Starting phenix.real_space_refine
on Wed Feb 12 19:34:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vwk_21419/02_2025/6vwk_21419_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vwk_21419/02_2025/6vwk_21419.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vwk_21419/02_2025/6vwk_21419.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vwk_21419/02_2025/6vwk_21419.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vwk_21419/02_2025/6vwk_21419_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vwk_21419/02_2025/6vwk_21419_neut.cif"
  }
  resolution = 3.3
  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=   1.000
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: 4
    Type Number    sf(0)   Gaussians
     S      86      5.16       5
     C    5615      2.51       5
     N    1328      2.21       5
     O    1394      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8423
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "I"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "J"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "L"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "M"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "N"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "O"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "P"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "Q"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "R"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "S"
      Number of atoms: 557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 557
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "X"
      Number of atoms: 362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 362
          Classifications: {'peptide': 47}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 44}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "Y"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "a"
      Number of atoms: 2104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2104
          Classifications: {'peptide': 266}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250}
  Time building chain proxies: 5.79, per 1000 atoms: 0.69
  Number of scatterers: 8423
  At special positions: 0
  Unit cell: (89.557, 99.268, 102.505, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      86     16.00
     O    1394      8.00
     N    1328      7.00
     C    5615      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: 2.16
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2024

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 1 sheets defined
      90.1% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'I' and resid 3 through 42
      removed outlier: 3.703A  pdb=" N   MET I  11 " --> pdb=" O   ASP I   7 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 45 through 77
      removed outlier: 3.722A  pdb=" N   LEU I  59 " --> pdb=" O   ILE I  55 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ILE I  63 " --> pdb=" O   LEU I  59 " (cutoff:3.500A)
      Proline residue:  I  64  - end of helix
    Processing helix  chain 'J' and resid 4 through 42
    Processing helix  chain 'J' and resid 45 through 77
      removed outlier: 3.750A  pdb=" N   LEU J  59 " --> pdb=" O   ILE J  55 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ILE J  63 " --> pdb=" O   LEU J  59 " (cutoff:3.500A)
      Proline residue:  J  64  - end of helix
    Processing helix  chain 'L' and resid 4 through 42
    Processing helix  chain 'L' and resid 45 through 77
      removed outlier: 3.716A  pdb=" N   LEU L  59 " --> pdb=" O   ILE L  55 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ILE L  63 " --> pdb=" O   LEU L  59 " (cutoff:3.500A)
      Proline residue:  L  64  - end of helix
    Processing helix  chain 'M' and resid 4 through 42
      removed outlier: 3.743A  pdb=" N   GLN M  42 " --> pdb=" O   GLY M  38 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 45 through 77
      removed outlier: 3.789A  pdb=" N   LEU M  59 " --> pdb=" O   ILE M  55 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ILE M  63 " --> pdb=" O   LEU M  59 " (cutoff:3.500A)
      Proline residue:  M  64  - end of helix
    Processing helix  chain 'N' and resid 4 through 42
      removed outlier: 3.589A  pdb=" N   TYR N  10 " --> pdb=" O   MET N   6 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA N  40 " --> pdb=" O   LEU N  36 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 45 through 77
      removed outlier: 3.837A  pdb=" N   LEU N  59 " --> pdb=" O   ILE N  55 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ILE N  63 " --> pdb=" O   LEU N  59 " (cutoff:3.500A)
      Proline residue:  N  64  - end of helix
    Processing helix  chain 'O' and resid 4 through 42
      removed outlier: 3.628A  pdb=" N   LEU O   8 " --> pdb=" O   LEU O   4 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR O  10 " --> pdb=" O   MET O   6 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 45 through 77
      removed outlier: 3.861A  pdb=" N   LEU O  59 " --> pdb=" O   ILE O  55 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ILE O  63 " --> pdb=" O   LEU O  59 " (cutoff:3.500A)
      Proline residue:  O  64  - end of helix
    Processing helix  chain 'P' and resid 4 through 42
    Processing helix  chain 'P' and resid 45 through 77
