Starting phenix.real_space_refine
on Wed Mar 12 20:20:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vwk_21419/03_2025/6vwk_21419_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vwk_21419/03_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_21419/03_2025/6vwk_21419.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vwk_21419/03_2025/6vwk_21419.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vwk_21419/03_2025/6vwk_21419_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vwk_21419/03_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-5624/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: 6.08, per 1000 atoms: 0.72
  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: 2.19
  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: 0.68
  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: 2.35

  Time building geometry restraints manager: 2.59 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:             3.250
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.360
  Find NCS groups from input model:        0.220
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.990
-------------------------------------------------------------------------------
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  : 0.851 
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: 0.2147
  time to fit residues: 49.9618
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  : 0.862 
-------------------------------------------------------------------------------
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 = 68)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.106659 restraints weight = 10052.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 0.95
r_work: 0.3038 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
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  : 0.932 
Fit side-chains
REVERT: J   11 MET cc_start: 0.8120 (tpp) cc_final: 0.7856 (tpt)
REVERT: L   11 MET cc_start: 0.8417 (tpt) cc_final: 0.7785 (tpt)
REVERT: M    6 MET cc_start: 0.5890 (mtt) cc_final: 0.5559 (mtt)
REVERT: Q   41 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7882 (ttm-80)
REVERT: S    6 MET cc_start: 0.6042 (mmt) cc_final: 0.5521 (mmt)
REVERT: X    2 ASN cc_start: 0.6261 (t0) cc_final: 0.5786 (p0)
REVERT: Y   18 VAL cc_start: 0.8044 (t) cc_final: 0.7764 (t)
REVERT: a  116 ASN cc_start: 0.8684 (m-40) cc_final: 0.8123 (m110)
  outliers start: 13
  outliers final: 7
  residues processed: 148
  average time/residue: 0.2570
  time to fit residues: 54.0377
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  : 1.213 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 245 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.124019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.105506 restraints weight = 10191.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 0.97
r_work: 0.3020 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8577  Z= 0.308
  Angle     :  0.670   8.162  11626  Z= 0.338
  Chirality :  0.043   0.299   1415
  Planarity :  0.005   0.047   1434
  Dihedral  :  4.611  42.978   1176
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  9.56 %
    Favored  : 88.19 %
  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:  2.63 (0.24), residues: 1107
  helix:  2.03 (0.15), residues: 978
  sheet:  None (None), residues: 0
  loop : -0.41 (0.56), residues: 129

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   0.015   0.002   PHE a  85 
 TYR   0.023   0.002   TYR M  10 
 ARG   0.006   0.001   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
  151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.873 
Fit side-chains
REVERT: J   11 MET cc_start: 0.8094 (tpp) cc_final: 0.7773 (tpt)
REVERT: L   11 MET cc_start: 0.8417 (tpt) cc_final: 0.7750 (tpt)
REVERT: M    6 MET cc_start: 0.5826 (mtt) cc_final: 0.5541 (mtt)
REVERT: O   42 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7138 (mm110)
REVERT: Q   41 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7829 (ttm-80)
REVERT: R   57 MET cc_start: 0.8467 (ttp) cc_final: 0.7961 (ttt)
REVERT: X    2 ASN cc_start: 0.6760 (t0) cc_final: 0.6301 (p0)
REVERT: X   23 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7652 (mttt)
REVERT: X   24 TYR cc_start: 0.8268 (m-10) cc_final: 0.7968 (m-10)
REVERT: Y   18 VAL cc_start: 0.7971 (t) cc_final: 0.7728 (t)
