Starting phenix.real_space_refine
on Sat Jun 14 20:24:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hal_34595/06_2025/8hal_34595.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hal_34595/06_2025/8hal_34595.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hal_34595/06_2025/8hal_34595.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hal_34595/06_2025/8hal_34595.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hal_34595/06_2025/8hal_34595.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hal_34595/06_2025/8hal_34595.cif"
  }
  resolution = 4.4
  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=   0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     P     302      5.49       5
     S      46      5.16       5
     C    9551      2.51       5
     N    3022      2.21       5
     O    3664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 111 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16585
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 819
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 728
          Classifications: {'peptide': 92}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ALY:plan-2': 2, 'ALY:plan-1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 673
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 764
          Classifications: {'peptide': 101}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 98}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "I"
      Number of atoms: 3094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 3094
          Classifications: {'DNA': 151}
          Link IDs: {'rna3p': 150}
    Chain: "J"
      Number of atoms: 3097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 3097
          Classifications: {'DNA': 151}
          Link IDs: {'rna3p': 150}
    Chain: "K"
      Number of atoms: 4238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 4238
          Classifications: {'peptide': 513}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 481}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA C  14 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA C  14 " occ=0.00
  Time building chain proxies: 9.14, per 1000 atoms: 0.55
  Number of scatterers: 16585
  At special positions: 0
  Unit cell: (110.25, 170.52, 136.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     P     302     15.00
     O    3664      8.00
     N    3022      7.00
     C    9551      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: 3.98
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2428

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 13 sheets defined
      61.0% alpha, 6.8% beta
      117 base pairs and 228 stacking pairs defined.
    Time for finding SS restraints: 6.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.730A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
      removed outlier: 3.666A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.124A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLU B  74 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.289A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.543A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.504A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.948A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.605A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 4.078A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.376A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.742A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.684A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'K' and resid 1087 through 1104
      Proline residue:  K1096  - end of helix
      removed outlier: 3.657A  pdb=" N   GLN K1104 " --> pdb=" O   ALA K1100 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1108 through 1112
    Processing helix  chain 'K' and resid 1116 through 1121
    Processing helix  chain 'K' and resid 1124 through 1129
    Processing helix  chain 'K' and resid 1134 through 1144
    Processing helix  chain 'K' and resid 1150 through 1168
    Processing helix  chain 'K' and resid 1172 through 1195
      removed outlier: 3.711A  pdb=" N   LYS K1176 " --> pdb=" O   SER K1172 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ASP K1190 " --> pdb=" O   GLU K1186 " (cutoff:3.500A)
      Proline residue:  K1191  - end of helix
      removed outlier: 3.762A  pdb=" N   SER K1195 " --> pdb=" O   PRO K1191 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1292 through 1296
    Processing helix  chain 'K' and resid 1308 through 1314
    Processing helix  chain 'K' and resid 1332 through 1350
    Processing helix  chain 'K' and resid 1372 through 1380
    Processing helix  chain 'K' and resid 1442 through 1465
      removed outlier: 4.135A  pdb=" N   THR K1447 " --> pdb=" O   ARG K1443 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   ALA K1448 " --> pdb=" O   CYS K1444 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU K1452 " --> pdb=" O   ALA K1448 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1495 through 1513
    Processing helix  chain 'K' and resid 1522 through 1530
    Processing helix  chain 'K' and resid 1533 through 1537
    Processing helix  chain 'K' and resid 1543 through 1555
      removed outlier: 3.833A  pdb=" N   ASN K1547 " --> pdb=" O   ASP K1543 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1621 through 1628
    Processing helix  chain 'K' and resid 1663 through 1675
      removed outlier: 4.352A  pdb=" N   PHE K1667 " --> pdb=" O   GLY K1663 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1680 through 1698
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.745A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.015A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.738A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.498A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.393A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 1226 through 1229
      removed outlier: 3.740A  pdb=" N   LYS K1270 " --> pdb=" O   TYR K1227 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   SER K1229 " --> pdb=" O   GLU K1268 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU K1268 " --> pdb=" O   SER K1229 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1280 through 1282
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1357 through 1370
      removed outlier: 6.825A  pdb=" N   ALA K1395 " --> pdb=" O   VAL K1362 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   SER K1364 " --> pdb=" O   THR K1393 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   THR K1393 " --> pdb=" O   SER K1364 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   ASP K1366 " --> pdb=" O   TYR K1391 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   TYR K1391 " --> pdb=" O   ASP K1366 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   THR K1368 " --> pdb=" O   PHE K1389 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   PHE K1389 " --> pdb=" O   THR K1368 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE K1410 " --> pdb=" O   ALA K1398 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   GLU K1400 " --> pdb=" O   CYS K1408 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   CYS K1408 " --> pdb=" O   GLU K1400 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE K1402 " --> pdb=" O   ASP K1406 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   ASP K1406 " --> pdb=" O   ILE K1402 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   TYR K1433 " --> pdb=" O   HIS K1413 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLN K1415 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   ILE K1431 " --> pdb=" O   GLN K1415 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   TYR K1417 " --> pdb=" O   VAL K1429 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   VAL K1429 " --> pdb=" O   TYR K1417 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   TRP K1472 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   TYR K1433 " --> pdb=" O   TRP K1472 " (cutoff:3.500A)

    583 hydrogen bonds defined for protein.