      removed outlier: 3.789A  pdb=" N   LEU P  59 " --> pdb=" O   ILE P  55 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ILE P  63 " --> pdb=" O   LEU P  59 " (cutoff:3.500A)
      Proline residue:  P  64  - end of helix
      removed outlier: 3.671A  pdb=" N   ALA P  67 " --> pdb=" O   ILE P  63 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 4 through 42
    Processing helix  chain 'Q' and resid 45 through 77
      removed outlier: 3.602A  pdb=" N   LEU Q  59 " --> pdb=" O   ILE Q  55 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ILE Q  63 " --> pdb=" O   LEU Q  59 " (cutoff:3.500A)
      Proline residue:  Q  64  - end of helix
    Processing helix  chain 'R' and resid 4 through 42
    Processing helix  chain 'R' and resid 45 through 77
      removed outlier: 3.811A  pdb=" N   LEU R  59 " --> pdb=" O   ILE R  55 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ILE R  63 " --> pdb=" O   LEU R  59 " (cutoff:3.500A)
      Proline residue:  R  64  - end of helix
    Processing helix  chain 'S' and resid 4 through 42
      removed outlier: 3.808A  pdb=" N   LEU S   8 " --> pdb=" O   LEU S   4 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 45 through 61
      removed outlier: 3.767A  pdb=" N   LEU S  59 " --> pdb=" O   ILE S  55 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 61 through 77
      removed outlier: 3.541A  pdb=" N   ALA S  67 " --> pdb=" O   ILE S  63 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 5 through 25
    Processing helix  chain 'X' and resid 25 through 46
    Processing helix  chain 'Y' and resid 2 through 50
      Proline residue:  Y  27  - end of helix
    Processing helix  chain 'a' and resid 7 through 16
    Processing helix  chain 'a' and resid 43 through 67
    Processing helix  chain 'a' and resid 73 through 94
    Processing helix  chain 'a' and resid 100 through 118
    Processing helix  chain 'a' and resid 119 through 121
      No H-bonds generated for 'chain 'a' and resid 119 through 121'
    Processing helix  chain 'a' and resid 124 through 133
    Processing helix  chain 'a' and resid 146 through 169
      removed outlier: 3.878A  pdb=" N   THR a 150 " --> pdb=" O   ASP a 146 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 172 through 180
    Processing helix  chain 'a' and resid 185 through 187
      No H-bonds generated for 'chain 'a' and resid 185 through 187'
    Processing helix  chain 'a' and resid 188 through 229
      Proline residue:  a 204  - end of helix
      removed outlier: 3.568A  pdb=" N   PHE a 222 " --> pdb=" O   GLY a 218 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU a 229 " --> pdb=" O   ILE a 225 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 230 through 269
      removed outlier: 4.692A  pdb=" N   TRP a 235 " --> pdb=" O   TRP a 231 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ILE a 236 " --> pdb=" O   TRP a 232 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   LEU a 237 " --> pdb=" O   SER a 233 " (cutoff:3.500A)
      Proline residue:  a 240  - end of helix
      removed outlier: 3.892A  pdb=" N   LEU a 247 " --> pdb=" O   ILE a 243 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR a 250 " --> pdb=" O   ILE a 246 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22

    813 hydrogen bonds defined for protein.
    2439 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 2.49 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1336
        1.32 -     1.44: 2020
        1.44 -     1.57: 5049
        1.57 -     1.69: 0
        1.69 -     1.81: 172
  Bond restraints: 8577
  Sorted by residual:
  bond pdb=" C   ARG a 210 "
       pdb=" O   ARG a 210 "
    ideal  model  delta    sigma   weight residual
    1.236  1.196  0.041 1.15e-02 7.56e+03 1.24e+01
  bond pdb=" N   VAL S  60 "
       pdb=" CA  VAL S  60 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.17e-02 7.31e+03 8.31e+00
  bond pdb=" C   LEU S   8 "
       pdb=" O   LEU S   8 "
    ideal  model  delta    sigma   weight residual
    1.236  1.202  0.034 1.26e-02 6.30e+03 7.37e+00
  bond pdb=" N   MET S  11 "
       pdb=" CA  MET S  11 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.33e-02 5.65e+03 6.72e+00
  bond pdb=" C   ASP S   7 "
       pdb=" O   ASP S   7 "
    ideal  model  delta    sigma   weight residual
    1.237  1.267 -0.031 1.19e-02 7.06e+03 6.61e+00
  ... (remaining 8572 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 9466
        1.56 -     3.12: 1802
        3.12 -     4.68: 274
        4.68 -     6.24: 70
        6.24 -     7.80: 14
  Bond angle restraints: 11626
  Sorted by residual:
  angle pdb=" N   ALA M  62 "
        pdb=" CA  ALA M  62 "
        pdb=" C   ALA M  62 "
      ideal   model   delta    sigma   weight residual
     111.07  116.01   -4.94 1.07e+00 8.73e-01 2.13e+01
  angle pdb=" N   ALA Q  62 "
        pdb=" CA  ALA Q  62 "
        pdb=" C   ALA Q  62 "
      ideal   model   delta    sigma   weight residual
     111.28  116.29   -5.01 1.09e+00 8.42e-01 2.11e+01
  angle pdb=" CA  VAL S  60 "
        pdb=" C   VAL S  60 "
        pdb=" O   VAL S  60 "
      ideal   model   delta    sigma   weight residual
     121.17  116.64    4.53 1.06e+00 8.90e-01 1.83e+01
  angle pdb=" N   PRO X  27 "
        pdb=" CA  PRO X  27 "
        pdb=" C   PRO X  27 "
      ideal   model   delta    sigma   weight residual