REVERT: a   46 MET cc_start: 0.7367 (mmm) cc_final: 0.6974 (mtp)
  outliers start: 19
  outliers final: 11
  residues processed: 144
  average time/residue: 0.1962
  time to fit residues: 39.4900
Evaluate side-chains
  140 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   21 LEU
Chi-restraints excluded: chain a residue   71 VAL
Chi-restraints excluded: chain a residue   93 MET
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0980
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 48 optimal weight:    0.1980
   chunk 92 optimal weight:    4.9990
   chunk 26 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
a  20 GLN

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 = 0.129744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.109915 restraints weight = 10006.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.07
r_work: 0.3087 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8577  Z= 0.221
  Angle     :  0.611   8.312  11626  Z= 0.306
  Chirality :  0.040   0.271   1415
  Planarity :  0.005   0.048   1434
  Dihedral  :  4.457  47.294   1176
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 10.27 %
    Favored  : 87.01 %
  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:  3.09 (0.24), residues: 1107
  helix:  2.42 (0.15), residues: 958
  sheet:  None (None), residues: 0
  loop : -0.56 (0.48), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP a 231 
 HIS   0.016   0.002   HIS a 245 
 PHE   0.016   0.001   PHE a 244 
 TYR   0.021   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
  158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
REVERT: J   11 MET cc_start: 0.8047 (tpp) cc_final: 0.7762 (tpt)
REVERT: J   57 MET cc_start: 0.8464 (tmm) cc_final: 0.8093 (ttp)
REVERT: L   11 MET cc_start: 0.8391 (tpt) cc_final: 0.7711 (tpt)
REVERT: M    6 MET cc_start: 0.5863 (mtt) cc_final: 0.5590 (mtt)
REVERT: O   57 MET cc_start: 0.8786 (tmm) cc_final: 0.8497 (ttp)
REVERT: R   17 MET cc_start: 0.8462 (mmm) cc_final: 0.7924 (mmm)
REVERT: R   57 MET cc_start: 0.8567 (ttp) cc_final: 0.8135 (ttt)
REVERT: X    1 MET cc_start: 0.5585 (mtt) cc_final: 0.4865 (ttm)
REVERT: X   24 TYR cc_start: 0.8301 (m-10) cc_final: 0.7944 (m-10)
REVERT: Y   18 VAL cc_start: 0.7980 (t) cc_final: 0.7711 (t)
REVERT: a   46 MET cc_start: 0.7273 (mmm) cc_final: 0.6897 (mtp)
REVERT: a  116 ASN cc_start: 0.8655 (m-40) cc_final: 0.8179 (m110)
REVERT: a  246 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8062 (mt)
  outliers start: 23
  outliers final: 9
  residues processed: 149
  average time/residue: 0.1807
  time to fit residues: 38.4212
Evaluate side-chains
  141 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
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   93 MET
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 83 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3419 r_free = 0.3419 target = 0.129155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.109676 restraints weight = 10047.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.06
r_work: 0.3075 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8577  Z= 0.261
  Angle     :  0.622   8.169  11626  Z= 0.310
  Chirality :  0.041   0.332   1415
  Planarity :  0.005   0.049   1434
  Dihedral  :  4.409  51.899   1176
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 11.10 %
    Favored  : 86.78 %
  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:  3.19 (0.23), residues: 1107
  helix:  2.50 (0.15), residues: 957
  sheet:  None (None), residues: 0
  loop : -0.58 (0.47), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP a 231 
 HIS   0.002   0.001   HIS a  95 
 PHE   0.013   0.001   PHE a  85 
 TYR   0.020   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
  151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
REVERT: I   57 MET cc_start: 0.8137 (tmm) cc_final: 0.7904 (ttp)
REVERT: J   11 MET cc_start: 0.8052 (tpp) cc_final: 0.7754 (tpt)
REVERT: O   42 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7285 (mm110)
REVERT: O   57 MET cc_start: 0.8789 (tmm) cc_final: 0.8503 (ttp)
REVERT: P    6 MET cc_start: 0.4724 (ptt) cc_final: 0.4301 (mtp)
REVERT: R   17 MET cc_start: 0.8540 (mmm) cc_final: 0.8027 (mmm)
REVERT: R   57 MET cc_start: 0.8639 (ttp) cc_final: 0.8133 (ttt)
REVERT: X    1 MET cc_start: 0.5631 (mtt) cc_final: 0.5028 (ttm)