    1725 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      280 hydrogen bonds
      560 hydrogen bond angles
      0 basepair planarities
      117 basepair parallelities
      228 stacking parallelities
  Total time for adding SS restraints: 7.05

  Time building geometry restraints manager: 4.73 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2780
        1.33 -     1.45: 5676
        1.45 -     1.57: 8411
        1.57 -     1.69: 602
        1.69 -     1.81: 68
  Bond restraints: 17537
  Sorted by residual:
  bond pdb=" NZ  ALY B  16 "
       pdb=" CH  ALY B  16 "
    ideal  model  delta    sigma   weight residual
    1.343  1.384 -0.041 2.00e-02 2.50e+03 4.25e+00
  bond pdb=" C3'  DT I 136 "
       pdb=" O3'  DT I 136 "
    ideal  model  delta    sigma   weight residual
    1.422  1.471 -0.049 3.00e-02 1.11e+03 2.71e+00
  bond pdb=" CG  GLU F  63 "
       pdb=" CD  GLU F  63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.484  0.032 2.50e-02 1.60e+03 1.62e+00
  bond pdb=" C3'  DA J  59 "
       pdb=" O3'  DA J  59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.56e+00
  bond pdb=" CD  GLU F  63 "
       pdb=" OE1 GLU F  63 "
    ideal  model  delta    sigma   weight residual
    1.249  1.226  0.023 1.90e-02 2.77e+03 1.44e+00
  ... (remaining 17532 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 24357
        1.84 -     3.67: 555
        3.67 -     5.51: 45
        5.51 -     7.34: 15
        7.34 -     9.18: 3
  Bond angle restraints: 24975
  Sorted by residual:
  angle pdb=" C   LEU H 101 "
        pdb=" N   LEU H 102 "
        pdb=" CA  LEU H 102 "
      ideal   model   delta    sigma   weight residual
     122.70  113.52    9.18 1.98e+00 2.55e-01 2.15e+01
  angle pdb=" N   GLU F  63 "
        pdb=" CA  GLU F  63 "
        pdb=" CB  GLU F  63 "
      ideal   model   delta    sigma   weight residual
     110.28  117.11   -6.83 1.55e+00 4.16e-01 1.94e+01
  angle pdb=" N   GLU A 105 "
        pdb=" CA  GLU A 105 "
        pdb=" CB  GLU A 105 "
      ideal   model   delta    sigma   weight residual
     110.12  115.86   -5.74 1.47e+00 4.63e-01 1.52e+01
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     111.02  118.05   -7.03 1.86e+00 2.89e-01 1.43e+01
  angle pdb=" N   GLU K1186 "
        pdb=" CA  GLU K1186 "
        pdb=" CB  GLU K1186 "
      ideal   model   delta    sigma   weight residual
     110.12  115.43   -5.31 1.47e+00 4.63e-01 1.30e+01
  ... (remaining 24970 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.55: 8491
       35.55 -    71.11: 1338
       71.11 -   106.66: 23
      106.66 -   142.21: 1
      142.21 -   177.77: 2
  Dihedral angle restraints: 9855
    sinusoidal: 6092
      harmonic: 3763
  Sorted by residual:
  dihedral pdb=" CA  ARG E  63 "
           pdb=" C   ARG E  63 "
           pdb=" N   LYS E  64 "
           pdb=" CA  LYS E  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.34  -26.66     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" C4'  DT I 136 "
           pdb=" C3'  DT I 136 "
           pdb=" O3'  DT I 136 "
           pdb=" P    DT I 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.77 -177.77     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA J  59 "
           pdb=" C3'  DA J  59 "
           pdb=" O3'  DA J  59 "
           pdb=" P    DA J  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   61.88  158.12     1      3.50e+01 8.16e-04 1.51e+01
  ... (remaining 9852 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 2205
       0.039 -    0.079: 440
       0.079 -    0.118: 109
       0.118 -    0.157: 19
       0.157 -    0.196: 1
  Chirality restraints: 2774
  Sorted by residual:
  chirality pdb=" CA  GLU G  61 "
            pdb=" N   GLU G  61 "
            pdb=" C   GLU G  61 "
            pdb=" CB  GLU G  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.64e-01
  chirality pdb=" CA  MET K1095 "
            pdb=" N   MET K1095 "
            pdb=" C   MET K1095 "
            pdb=" CB  MET K1095 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.37e-01
  chirality pdb=" P    DA J  60 "
            pdb=" OP1  DA J  60 "
            pdb=" OP2  DA J  60 "
            pdb=" O5'  DA J  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.49   -0.14 2.00e-01 2.50e+01 5.02e-01
  ... (remaining 2771 not shown)

  Planarity restraints: 2132
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 102 "    0.037 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO H 103 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO H 103 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO H 103 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  69 "    0.011 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   ARG A  69 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ARG A  69 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A  70 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.032 5.00e-02 4.00e+02   4.77e-02 3.65e+00