     110.70  115.88   -5.18 1.22e+00 6.72e-01 1.80e+01
  angle pdb=" N   PHE R  76 "
        pdb=" CA  PHE R  76 "
        pdb=" C   PHE R  76 "
      ideal   model   delta    sigma   weight residual
     111.40  116.56   -5.16 1.22e+00 6.72e-01 1.79e+01
  ... (remaining 11621 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 4676
       17.07 -    34.15: 306
       34.15 -    51.22: 55
       51.22 -    68.29: 14
       68.29 -    85.36: 5
  Dihedral angle restraints: 5056
    sinusoidal: 1884
      harmonic: 3172
  Sorted by residual:
  dihedral pdb=" CA  LEU X   3 "
           pdb=" C   LEU X   3 "
           pdb=" N   ASN X   4 "
           pdb=" CA  ASN X   4 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.82  -28.18     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  MET a   6 "
           pdb=" C   MET a   6 "
           pdb=" N   THR a   7 "
           pdb=" CA  THR a   7 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.19   27.81     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  ARG a 140 "
           pdb=" C   ARG a 140 "
           pdb=" N   VAL a 141 "
           pdb=" CA  VAL a 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.75  -27.25     0      5.00e+00 4.00e-02 2.97e+01
  ... (remaining 5053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1148
       0.078 -    0.157: 213
       0.157 -    0.235: 33
       0.235 -    0.314: 17
       0.314 -    0.392: 4
  Chirality restraints: 1415
  Sorted by residual:
  chirality pdb=" CA  PHE S  76 "
            pdb=" N   PHE S  76 "
            pdb=" C   PHE S  76 "
            pdb=" CB  PHE S  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.84e+00
  chirality pdb=" CA  PHE P  76 "
            pdb=" N   PHE P  76 "
            pdb=" C   PHE P  76 "
            pdb=" CB  PHE P  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.43e+00
  chirality pdb=" CA  PHE J  76 "
            pdb=" N   PHE J  76 "
            pdb=" C   PHE J  76 "
            pdb=" CB  PHE J  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.39e+00
  ... (remaining 1412 not shown)

  Planarity restraints: 1434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU O   8 "   -0.027 2.00e-02 2.50e+03   5.49e-02 3.02e+01
        pdb=" C   LEU O   8 "    0.095 2.00e-02 2.50e+03
        pdb=" O   LEU O   8 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   LEU O   9 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET Y  22 "    0.024 2.00e-02 2.50e+03   4.69e-02 2.20e+01
        pdb=" C   MET Y  22 "   -0.081 2.00e-02 2.50e+03
        pdb=" O   MET Y  22 "    0.030 2.00e-02 2.50e+03
        pdb=" N   LYS Y  23 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA J  21 "   -0.022 2.00e-02 2.50e+03   4.35e-02 1.89e+01
        pdb=" C   ALA J  21 "    0.075 2.00e-02 2.50e+03
        pdb=" O   ALA J  21 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ILE J  22 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1431 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.86: 2295
        2.86 -     3.37: 8720
        3.37 -     3.88: 14108
        3.88 -     4.39: 15509
        4.39 -     4.90: 27755
  Nonbonded interactions: 68387
  Sorted by model distance:
  nonbonded pdb=" O   ASN a  33 "
            pdb=" OD1 ASN a  33 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   SER a 165 "
            pdb=" O   LYS a 169 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   ASN N   5 "
            pdb=" OD2 ASP O   7 "
     model   vdw
     2.395 3.040
  nonbonded pdb=" O   LEU L   4 "
            pdb=" OD1 ASP L   7 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" OD1 ASN O   5 "
            pdb=" N   MET O   6 "
     model   vdw
     2.510 3.120
  ... (remaining 68382 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 'I'
  selection = chain 'J'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
}
ncs_group {
  reference = chain 'X'
  selection = (chain 'Y' and resid 1 through 47)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.910
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     23.290
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
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      :  0.010   0.064   8577  Z= 0.640
  Angle     :  1.305   7.796  11626  Z= 0.848
  Chirality :  0.069   0.392   1415
  Planarity :  0.013   0.063   1434
  Dihedral  : 12.707  85.363   3032
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 0.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  5.19 %
    Favored  : 94.21 %
  Cbeta Deviations :  0.40 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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: -0.35 (0.22), residues: 1107
  helix:  0.01 (0.14), residues: 974
  sheet:  None (None), residues: 0
  loop : -0.96 (0.56), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.006   TRP Y  26 
 HIS   0.020   0.007   HIS a  15 
 PHE   0.032   0.004   PHE L  76 
 TYR   0.052   0.007   TYR O  10 
 ARG   0.047   0.009   ARG Y  36 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 168
  time to evaluate  : 0.943 
Fit side-chains
REVERT: I    6 MET cc_start: 0.5274 (mtm) cc_final: 0.4821 (mmp)
REVERT: J   11 MET cc_start: 0.8069 (tpp) cc_final: 0.7832 (tpt)
REVERT: L   11 MET cc_start: 0.8456 (tpt) cc_final: 0.7974 (tpt)
REVERT: M    6 MET cc_start: 0.5909 (mtt) cc_final: 0.5557 (mtm)
