   0.001   ARG L 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03955 (  645)
  hydrogen bonds       : angle       4.11653 ( 1851)
  metal coordination   : bond        0.00105 (    3)
  covalent geometry    : bond        0.00278 (11912)
  covalent geometry    : angle       0.54682 (16102)

*********************** 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
  99 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8101 (mp0)
REVERT: L  363 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8443 (ttp80)
REVERT: L  365 LYS cc_start: 0.8527 (mmtm) cc_final: 0.8299 (mmmt)
  outliers start: 7
  outliers final: 4
  residues processed: 95
  average time/residue: 0.2897
  time to fit residues: 38.9825
Evaluate side-chains
  85 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
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 1817 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0670
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    0.1980
   chunk 100 optimal weight:    3.9990
   overall best weight:    1.0522

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

Flipped N/Q/H residues before XYZ refinement:
** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 175 ASN
L1522 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.073423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.056966 restraints weight = 47021.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 3.10
r_work: 0.2951 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2954
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    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 = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2954
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.1946

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= 0.128
  Angle     :  0.511   9.511  16102  Z= 0.263
  Chirality :  0.039   0.153   1835
  Planarity :  0.004   0.058   2015
  Dihedral  :  7.440  73.382   1645
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.69 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  6.23 %
    Favored  : 93.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.23), residues: 1413
  helix:  2.18 (0.18), residues: 806
  sheet:  0.03 (0.52), residues: 92
  loop : -0.94 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L1194 
 HIS   0.003   0.001   HIS L 364 
 PHE   0.013   0.001   PHE L 539 
 TYR   0.023   0.001   TYR L  15 
 ARG   0.007   0.000   ARG L 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  645)
  hydrogen bonds       : angle       3.98373 ( 1851)
  metal coordination   : bond        0.00116 (    3)
  covalent geometry    : bond        0.00292 (11912)
  covalent geometry    : angle       0.51134 (16102)

*********************** 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
  99 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8034 (mp0)
REVERT: L  363 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8311 (ttp80)
REVERT: L  415 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8655 (mp10)
REVERT: L  691 MET cc_start: 0.8849 (mtp) cc_final: 0.8597 (mtm)
  outliers start: 10
  outliers final: 5
  residues processed: 97
  average time/residue: 0.3047
  time to fit residues: 41.0053
Evaluate side-chains
  84 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
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  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 120 optimal weight:    1.9990
   chunk 118 optimal weight:    0.0270
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 139 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.7240

-------------------------------------------------------------------------------
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 ** 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 = 0.3519 r_free = 0.3519 target = 0.073632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.056934 restraints weight = 50934.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 3.27
r_work: 0.2956 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11915  Z= 0.105
  Angle     :  0.484  10.142  16102  Z= 0.247
  Chirality :  0.038   0.173   1835
  Planarity :  0.004   0.053   2015
  Dihedral  :  7.323  73.455   1645
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.23), residues: 1413
  helix:  2.26 (0.18), residues: 807
  sheet: -0.02 (0.52), residues: 92
  loop : -0.90 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L1194 
 HIS   0.002   0.000   HIS L1359 
 PHE   0.018   0.001   PHE L 539 
 TYR   0.012   0.001   TYR L  15 
 ARG   0.007   0.000   ARG L 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  645)
  hydrogen bonds       : angle       3.90280 ( 1851)
  metal coordination   : bond        0.00106 (    3)
  covalent geometry    : bond        0.00237 (11912)
  covalent geometry    : angle       0.48417 (16102)

*********************** 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
  95 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7997 (mp0)
REVERT: L  363 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8277 (ttp80)
REVERT: L  415 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8656 (mp10)
REVERT: L  691 MET cc_start: 0.8845 (mtp) cc_final: 0.8584 (mtm)
REVERT: L 1345 MET cc_start: 0.8855 (ttp) cc_final: 0.8572 (ttm)
  outliers start: 9
  outliers final: 9
  residues processed: 92
  average time/residue: 0.3269
  time to fit residues: 41.4421
Evaluate side-chains
  89 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
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 1298 HIS
Chi-restraints excluded: chain L residue 1533 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 127 optimal weight:    0.9980
   chunk 129 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 62 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 141 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
L 175 ASN
L 324 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.073019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.056675 restraints weight = 45277.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 3.03
r_work: 0.2950 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    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 = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.2279