        pdb=" N   PRO D 103 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.026 5.00e-02 4.00e+02
  ... (remaining 2129 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1032
        2.73 -     3.27: 15993
        3.27 -     3.81: 32542
        3.81 -     4.36: 37765
        4.36 -     4.90: 55123
  Nonbonded interactions: 142455
  Sorted by model distance:
  nonbonded pdb=" O2   DT J 140 "
            pdb=" N6   DA J 141 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" OD2 ASP F  68 "
            pdb=" NE2 GLN F  93 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   ILE E  62 "
            pdb=" NE2 GLN E  93 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O2   DT I 107 "
            pdb=" N2   DG J  75 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" N   THR D  90 "
            pdb=" OE2 GLU D  93 "
     model   vdw
     2.258 3.120
  ... (remaining 142450 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 19 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and ((resid 31 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 32 through 124))
  selection = (chain 'H' and resid 31 through 124)
}
ncs_group {
  reference = (chain 'I' and resid 16 through 165)
  selection = (chain 'J' and resid 16 through 165)
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     41.530
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
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      :  0.003   0.049  17537  Z= 0.155
  Angle     :  0.631   9.177  24975  Z= 0.383
  Chirality :  0.035   0.196   2774
  Planarity :  0.004   0.056   2132
  Dihedral  : 24.758 177.765   7427
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.26 (0.23), residues: 1261
  helix:  1.26 (0.19), residues: 749
  sheet:  0.06 (0.66), residues: 58
  loop :  0.41 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP K1502 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.015   0.001   PHE A 104 
 TYR   0.019   0.001   TYR G  57 
 ARG   0.019   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13883 (  863)
  hydrogen bonds       : angle       5.77810 ( 2285)
  covalent geometry    : bond        0.00302 (17537)
  covalent geometry    : angle       0.63059 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   41 GLU cc_start: 0.7537 (mp0) cc_final: 0.7323 (mm-30)
REVERT: E  110 CYS cc_start: 0.8206 (t) cc_final: 0.7997 (t)
REVERT: E  120 MET cc_start: 0.7713 (ptp) cc_final: 0.7493 (mpp)
REVERT: F   97 LEU cc_start: 0.8693 (tp) cc_final: 0.8338 (tp)
REVERT: K 1148 GLN cc_start: 0.6269 (pp30) cc_final: 0.5746 (tp40)
REVERT: K 1193 MET cc_start: -0.3248 (ttt) cc_final: -0.3778 (tpp)
REVERT: K 1385 MET cc_start: -0.2374 (mtt) cc_final: -0.3087 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.2460
  time to fit residues: 36.1548
Evaluate side-chains
  54 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    6.9990
   chunk 117 optimal weight:    0.0010
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 79 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 121 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 140 optimal weight:    2.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E  93 GLN
E 108 ASN
F  93 GLN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.056561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.040825 restraints weight = 205927.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.041839 restraints weight = 108972.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.042417 restraints weight = 73236.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  17537  Z= 0.164
  Angle     :  0.578   8.267  24975  Z= 0.336
  Chirality :  0.036   0.177   2774
  Planarity :  0.005   0.061   2132
  Dihedral  : 28.405 172.730   4825
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.08 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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: 1261
  helix:  1.43 (0.18), residues: 769
  sheet:  0.31 (0.67), residues: 58
  loop :  0.47 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP K1502 
 HIS   0.007   0.001   HIS K1451 
 PHE   0.014   0.001   PHE A  67 
 TYR   0.012   0.001   TYR H  83 
 ARG   0.007   0.000   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05093 (  863)
  hydrogen bonds       : angle       3.89533 ( 2285)
  covalent geometry    : bond        0.00349 (17537)
  covalent geometry    : angle       0.57826 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 1.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9514 (mt) cc_final: 0.9271 (mt)
REVERT: B   84 MET cc_start: 0.7569 (ppp) cc_final: 0.7258 (ppp)
REVERT: F   58 LEU cc_start: 0.9500 (tp) cc_final: 0.9181 (pp)
REVERT: F   97 LEU cc_start: 0.8795 (tp) cc_final: 0.8462 (tp)
REVERT: K 1148 GLN cc_start: 0.6804 (pp30) cc_final: 0.6575 (tp40)