REVERT: Q   28 ILE cc_start: 0.9184 (mt) cc_final: 0.8977 (mp)
REVERT: S    6 MET cc_start: 0.5895 (mmt) cc_final: 0.5233 (mmt)
REVERT: S   11 MET cc_start: 0.8581 (tpp) cc_final: 0.8263 (tpt)
REVERT: S   65 MET cc_start: 0.8400 (mmt) cc_final: 0.8186 (mmt)
REVERT: Y   16 LEU cc_start: 0.8865 (mp) cc_final: 0.8557 (mp)
REVERT: a  257 MET cc_start: 0.8137 (ttp) cc_final: 0.7927 (ttt)
  outliers start: 5
  outliers final: 2
  residues processed: 172
  average time/residue: 0.2250
  time to fit residues: 52.1600
Evaluate side-chains
  133 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   33 ASN
Chi-restraints excluded: chain a residue  149 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 27 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
R   5 ASN
S   3 ASN
a 132 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.124978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.106645 restraints weight = 10053.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 0.96
r_work: 0.3038 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 2.52 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8577  Z= 0.293
  Angle     :  0.714   8.231  11626  Z= 0.371
  Chirality :  0.045   0.351   1415
  Planarity :  0.006   0.050   1434
  Dihedral  :  4.990  34.844   1178
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.09 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  2.19 (0.23), residues: 1107
  helix:  1.73 (0.15), residues: 976
  sheet:  None (None), residues: 0
  loop : -0.44 (0.55), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP a 111 
 HIS   0.007   0.002   HIS a 132 
 PHE   0.017   0.002   PHE a  75 
 TYR   0.023   0.002   TYR M  10 
 ARG   0.007   0.001   ARG Q  41 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 0.815 
Fit side-chains
REVERT: J   11 MET cc_start: 0.8124 (tpp) cc_final: 0.7860 (tpt)
REVERT: L   11 MET cc_start: 0.8422 (tpt) cc_final: 0.7792 (tpt)
REVERT: M    6 MET cc_start: 0.5894 (mtt) cc_final: 0.5563 (mtt)
REVERT: Q   41 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7883 (ttm-80)
REVERT: S    6 MET cc_start: 0.6045 (mmt) cc_final: 0.5526 (mmt)
REVERT: X    2 ASN cc_start: 0.6261 (t0) cc_final: 0.5786 (p0)
REVERT: Y   18 VAL cc_start: 0.8045 (t) cc_final: 0.7765 (t)
REVERT: a  116 ASN cc_start: 0.8682 (m-40) cc_final: 0.8120 (m110)
  outliers start: 13
  outliers final: 7
  residues processed: 148
  average time/residue: 0.2017
  time to fit residues: 41.4922
Evaluate side-chains
  135 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   37 GLU
Chi-restraints excluded: chain P residue   44 ASP
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue  147 VAL
Chi-restraints excluded: chain a residue  149 VAL
Chi-restraints excluded: chain a residue  246 ILE
Chi-restraints excluded: chain a residue  265 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 69 optimal weight:    0.2980
   chunk 80 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
R  52 GLN
a  14 HIS
a  20 GLN
a 245 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.125382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.107112 restraints weight = 10178.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 0.93
r_work: 0.3042 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8577  Z= 0.271
  Angle     :  0.649   8.339  11626  Z= 0.328
  Chirality :  0.043   0.319   1415
  Planarity :  0.005   0.047   1434
  Dihedral  :  4.532  41.534   1176
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  9.80 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  2.79 (0.24), residues: 1107
  helix:  2.14 (0.15), residues: 977
  sheet:  None (None), residues: 0
  loop : -0.42 (0.55), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP a 111 
 HIS   0.003   0.001   HIS a  95 
 PHE   0.013   0.001   PHE a  75 
 TYR   0.024   0.002   TYR M  10 
 ARG   0.006   0.000   ARG I  41 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.801 
Fit side-chains
REVERT: J   11 MET cc_start: 0.8048 (tpp) cc_final: 0.7749 (tpt)
REVERT: L   11 MET cc_start: 0.8385 (tpt) cc_final: 0.7726 (tpt)
REVERT: M    6 MET cc_start: 0.5753 (mtt) cc_final: 0.5415 (mtt)
REVERT: R   57 MET cc_start: 0.8432 (ttp) cc_final: 0.7949 (ttt)
REVERT: X    2 ASN cc_start: 0.6727 (t0) cc_final: 0.6289 (p0)
REVERT: X   23 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7558 (mttt)
REVERT: X   24 TYR cc_start: 0.8244 (m-10) cc_final: 0.7966 (m-10)
REVERT: Y   18 VAL cc_start: 0.7961 (t) cc_final: 0.7699 (t)
REVERT: a   46 MET cc_start: 0.7293 (mmm) cc_final: 0.6894 (mtp)
  outliers start: 16
  outliers final: 10
  residues processed: 147
  average time/residue: 0.2036
  time to fit residues: 41.9048
Evaluate side-chains
  139 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   37 GLU
Chi-restraints excluded: chain O residue   16 MET
Chi-restraints excluded: chain P residue   44 ASP
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue   71 VAL
Chi-restraints excluded: chain a residue   93 MET
Chi-restraints excluded: chain a residue  149 VAL
Chi-restraints excluded: chain a residue  245 HIS
Chi-restraints excluded: chain a residue  246 ILE
Chi-restraints excluded: chain a residue  265 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 92 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.128010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.108816 restraints weight = 10030.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 1.02