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= 0.120
  Angle     :  0.482  10.244  16102  Z= 0.245
  Chirality :  0.038   0.174   1835
  Planarity :  0.004   0.050   2015
  Dihedral  :  7.315  73.399   1645
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  8.21 %
    Favored  : 90.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.23), residues: 1413
  helix:  2.28 (0.18), residues: 808
  sheet: -0.09 (0.53), residues: 90
  loop : -0.95 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L1194 
 HIS   0.002   0.000   HIS L 653 
 PHE   0.014   0.001   PHE L 539 
 TYR   0.011   0.001   TYR L  15 
 ARG   0.004   0.000   ARG L 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03402 (  645)
  hydrogen bonds       : angle       3.88805 ( 1851)
  metal coordination   : bond        0.00096 (    3)
  covalent geometry    : bond        0.00275 (11912)
  covalent geometry    : angle       0.48153 (16102)

*********************** 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
  93 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8010 (mp0)
REVERT: L  415 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8671 (mp10)
REVERT: L  691 MET cc_start: 0.8892 (mtp) cc_final: 0.8648 (mtm)
  outliers start: 12
  outliers final: 9
  residues processed: 90
  average time/residue: 0.3127
  time to fit residues: 39.1920
Evaluate side-chains
  89 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
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 1533 LEU
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 96 optimal weight:    6.9990
   chunk 115 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 122 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 126 optimal weight:    0.0020
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
L  62 HIS
L1171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.072159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.054778 restraints weight = 74733.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 3.95
r_work: 0.2881 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2885
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    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 = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2885
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11915  Z= 0.131
  Angle     :  0.488  10.519  16102  Z= 0.249
  Chirality :  0.039   0.195   1835
  Planarity :  0.004   0.050   2015
  Dihedral  :  7.335  73.378   1645
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  8.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.23), residues: 1413
  helix:  2.31 (0.18), residues: 808
  sheet: -0.29 (0.51), residues: 98
  loop : -1.01 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L1194 
 HIS   0.003   0.001   HIS L 364 
 PHE   0.014   0.001   PHE L 539 
 TYR   0.010   0.001   TYR L1450 
 ARG   0.004   0.000   ARG L 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03488 (  645)
  hydrogen bonds       : angle       3.90013 ( 1851)
  metal coordination   : bond        0.00166 (    3)
  covalent geometry    : bond        0.00301 (11912)
  covalent geometry    : angle       0.48767 (16102)

*********************** 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
  97 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7983 (mp0)
REVERT: L  169 ARG cc_start: 0.8759 (mtm180) cc_final: 0.8247 (mtm110)
REVERT: L  363 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8315 (ttp80)
REVERT: L  415 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8705 (mp10)
REVERT: L  691 MET cc_start: 0.8919 (mtp) cc_final: 0.8662 (mtm)
REVERT: L 1345 MET cc_start: 0.8907 (ttp) cc_final: 0.8619 (ttm)
  outliers start: 11
  outliers final: 9
  residues processed: 95
  average time/residue: 0.3050
  time to fit residues: 40.5694
Evaluate side-chains
  93 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 1.566 
-------------------------------------------------------------------------------
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 1533 LEU
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 57 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0980
   chunk 107 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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**
L1554 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.071769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.054447 restraints weight = 71008.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 3.85
r_work: 0.2879 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    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 = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11915  Z= 0.136
  Angle     :  0.496  10.551  16102  Z= 0.253
  Chirality :  0.039   0.180   1835
  Planarity :  0.004   0.049   2015
  Dihedral  :  7.339  73.378   1645
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  8.97 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.23), residues: 1413
  helix:  2.31 (0.18), residues: 808
  sheet: -0.31 (0.52), residues: 98
  loop : -1.02 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L1194 
 HIS   0.003   0.001   HIS L 653 
 PHE   0.015   0.001   PHE L 539 
 TYR   0.012   0.001   TYR L  15 
 ARG   0.005   0.000   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03506 (  645)
  hydrogen bonds       : angle       3.92227 ( 1851)
  metal coordination   : bond        0.00138 (    3)
  covalent geometry    : bond        0.00314 (11912)
  covalent geometry    : angle       0.49644 (16102)