REVERT: K 1193 MET cc_start: 0.0003 (ttt) cc_final: -0.1616 (tpp)
  outliers start: 2
  outliers final: 2
  residues processed: 80
  average time/residue: 0.3142
  time to fit residues: 41.3769
Evaluate side-chains
  51 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 2.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 87 optimal weight:   10.0000
   chunk 146 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 115 optimal weight:    9.9990
   chunk 106 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 86 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
D 109 HIS
E  93 GLN
F  93 GLN
G  38 ASN
G 104 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.052201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.036767 restraints weight = 206377.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.037733 restraints weight = 108632.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.038163 restraints weight = 73190.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  17537  Z= 0.234
  Angle     :  0.635   6.755  24975  Z= 0.369
  Chirality :  0.038   0.209   2774
  Planarity :  0.005   0.056   2132
  Dihedral  : 29.024 162.691   4825
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.63 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.23 (0.23), residues: 1261
  helix:  1.22 (0.18), residues: 780
  sheet:  0.47 (0.66), residues: 62
  loop :  0.30 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP K1502 
 HIS   0.010   0.002   HIS D 109 
 PHE   0.014   0.002   PHE K1206 
 TYR   0.016   0.002   TYR H  83 
 ARG   0.014   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06449 (  863)
  hydrogen bonds       : angle       4.08229 ( 2285)
  covalent geometry    : bond        0.00507 (17537)
  covalent geometry    : angle       0.63528 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 1.603 
Fit side-chains
REVERT: A   92 LEU cc_start: 0.9558 (mt) cc_final: 0.9324 (mt)
REVERT: A  105 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8316 (tm-30)
REVERT: C   87 ILE cc_start: 0.9168 (tp) cc_final: 0.8815 (pt)
REVERT: D   62 MET cc_start: 0.8823 (tpp) cc_final: 0.8612 (tpp)
REVERT: F   68 ASP cc_start: 0.8448 (m-30) cc_final: 0.8186 (m-30)
REVERT: F   97 LEU cc_start: 0.8865 (tp) cc_final: 0.8606 (tp)
REVERT: K 1095 MET cc_start: 0.1562 (mmm) cc_final: 0.1038 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 71
  average time/residue: 0.3871
  time to fit residues: 46.4743
Evaluate side-chains
  47 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 3.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 153 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 129 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 57 optimal weight:    3.9990
   chunk 64 optimal weight:   30.0000
   chunk 7 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 141 optimal weight:    9.9990
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
K1113 GLN
** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1297 HIS
** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1628 HIS
** K1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.048644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.033624 restraints weight = 215860.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.034548 restraints weight = 113923.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.035055 restraints weight = 76205.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.4592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  17537  Z= 0.292
  Angle     :  0.724   6.996  24975  Z= 0.418
  Chirality :  0.041   0.193   2774
  Planarity :  0.006   0.058   2132
  Dihedral  : 29.851 168.087   4825
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 19.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.71 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.61 (0.22), residues: 1261
  helix:  0.77 (0.17), residues: 777
  sheet:  0.41 (0.66), residues: 64
  loop : -0.09 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP K1158 
 HIS   0.007   0.002   HIS B  75 
 PHE   0.018   0.002   PHE A  67 
 TYR   0.019   0.002   TYR G  57 
 ARG   0.022   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07686 (  863)
  hydrogen bonds       : angle       4.50255 ( 2285)
  covalent geometry    : bond        0.00631 (17537)
  covalent geometry    : angle       0.72408 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 1.371 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9597 (mt) cc_final: 0.9369 (mt)
REVERT: A  105 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8344 (tm-30)
REVERT: K 1095 MET cc_start: 0.1542 (mmm) cc_final: 0.1263 (mmm)
REVERT: K 1158 TRP cc_start: 0.8608 (m100) cc_final: 0.8381 (m100)
REVERT: K 1193 MET cc_start: 0.1575 (ttt) cc_final: 0.0979 (ttm)
  outliers start: 2
  outliers final: 1
  residues processed: 70