r_work: 0.3070 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8577  Z= 0.299
  Angle     :  0.646   8.342  11626  Z= 0.323
  Chirality :  0.042   0.266   1415
  Planarity :  0.005   0.049   1434
  Dihedral  :  4.491  47.795   1176
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 10.51 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  2.89 (0.24), residues: 1107
  helix:  2.22 (0.15), residues: 978
  sheet:  None (None), residues: 0
  loop : -0.42 (0.55), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP a 241 
 HIS   0.017   0.003   HIS a 245 
 PHE   0.015   0.001   PHE a  85 
 TYR   0.022   0.001   TYR M  10 
 ARG   0.004   0.000   ARG I  41 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: I   57 MET cc_start: 0.8134 (tmm) cc_final: 0.7897 (ttp)
REVERT: J   11 MET cc_start: 0.8072 (tpp) cc_final: 0.7748 (tpt)
REVERT: L   11 MET cc_start: 0.8375 (tpt) cc_final: 0.7690 (tpt)
REVERT: M    6 MET cc_start: 0.6066 (mtt) cc_final: 0.5796 (mtt)
REVERT: O   42 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7216 (mm110)
REVERT: O   57 MET cc_start: 0.8786 (tmm) cc_final: 0.8514 (ttp)
REVERT: R   17 MET cc_start: 0.8424 (mmm) cc_final: 0.7912 (mmm)
REVERT: R   57 MET cc_start: 0.8529 (ttp) cc_final: 0.8114 (ttt)
REVERT: X    1 MET cc_start: 0.5601 (mtt) cc_final: 0.4926 (ttm)
REVERT: X   24 TYR cc_start: 0.8297 (m-10) cc_final: 0.7934 (m-10)
REVERT: Y   18 VAL cc_start: 0.7984 (t) cc_final: 0.7716 (t)
REVERT: a   46 MET cc_start: 0.7330 (mmm) cc_final: 0.6946 (mtp)
REVERT: a  116 ASN cc_start: 0.8672 (m-40) cc_final: 0.8225 (m110)
  outliers start: 22
  outliers final: 10
  residues processed: 144
  average time/residue: 0.1957
  time to fit residues: 39.5748
Evaluate side-chains
  137 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain O residue   16 MET
Chi-restraints excluded: chain P residue   44 ASP
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue   71 VAL
Chi-restraints excluded: chain a residue  147 VAL
Chi-restraints excluded: chain a residue  149 VAL
Chi-restraints excluded: chain a residue  245 HIS
Chi-restraints excluded: chain a residue  246 ILE
Chi-restraints excluded: chain a residue  265 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 75 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 48 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0030
   chunk 31 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
J   3 ASN
J   5 ASN
a  15 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.129486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.110127 restraints weight = 10055.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.05
r_work: 0.3083 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8577  Z= 0.243
  Angle     :  0.614   8.481  11626  Z= 0.306
  Chirality :  0.041   0.340   1415
  Planarity :  0.005   0.049   1434
  Dihedral  :  4.404  51.740   1176
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.45 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  3.23 (0.24), residues: 1107
  helix:  2.53 (0.15), residues: 957
  sheet:  None (None), residues: 0
  loop : -0.61 (0.47), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP a 231 
 HIS   0.004   0.001   HIS a 245 
 PHE   0.012   0.001   PHE a  85 
 TYR   0.021   0.001   TYR M  10 
 ARG   0.003   0.000   ARG a 210 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: I   57 MET cc_start: 0.8119 (tmm) cc_final: 0.7877 (ttp)
REVERT: J   11 MET cc_start: 0.8026 (tpp) cc_final: 0.7741 (tpt)
REVERT: M    6 MET cc_start: 0.5979 (mtt) cc_final: 0.5688 (mtt)
REVERT: O   57 MET cc_start: 0.8784 (tmm) cc_final: 0.8497 (ttp)
REVERT: P    6 MET cc_start: 0.4700 (ptt) cc_final: 0.4303 (mtp)
REVERT: R   57 MET cc_start: 0.8665 (ttp) cc_final: 0.8196 (ttt)
REVERT: X    1 MET cc_start: 0.5622 (mtt) cc_final: 0.5051 (ttm)
REVERT: X   24 TYR cc_start: 0.8217 (m-10) cc_final: 0.7740 (m-10)
REVERT: Y   18 VAL cc_start: 0.8007 (t) cc_final: 0.7721 (t)
REVERT: a   46 MET cc_start: 0.7214 (mmm) cc_final: 0.6865 (mtp)
REVERT: a  116 ASN cc_start: 0.8679 (m-40) cc_final: 0.8212 (m110)
  outliers start: 17
  outliers final: 11
  residues processed: 146
  average time/residue: 0.2111
  time to fit residues: 43.3384
Evaluate side-chains
  145 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   78 VAL
Chi-restraints excluded: chain M residue   37 GLU
Chi-restraints excluded: chain O residue   16 MET
Chi-restraints excluded: chain P residue   44 ASP
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue   71 VAL
Chi-restraints excluded: chain a residue  149 VAL
Chi-restraints excluded: chain a residue  246 ILE
Chi-restraints excluded: chain a residue  259 LEU
Chi-restraints excluded: chain a residue  265 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
a  15 HIS

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 = 0.127862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.108362 restraints weight = 10137.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.07
r_work: 0.3070 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8577  Z= 0.292
  Angle     :  0.636   8.682  11626  Z= 0.316
  Chirality :  0.042   0.326   1415
  Planarity :  0.005   0.048   1434