*********************** 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
  93 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7996 (mp0)
REVERT: L  165 PHE cc_start: 0.9248 (t80) cc_final: 0.8363 (t80)
REVERT: L  169 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8171 (mtm180)
REVERT: L  363 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8297 (ttp80)
REVERT: L  415 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8713 (mp10)
REVERT: L  691 MET cc_start: 0.8904 (mtp) cc_final: 0.8648 (mtm)
  outliers start: 10
  outliers final: 8
  residues processed: 92
  average time/residue: 0.3154
  time to fit residues: 40.1159
Evaluate side-chains
  90 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
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 1533 LEU
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 82 optimal weight:    0.3980
   chunk 104 optimal weight:    2.9990
   chunk 140 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 117 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3488 r_free = 0.3488 target = 0.072025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.055065 restraints weight = 64602.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 3.64
r_work: 0.2898 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2900
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2900 r_free = 0.2900    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 = 0.2900 r_free = 0.2900    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2900
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11915  Z= 0.119
  Angle     :  0.485  10.613  16102  Z= 0.247
  Chirality :  0.038   0.180   1835
  Planarity :  0.003   0.048   2015
  Dihedral  :  7.299  73.410   1645
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  9.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.23), residues: 1413
  helix:  2.33 (0.18), residues: 808
  sheet: -0.03 (0.55), residues: 88
  loop : -1.04 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L1194 
 HIS   0.002   0.000   HIS L 653 
 PHE   0.014   0.001   PHE L 539 
 TYR   0.010   0.001   TYR L1450 
 ARG   0.005   0.000   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03392 (  645)
  hydrogen bonds       : angle       3.89291 ( 1851)
  metal coordination   : bond        0.00112 (    3)
  covalent geometry    : bond        0.00272 (11912)
  covalent geometry    : angle       0.48455 (16102)

*********************** 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
  94 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
REVERT: L  150 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7977 (mp0)
REVERT: L  165 PHE cc_start: 0.9225 (t80) cc_final: 0.8202 (t80)
REVERT: L  169 ARG cc_start: 0.8756 (mtm180) cc_final: 0.8309 (mtm110)
REVERT: L  363 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8306 (ttp80)
REVERT: L  415 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8693 (mp10)
REVERT: L  691 MET cc_start: 0.8879 (mtp) cc_final: 0.8636 (mtm)
REVERT: L 1345 MET cc_start: 0.8920 (ttp) cc_final: 0.8640 (ttm)
  outliers start: 9
  outliers final: 7
  residues processed: 93
  average time/residue: 0.3126
  time to fit residues: 40.6256
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  : 1.320 
-------------------------------------------------------------------------------
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 99 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 128 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 140 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3467 r_free = 0.3467 target = 0.071102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.054882 restraints weight = 45603.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 3.00
r_work: 0.2905 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    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 = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
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      :  0.004   0.033  11915  Z= 0.154
  Angle     :  0.509  10.487  16102  Z= 0.261
  Chirality :  0.039   0.189   1835
  Planarity :  0.004   0.048   2015
  Dihedral  :  7.368  73.312   1645
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  9.65 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.23), residues: 1413
  helix:  2.27 (0.18), residues: 808
  sheet: -0.31 (0.52), residues: 98
  loop : -1.07 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L1194 
 HIS   0.003   0.001   HIS L 653 
 PHE   0.014   0.001   PHE L 539 
 TYR   0.010   0.001   TYR L1450 
 ARG   0.005   0.000   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03662 (  645)
  hydrogen bonds       : angle       3.97555 ( 1851)
  metal coordination   : bond        0.00173 (    3)
  covalent geometry    : bond        0.00353 (11912)
  covalent geometry    : angle       0.50912 (16102)