  average time/residue: 0.2472
  time to fit residues: 29.8479
Evaluate side-chains
  43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 127 optimal weight:    7.9990
   chunk 106 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   chunk 121 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1336 ASN
** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1638 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.048668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.033742 restraints weight = 214755.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.034641 restraints weight = 112026.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.035143 restraints weight = 74729.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  17537  Z= 0.220
  Angle     :  0.651   7.794  24975  Z= 0.378
  Chirality :  0.038   0.196   2774
  Planarity :  0.005   0.127   2132
  Dihedral  : 30.008 170.817   4825
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.45 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.86 (0.23), residues: 1261
  helix:  1.02 (0.18), residues: 778
  sheet:  0.40 (0.67), residues: 64
  loop : -0.08 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP K1502 
 HIS   0.005   0.001   HIS K1451 
 PHE   0.023   0.002   PHE G  25 
 TYR   0.011   0.002   TYR D  40 
 ARG   0.020   0.001   ARG K1173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06153 (  863)
  hydrogen bonds       : angle       4.23973 ( 2285)
  covalent geometry    : bond        0.00478 (17537)
  covalent geometry    : angle       0.65120 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9543 (mt) cc_final: 0.9311 (mt)
REVERT: A  105 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8262 (tm-30)
REVERT: B   88 TYR cc_start: 0.8585 (m-10) cc_final: 0.8116 (m-10)
REVERT: C   41 GLU cc_start: 0.8280 (pm20) cc_final: 0.7900 (pm20)
REVERT: C   87 ILE cc_start: 0.9317 (tp) cc_final: 0.8950 (pt)
REVERT: F   63 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8118 (pm20)
REVERT: K 1095 MET cc_start: 0.1491 (mmm) cc_final: 0.1151 (mmm)
REVERT: K 1661 MET cc_start: 0.2261 (mmm) cc_final: 0.2016 (mmm)
REVERT: K 1691 MET cc_start: 0.6167 (mmm) cc_final: 0.5871 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 75
  average time/residue: 0.2422
  time to fit residues: 29.8642
Evaluate side-chains
  47 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 150 optimal weight:   40.0000
   chunk 56 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1272 ASN
K1292 GLN
** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1547 ASN
** K1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.046290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.031678 restraints weight = 222267.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.032404 restraints weight = 123132.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.032929 restraints weight = 81430.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.6214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058  17537  Z= 0.326
  Angle     :  0.769   7.987  24975  Z= 0.442
  Chirality :  0.043   0.200   2774
  Planarity :  0.006   0.064   2132
  Dihedral  : 30.790 169.862   4825
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 23.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.22 (0.22), residues: 1261
  helix:  0.53 (0.18), residues: 780
  sheet:  0.50 (0.66), residues: 64
  loop : -0.44 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP K1472 
 HIS   0.008   0.002   HIS E  39 
 PHE   0.022   0.002   PHE G  25 
 TYR   0.017   0.003   TYR C  39 
 ARG   0.012   0.001   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09340 (  863)
  hydrogen bonds       : angle       4.72963 ( 2285)
  covalent geometry    : bond        0.00708 (17537)
  covalent geometry    : angle       0.76879 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9602 (mt) cc_final: 0.9386 (mt)
REVERT: A  105 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: B   88 TYR cc_start: 0.8642 (m-10) cc_final: 0.8273 (m-10)
REVERT: C   41 GLU cc_start: 0.8398 (pm20) cc_final: 0.7857 (pm20)
REVERT: E  105 GLU cc_start: 0.8598 (pm20) cc_final: 0.8319 (pm20)
REVERT: K 1095 MET cc_start: 0.1695 (mmm) cc_final: 0.1353 (mmm)
REVERT: K 1158 TRP cc_start: 0.8826 (m100) cc_final: 0.8469 (m100)
REVERT: K 1193 MET cc_start: 0.2054 (ttt) cc_final: 0.1628 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.2453
  time to fit residues: 27.5126
Evaluate side-chains
  47 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0370
   chunk 111 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
C  24 GLN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1272 ASN
K1292 GLN
** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.048629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.033658 restraints weight = 213139.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.034527 restraints weight = 109864.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.035090 restraints weight = 73636.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.5816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  17537  Z= 0.158
  Angle     :  0.641   7.776  24975  Z= 0.369
  Chirality :  0.038   0.161   2774
  Planarity :  0.004   0.059   2132
  Dihedral  : 30.499 172.642   4825
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.86 (0.23), residues: 1261
  helix:  1.05 (0.18), residues: 775
  sheet:  0.50 (0.67), residues: 64
  loop : -0.16 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP K1502 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.017   0.001   PHE A  67 
 TYR   0.011   0.001   TYR B  72 
 ARG   0.007   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04891 (  863)
  hydrogen bonds       : angle       4.08721 ( 2285)
  covalent geometry    : bond        0.00343 (17537)
  covalent geometry    : angle       0.64143 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9528 (mt) cc_final: 0.9301 (mt)
REVERT: A  105 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8265 (tm-30)
REVERT: B   88 TYR cc_start: 0.8549 (m-10) cc_final: 0.8183 (m-10)
REVERT: C   41 GLU cc_start: 0.8297 (pm20) cc_final: 0.7927 (pm20)
REVERT: D  105 GLU cc_start: 0.8192 (pm20) cc_final: 0.7947 (pm20)
REVERT: K 1506 MET cc_start: -0.4930 (mtt) cc_final: -0.5156 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2408
  time to fit residues: 32.1297
Evaluate side-chains
  54 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 137 optimal weight:    2.9990
   chunk 131 optimal weight:    8.9990
   chunk 152 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 149 optimal weight:   20.0000
   chunk 127 optimal weight:    8.9990
   chunk 67 optimal weight:    8.9990
   chunk 57 optimal weight:    4.9990
   chunk 118 optimal weight:   20.0000
   chunk 79 optimal weight:    8.9990
   chunk 125 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1272 ASN
** K1351 HIS ** 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 = 0.3365 r_free = 0.3365 target = 0.045345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.030870 restraints weight = 224073.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.031694 restraints weight = 119197.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.032192 restraints weight = 81201.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.6823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.096  17537  Z= 0.368
  Angle     :  0.801   8.004  24975  Z= 0.458
  Chirality :  0.044   0.206   2774
  Planarity :  0.006   0.079   2132
  Dihedral  : 30.966 169.119   4825
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 25.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.06 (0.22), residues: 1261
  helix:  0.41 (0.18), residues: 781
  sheet:  0.53 (0.67), residues: 63
  loop : -0.56 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP K1158 
 HIS   0.008   0.002   HIS E 113 
 PHE   0.032   0.003   PHE G  25 
 TYR   0.017   0.002   TYR K1298 
 ARG   0.012   0.001   ARG D  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10251 (  863)
  hydrogen bonds       : angle       4.81004 ( 2285)
  covalent geometry    : bond        0.00796 (17537)
  covalent geometry    : angle       0.80062 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9604 (mt) cc_final: 0.9387 (mt)
REVERT: B   88 TYR cc_start: 0.8720 (m-10) cc_final: 0.8358 (m-80)
REVERT: C   41 GLU cc_start: 0.8460 (pm20) cc_final: 0.8023 (pm20)
REVERT: C   87 ILE cc_start: 0.9224 (tp) cc_final: 0.8861 (pt)
REVERT: K 1193 MET cc_start: 0.2372 (ttt) cc_final: 0.1874 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.2517
  time to fit residues: 28.0345
Evaluate side-chains
  44 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 149 optimal weight:    8.9990
   chunk 131 optimal weight:   20.0000
   chunk 28 optimal weight:    0.5980
   chunk 100 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 53 optimal weight:    0.3980
   chunk 134 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1297 HIS
** K1351 HIS ** 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 = 0.3406 r_free = 0.3406 target = 0.046999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.032301 restraints weight = 216247.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.033177 restraints weight = 112385.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.033698 restraints weight = 74967.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.6629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  17537  Z= 0.190
  Angle     :  0.672   8.625  24975  Z= 0.387
  Chirality :  0.038   0.168   2774
  Planarity :  0.006   0.173   2132
  Dihedral  : 30.899 173.473   4825
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.46 (0.23), residues: 1261