  Dihedral  :  4.416  51.902   1176
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.04 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  3.14 (0.23), residues: 1107
  helix:  2.47 (0.15), residues: 958
  sheet:  None (None), residues: 0
  loop : -0.61 (0.47), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP a 231 
 HIS   0.002   0.001   HIS a 245 
 PHE   0.014   0.001   PHE a  85 
 TYR   0.019   0.001   TYR M  10 
 ARG   0.003   0.000   ARG a 210 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
REVERT: I   57 MET cc_start: 0.8109 (tmm) cc_final: 0.7865 (ttp)
REVERT: J   11 MET cc_start: 0.8120 (tpp) cc_final: 0.7810 (tpt)
REVERT: J   41 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.6796 (ttm-80)
REVERT: L   11 MET cc_start: 0.8339 (tpt) cc_final: 0.7615 (tpt)
REVERT: N   16 MET cc_start: 0.8241 (ttp) cc_final: 0.7984 (ttp)
REVERT: O   42 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7181 (mm-40)
REVERT: O   57 MET cc_start: 0.8736 (tmm) cc_final: 0.8461 (ttp)
REVERT: P    6 MET cc_start: 0.4854 (ptt) cc_final: 0.4387 (mtp)
REVERT: R   17 MET cc_start: 0.8437 (mmm) cc_final: 0.7948 (mmm)
REVERT: R   57 MET cc_start: 0.8558 (ttp) cc_final: 0.8200 (ttt)
REVERT: R   75 MET cc_start: 0.8919 (ttp) cc_final: 0.8445 (mtp)
REVERT: X    1 MET cc_start: 0.5238 (mtt) cc_final: 0.4779 (ttm)
REVERT: X   24 TYR cc_start: 0.8202 (m-10) cc_final: 0.7814 (m-10)
REVERT: Y   18 VAL cc_start: 0.8061 (t) cc_final: 0.7787 (t)
REVERT: a    6 MET cc_start: 0.6957 (mmp) cc_final: 0.6719 (mmt)
REVERT: a   40 THR cc_start: 0.7131 (OUTLIER) cc_final: 0.6859 (p)
REVERT: a   46 MET cc_start: 0.7287 (mmm) cc_final: 0.6900 (mtp)
REVERT: a  116 ASN cc_start: 0.8676 (m-40) cc_final: 0.8215 (m110)
  outliers start: 20
  outliers final: 13
  residues processed: 148
  average time/residue: 0.1991
  time to fit residues: 41.3189
Evaluate side-chains
  147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   78 VAL
Chi-restraints excluded: chain L residue   37 GLU
Chi-restraints excluded: chain M residue   37 GLU
Chi-restraints excluded: chain O residue   16 MET
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue   15 HIS
Chi-restraints excluded: chain a residue   40 THR
Chi-restraints excluded: chain a residue   56 PHE
Chi-restraints excluded: chain a residue   71 VAL
Chi-restraints excluded: chain a residue  149 VAL
Chi-restraints excluded: chain a residue  246 ILE
Chi-restraints excluded: chain a residue  259 LEU
Chi-restraints excluded: chain a residue  265 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 61 optimal weight:    0.2980
   chunk 93 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 98 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 102 optimal weight:    0.5980
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
a  15 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.129579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.109908 restraints weight = 10214.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 1.09
r_work: 0.3084 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8577  Z= 0.231
  Angle     :  0.608   8.710  11626  Z= 0.302
  Chirality :  0.040   0.319   1415
  Planarity :  0.005   0.048   1434
  Dihedral  :  4.346  51.847   1176
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.63 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  3.34 (0.24), residues: 1107
  helix:  2.62 (0.15), residues: 958
  sheet:  None (None), residues: 0
  loop : -0.70 (0.47), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP a 231 
 HIS   0.015   0.003   HIS a  15 
 PHE   0.011   0.001   PHE a  85 
 TYR   0.016   0.001   TYR M  10 
 ARG   0.004   0.000   ARG I  41 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: I    6 MET cc_start: 0.4782 (mtm) cc_final: 0.3801 (ppp)
REVERT: I   16 MET cc_start: 0.8342 (ttm) cc_final: 0.8025 (ttp)
REVERT: I   57 MET cc_start: 0.8116 (tmm) cc_final: 0.7864 (ttp)
REVERT: J   11 MET cc_start: 0.8114 (tpp) cc_final: 0.7836 (tpt)
REVERT: O   42 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7151 (mm-40)
REVERT: O   57 MET cc_start: 0.8753 (tmm) cc_final: 0.8479 (ttp)
REVERT: P    6 MET cc_start: 0.4848 (ptt) cc_final: 0.4358 (mtp)
REVERT: R   57 MET cc_start: 0.8479 (ttp) cc_final: 0.8176 (ttt)
REVERT: R   75 MET cc_start: 0.8979 (ttp) cc_final: 0.8544 (mtp)
REVERT: X    1 MET cc_start: 0.5303 (mtt) cc_final: 0.4889 (ttm)
REVERT: X   24 TYR cc_start: 0.8216 (m-10) cc_final: 0.7775 (m-10)
REVERT: Y   18 VAL cc_start: 0.8067 (t) cc_final: 0.7782 (t)
REVERT: a   40 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6850 (p)
REVERT: a   46 MET cc_start: 0.7311 (mmm) cc_final: 0.6938 (mtp)
REVERT: a  116 ASN cc_start: 0.8691 (m-40) cc_final: 0.8201 (m110)
  outliers start: 17
  outliers final: 13
  residues processed: 146
  average time/residue: 0.1944
  time to fit residues: 40.0919
Evaluate side-chains
  146 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   78 VAL
Chi-restraints excluded: chain L residue   37 GLU
Chi-restraints excluded: chain M residue   37 GLU
Chi-restraints excluded: chain O residue   16 MET
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue   40 THR
Chi-restraints excluded: chain a residue   56 PHE
Chi-restraints excluded: chain a residue   71 VAL
Chi-restraints excluded: chain a residue  149 VAL