*********************** 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
  95 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
REVERT: L  165 PHE cc_start: 0.9234 (t80) cc_final: 0.8282 (t80)
REVERT: L  169 ARG cc_start: 0.8787 (mtm180) cc_final: 0.8306 (mtm110)
REVERT: L  363 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8300 (ttp80)
REVERT: L  415 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8670 (mp10)
REVERT: L  691 MET cc_start: 0.8848 (mtp) cc_final: 0.8602 (mtm)
  outliers start: 8
  outliers final: 8
  residues processed: 93
  average time/residue: 0.3536
  time to fit residues: 45.8195
Evaluate side-chains
  93 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 1.670 
-------------------------------------------------------------------------------
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 1092 MET
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 62 optimal weight:    6.9990
   chunk 86 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0770
   chunk 101 optimal weight:    0.5980
   chunk 119 optimal weight:    0.8980
   chunk 141 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   chunk 123 optimal weight:    0.8980
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 = 0.3497 r_free = 0.3497 target = 0.072492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.055753 restraints weight = 57646.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 3.43
r_work: 0.2924 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    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 = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11915  Z= 0.101
  Angle     :  0.480  10.565  16102  Z= 0.244
  Chirality :  0.038   0.217   1835
  Planarity :  0.003   0.047   2015
  Dihedral  :  7.272  73.466   1645
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  9.80 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.23), residues: 1413
  helix:  2.33 (0.18), residues: 808
  sheet: -0.07 (0.57), residues: 82
  loop : -1.02 (0.27), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L1194 
 HIS   0.002   0.000   HIS L  74 
 PHE   0.015   0.001   PHE L 539 
 TYR   0.009   0.001   TYR L  15 
 ARG   0.007   0.000   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03259 (  645)
  hydrogen bonds       : angle       3.86126 ( 1851)
  metal coordination   : bond        0.00075 (    3)
  covalent geometry    : bond        0.00225 (11912)
  covalent geometry    : angle       0.47961 (16102)

********************** 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
  96 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 1.713 
Fit side-chains
   revert: symmetry clash
REVERT: L  165 PHE cc_start: 0.9197 (t80) cc_final: 0.8191 (t80)
REVERT: L  169 ARG cc_start: 0.8775 (mtm180) cc_final: 0.8316 (mtm110)
REVERT: L  363 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8305 (ttp80)
REVERT: L  415 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8675 (mp10)
REVERT: L  691 MET cc_start: 0.8837 (mtp) cc_final: 0.8597 (mtm)
  outliers start: 8
  outliers final: 7
  residues processed: 95
  average time/residue: 0.4726
  time to fit residues: 64.2125
Evaluate side-chains
  93 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
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 140 optimal weight:    0.0870
   chunk 82 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 115 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.9964

-------------------------------------------------------------------------------
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 = 0.3454 r_free = 0.3454 target = 0.070479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.053292 restraints weight = 65650.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 3.72
r_work: 0.2853 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11915  Z= 0.189
  Angle     :  0.530  10.145  16102  Z= 0.272
  Chirality :  0.040   0.212   1835
  Planarity :  0.004   0.047   2015
  Dihedral  :  7.411  73.294   1645
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  9.80 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.23), residues: 1413
  helix:  2.23 (0.18), residues: 808
  sheet: -0.35 (0.52), residues: 98
  loop : -1.09 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L1547 
 HIS   0.004   0.001   HIS L 653 
 PHE   0.014   0.002   PHE L 539 
 TYR   0.011   0.001   TYR L1450 
 ARG   0.005   0.000   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  645)
  hydrogen bonds       : angle       4.02135 ( 1851)
  metal coordination   : bond        0.00179 (    3)
  covalent geometry    : bond        0.00436 (11912)
  covalent geometry    : angle       0.53026 (16102)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6876.50 seconds
wall clock time: 120 minutes 26.14 seconds (7226.14 seconds total)