  helix:  0.79 (0.18), residues: 781
  sheet:  0.32 (0.66), residues: 63
  loop : -0.46 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP K1502 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.022   0.001   PHE G  25 
 TYR   0.011   0.001   TYR G  57 
 ARG   0.010   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05744 (  863)
  hydrogen bonds       : angle       4.35314 ( 2285)
  covalent geometry    : bond        0.00415 (17537)
  covalent geometry    : angle       0.67181 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9538 (mt) cc_final: 0.9316 (mt)
REVERT: A  105 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8290 (tm-30)
REVERT: B   88 TYR cc_start: 0.8612 (m-10) cc_final: 0.8294 (m-80)
REVERT: C   41 GLU cc_start: 0.8283 (pm20) cc_final: 0.7923 (pm20)
REVERT: C   87 ILE cc_start: 0.9360 (tp) cc_final: 0.9144 (pt)
REVERT: K 1193 MET cc_start: 0.2088 (ttt) cc_final: 0.1705 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2361
  time to fit residues: 27.4786
Evaluate side-chains
  49 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 125 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 151 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   chunk 80 optimal weight:    7.9990
   chunk 105 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0870
   chunk 33 optimal weight:    0.4980
   chunk 26 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.9164

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1351 HIS ** 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 = 0.3413 r_free = 0.3413 target = 0.047219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.032595 restraints weight = 215748.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.033499 restraints weight = 111778.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.034021 restraints weight = 74144.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.6635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  17537  Z= 0.182
  Angle     :  0.653   8.266  24975  Z= 0.376
  Chirality :  0.038   0.190   2774
  Planarity :  0.005   0.138   2132
  Dihedral  : 30.584 170.448   4825
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.69 (0.23), residues: 1261
  helix:  1.00 (0.18), residues: 777
  sheet:  0.12 (0.65), residues: 63
  loop : -0.35 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP K1472 
 HIS   0.010   0.001   HIS K1413 
 PHE   0.021   0.001   PHE A  67 
 TYR   0.013   0.001   TYR G  57 
 ARG   0.012   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05518 (  863)
  hydrogen bonds       : angle       4.18663 ( 2285)
  covalent geometry    : bond        0.00398 (17537)
  covalent geometry    : angle       0.65282 (24975)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9521 (mt) cc_final: 0.9293 (mt)
REVERT: A  105 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: B   88 TYR cc_start: 0.8652 (m-10) cc_final: 0.8334 (m-10)
REVERT: K 1095 MET cc_start: 0.2149 (mmm) cc_final: 0.1813 (mmm)
REVERT: K 1193 MET cc_start: 0.2234 (ttt) cc_final: 0.1810 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2549
  time to fit residues: 30.3985
Evaluate side-chains
  50 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 146 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 42 optimal weight:    0.7980
   chunk 129 optimal weight:    6.9990
   chunk 90 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 114 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0270
   chunk 142 optimal weight:    8.9990
   overall best weight:    1.1642

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.047803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.033118 restraints weight = 214313.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.034069 restraints weight = 109551.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.034470 restraints weight = 71617.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.6594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17537  Z= 0.158
  Angle     :  0.632   8.157  24975  Z= 0.364
  Chirality :  0.037   0.175   2774
  Planarity :  0.005   0.120   2132
  Dihedral  : 30.390 170.351   4825
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.93 (0.23), residues: 1261
  helix:  1.19 (0.18), residues: 777
  sheet:  0.23 (0.65), residues: 63
  loop : -0.26 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP K1472 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.017   0.001   PHE G  25 
 TYR   0.016   0.001   TYR K1298 
 ARG   0.011   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04784 (  863)
  hydrogen bonds       : angle       4.03533 ( 2285)
  covalent geometry    : bond        0.00341 (17537)
  covalent geometry    : angle       0.63231 (24975)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5785.91 seconds
wall clock time: 103 minutes 14.38 seconds (6194.38 seconds total)