Chi-restraints excluded: chain a residue  245 HIS
Chi-restraints excluded: chain a residue  246 ILE
Chi-restraints excluded: chain a residue  259 LEU
Chi-restraints excluded: chain a residue  265 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 67 optimal weight:    0.1980
   chunk 103 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 73 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0060
   chunk 95 optimal weight:    0.9980
   chunk 80 optimal weight:    0.2980
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
a  15 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.131107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.111626 restraints weight = 10174.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.08
r_work: 0.3115 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8577  Z= 0.207
  Angle     :  0.591   7.831  11626  Z= 0.294
  Chirality :  0.039   0.310   1415
  Planarity :  0.005   0.048   1434
  Dihedral  :  4.276  52.643   1176
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.75 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  3.51 (0.24), residues: 1107
  helix:  2.75 (0.15), residues: 958
  sheet:  None (None), residues: 0
  loop : -0.77 (0.47), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP a 231 
 HIS   0.002   0.001   HIS a  15 
 PHE   0.010   0.001   PHE a  85 
 TYR   0.018   0.001   TYR M  10 
 ARG   0.003   0.000   ARG a 210 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: I    6 MET cc_start: 0.4749 (mtm) cc_final: 0.3811 (ppp)
REVERT: I   16 MET cc_start: 0.8272 (ttm) cc_final: 0.7958 (ttp)
REVERT: I   57 MET cc_start: 0.8086 (tmm) cc_final: 0.7826 (ttp)
REVERT: J   11 MET cc_start: 0.8097 (tpp) cc_final: 0.7819 (tpt)
REVERT: O   57 MET cc_start: 0.8696 (tmm) cc_final: 0.8424 (ttp)
REVERT: P    6 MET cc_start: 0.4724 (ptt) cc_final: 0.4175 (mtp)
REVERT: R   57 MET cc_start: 0.8359 (ttp) cc_final: 0.8065 (ttt)
REVERT: R   75 MET cc_start: 0.8952 (ttp) cc_final: 0.8568 (mtp)
REVERT: X    1 MET cc_start: 0.5261 (mtt) cc_final: 0.4872 (ttm)
REVERT: X   24 TYR cc_start: 0.8222 (m-10) cc_final: 0.7727 (m-10)
REVERT: Y   18 VAL cc_start: 0.8024 (t) cc_final: 0.7739 (t)
REVERT: a    6 MET cc_start: 0.7135 (mmt) cc_final: 0.6341 (tpt)
REVERT: a   40 THR cc_start: 0.6990 (OUTLIER) cc_final: 0.6697 (p)
REVERT: a   46 MET cc_start: 0.7159 (mmm) cc_final: 0.6829 (mtp)
REVERT: a  116 ASN cc_start: 0.8669 (m-40) cc_final: 0.8138 (m110)
  outliers start: 17
  outliers final: 14
  residues processed: 146
  average time/residue: 0.1873
  time to fit residues: 38.6802
Evaluate side-chains
  148 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   78 VAL
Chi-restraints excluded: chain L residue   37 GLU
Chi-restraints excluded: chain M residue   37 GLU
Chi-restraints excluded: chain N residue   78 VAL
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue   15 HIS
Chi-restraints excluded: chain a residue   40 THR
Chi-restraints excluded: chain a residue   56 PHE
Chi-restraints excluded: chain a residue  149 VAL
Chi-restraints excluded: chain a residue  178 LEU
Chi-restraints excluded: chain a residue  245 HIS
Chi-restraints excluded: chain a residue  246 ILE
Chi-restraints excluded: chain a residue  259 LEU
Chi-restraints excluded: chain a residue  265 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0470
   chunk 11 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
a  15 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.130063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.110646 restraints weight = 10320.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 1.09
r_work: 0.3095 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8577  Z= 0.245
  Angle     :  0.611   8.389  11626  Z= 0.301
  Chirality :  0.040   0.306   1415
  Planarity :  0.005   0.049   1434
  Dihedral  :  4.286  52.815   1176
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.34 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  3.44 (0.24), residues: 1107
  helix:  2.70 (0.15), residues: 958
  sheet:  None (None), residues: 0
  loop : -0.76 (0.46), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP a 231 
 HIS   0.004   0.001   HIS a  15 
 PHE   0.011   0.001   PHE a  85 
 TYR   0.015   0.001   TYR M  10 
 ARG   0.003   0.000   ARG a 210 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: I    6 MET cc_start: 0.4873 (mtm) cc_final: 0.3913 (ppp)
REVERT: I   16 MET cc_start: 0.8334 (ttm) cc_final: 0.8022 (ttp)
REVERT: I   57 MET cc_start: 0.8114 (tmm) cc_final: 0.7851 (ttp)
REVERT: J   11 MET cc_start: 0.8152 (tpp) cc_final: 0.7865 (tpt)
REVERT: N   16 MET cc_start: 0.8235 (ttp) cc_final: 0.7994 (ttm)
REVERT: O   57 MET cc_start: 0.8735 (tmm) cc_final: 0.8457 (ttp)
REVERT: P    6 MET cc_start: 0.4818 (ptt) cc_final: 0.4259 (mtp)
REVERT: R   17 MET cc_start: 0.8339 (mmm) cc_final: 0.7977 (mtp)
REVERT: R   57 MET cc_start: 0.8419 (ttp) cc_final: 0.8150 (ttt)
REVERT: R   75 MET cc_start: 0.8984 (ttp) cc_final: 0.8585 (mtp)
REVERT: X    1 MET cc_start: 0.5205 (mtt) cc_final: 0.4822 (ttm)
REVERT: X   24 TYR cc_start: 0.8218 (m-10) cc_final: 0.7745 (m-10)
REVERT: Y   18 VAL cc_start: 0.8077 (t) cc_final: 0.7794 (t)
REVERT: a    6 MET cc_start: 0.7177 (mmt) cc_final: 0.6256 (tpt)
REVERT: a   40 THR cc_start: 0.7013 (OUTLIER) cc_final: 0.6719 (p)
REVERT: a   46 MET cc_start: 0.7226 (mmm) cc_final: 0.6897 (mtp)
REVERT: a  116 ASN cc_start: 0.8659 (m-40) cc_final: 0.8152 (m110)
  outliers start: 17
  outliers final: 14
  residues processed: 143
  average time/residue: 0.1814
  time to fit residues: 37.1772
Evaluate side-chains
  145 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   78 VAL
Chi-restraints excluded: chain L residue   37 GLU
Chi-restraints excluded: chain M residue   37 GLU
Chi-restraints excluded: chain N residue   78 VAL
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue   15 HIS
Chi-restraints excluded: chain a residue   40 THR
Chi-restraints excluded: chain a residue   56 PHE
Chi-restraints excluded: chain a residue  149 VAL
Chi-restraints excluded: chain a residue  178 LEU
Chi-restraints excluded: chain a residue  245 HIS
Chi-restraints excluded: chain a residue  246 ILE
Chi-restraints excluded: chain a residue  259 LEU
Chi-restraints excluded: chain a residue  265 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 99 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
a  15 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.128782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.107612 restraints weight = 10215.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.24
r_work: 0.3058 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   8577  Z= 0.298
  Angle     :  0.646   9.113  11626  Z= 0.317
  Chirality :  0.041   0.306   1415
  Planarity :  0.005   0.050   1434
  Dihedral  :  4.316  51.638   1176
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.34 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  3.28 (0.23), residues: 1107
  helix:  2.57 (0.15), residues: 959
  sheet:  None (None), residues: 0
  loop : -0.74 (0.46), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP a 241 
 HIS   0.006   0.001   HIS a  15 
 PHE   0.014   0.001   PHE a  85 
 TYR   0.014   0.001   TYR a  11 
 ARG   0.003   0.000   ARG a 210 

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: I    6 MET cc_start: 0.4822 (mtm) cc_final: 0.3835 (ppp)
REVERT: I   16 MET cc_start: 0.8311 (ttm) cc_final: 0.8023 (ttp)
REVERT: I   57 MET cc_start: 0.8063 (tmm) cc_final: 0.7840 (ttp)
REVERT: J   11 MET cc_start: 0.8183 (tpp) cc_final: 0.7873 (tpt)
REVERT: J   41 ARG cc_start: 0.7272 (ttt-90) cc_final: 0.6754 (ttm-80)
REVERT: J   57 MET cc_start: 0.8376 (tmm) cc_final: 0.7982 (ttp)
REVERT: O   42 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7088 (mm-40)
REVERT: O   57 MET cc_start: 0.8670 (tmm) cc_final: 0.8440 (ttp)
REVERT: P    6 MET cc_start: 0.4710 (ptt) cc_final: 0.4075 (mtp)
REVERT: R   17 MET cc_start: 0.8324 (mmm) cc_final: 0.7957 (mtp)
REVERT: R   57 MET cc_start: 0.8513 (ttp) cc_final: 0.8237 (ttt)
REVERT: R   75 MET cc_start: 0.8925 (ttp) cc_final: 0.8584 (mtp)
REVERT: X    1 MET cc_start: 0.5035 (mtt) cc_final: 0.4652 (ttm)
REVERT: X   24 TYR cc_start: 0.8193 (m-10) cc_final: 0.7726 (m-10)
REVERT: Y   18 VAL cc_start: 0.8044 (t) cc_final: 0.7777 (t)
REVERT: a    6 MET cc_start: 0.7099 (mmt) cc_final: 0.6171 (tpt)
REVERT: a   40 THR cc_start: 0.6937 (OUTLIER) cc_final: 0.6630 (p)
REVERT: a   46 MET cc_start: 0.7276 (mmm) cc_final: 0.6889 (mtp)
REVERT: a  116 ASN cc_start: 0.8714 (m-40) cc_final: 0.8234 (m110)
  outliers start: 19
  outliers final: 15
  residues processed: 145
  average time/residue: 0.1920
  time to fit residues: 39.0636
Evaluate side-chains
  147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
Chi-restraints excluded: chain I residue   78 VAL
Chi-restraints excluded: chain L residue   37 GLU
Chi-restraints excluded: chain M residue   37 GLU
Chi-restraints excluded: chain N residue   78 VAL
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue   15 HIS
Chi-restraints excluded: chain a residue   40 THR
Chi-restraints excluded: chain a residue   56 PHE
Chi-restraints excluded: chain a residue   71 VAL
Chi-restraints excluded: chain a residue  149 VAL
Chi-restraints excluded: chain a residue  178 LEU
Chi-restraints excluded: chain a residue  245 HIS
Chi-restraints excluded: chain a residue  246 ILE
Chi-restraints excluded: chain a residue  259 LEU
Chi-restraints excluded: chain a residue  265 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 104 optimal weight:    0.0980
   chunk 99 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3435 r_free = 0.3435 target = 0.129883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.109554 restraints weight = 10359.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.17
r_work: 0.3077 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8577  Z= 0.242
  Angle     :  0.618   9.265  11626  Z= 0.303
  Chirality :  0.040   0.305   1415
  Planarity :  0.005   0.050   1434
  Dihedral  :  4.287  51.108   1176
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.93 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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:  3.36 (0.23), residues: 1107
  helix:  2.64 (0.15), residues: 959
  sheet:  None (None), residues: 0
  loop : -0.79 (0.46), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP a 231 
 HIS   0.008   0.002   HIS a  15 
 PHE   0.011   0.001   PHE a  85 
 TYR   0.013   0.001   TYR a  11 
 ARG   0.003   0.000   ARG a 210 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4104.50 seconds
wall clock time: 73 minutes 28.32 seconds (4408.32 seconds total)