REVERT: X   24 TYR cc_start: 0.8209 (m-10) cc_final: 0.7748 (m-10)
REVERT: Y   18 VAL cc_start: 0.8034 (t) cc_final: 0.7748 (t)
REVERT: a   46 MET cc_start: 0.7250 (mmm) cc_final: 0.6910 (mtp)
REVERT: a  116 ASN cc_start: 0.8678 (m-40) cc_final: 0.8215 (m110)
  outliers start: 18
  outliers final: 10
  residues processed: 142
  average time/residue: 0.1947
  time to fit residues: 39.4258
Evaluate side-chains
  142 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
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  245 HIS
Chi-restraints excluded: chain a residue  246 ILE
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:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.127007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.107121 restraints weight = 10027.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.07
r_work: 0.3056 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8577  Z= 0.321
  Angle     :  0.656   8.661  11626  Z= 0.325
  Chirality :  0.042   0.336   1415
  Planarity :  0.005   0.049   1434
  Dihedral  :  4.441  51.611   1176
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.69 %
    Favored  : 85.95 %
  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:  3.03 (0.23), residues: 1107
  helix:  2.35 (0.15), residues: 962
  sheet:  None (None), residues: 0
  loop : -0.43 (0.48), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP a 241 
 HIS   0.003   0.001   HIS a  15 
 PHE   0.015   0.001   PHE a  85 
 TYR   0.015   0.001   TYR a  11 
 ARG   0.008   0.000   ARG I  41 

*********************** 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
  156 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: I   57 MET cc_start: 0.8175 (tmm) cc_final: 0.7930 (ttp)
REVERT: J   11 MET cc_start: 0.8215 (tpp) cc_final: 0.7901 (tpt)
REVERT: J   41 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.6848 (ttm-80)
REVERT: L   11 MET cc_start: 0.8359 (tpt) cc_final: 0.7639 (tpt)
REVERT: N   16 MET cc_start: 0.8276 (ttm) cc_final: 0.8034 (ttp)
REVERT: O   42 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7253 (mm-40)
REVERT: O   57 MET cc_start: 0.8731 (tmm) cc_final: 0.8460 (ttp)
REVERT: P    6 MET cc_start: 0.4813 (ptt) cc_final: 0.4336 (mtp)
REVERT: R   57 MET cc_start: 0.8453 (ttp) cc_final: 0.8124 (ttp)
REVERT: R   75 MET cc_start: 0.8857 (ttm) cc_final: 0.8647 (mtp)
REVERT: X    1 MET cc_start: 0.5174 (mtt) cc_final: 0.4689 (ttm)
REVERT: X   24 TYR cc_start: 0.8208 (m-10) cc_final: 0.7850 (m-10)
REVERT: Y   18 VAL cc_start: 0.8083 (t) cc_final: 0.7823 (t)
REVERT: a    6 MET cc_start: 0.6955 (mmp) cc_final: 0.6666 (mmt)
REVERT: a   46 MET cc_start: 0.7333 (mmm) cc_final: 0.6957 (mtp)
REVERT: a  116 ASN cc_start: 0.8679 (m-40) cc_final: 0.8222 (m110)
REVERT: a  119 ASP cc_start: 0.8331 (t0) cc_final: 0.8030 (t0)
  outliers start: 20
  outliers final: 15
  residues processed: 149
  average time/residue: 0.1980
  time to fit residues: 41.1304
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  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
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 P residue   44 ASP
Chi-restraints excluded: chain Q residue   37 GLU
Chi-restraints excluded: chain a residue   15 HIS
Chi-restraints excluded: chain a residue   56 PHE
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  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:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 98 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 102 optimal weight:    0.1980
   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
a 245 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.129224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.109683 restraints weight = 10206.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.08
r_work: 0.3084 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8577  Z= 0.230
  Angle     :  0.610   8.476  11626  Z= 0.303
  Chirality :  0.040   0.320   1415
  Planarity :  0.005   0.048   1434
  Dihedral  :  4.361  52.322   1176
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.40 %
    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:  3.25 (0.23), residues: 1107
  helix:  2.55 (0.15), residues: 958
  sheet:  None (None), residues: 0
  loop : -0.67 (0.47), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP a 231 
 HIS   0.015   0.002   HIS a  15 
 PHE   0.011   0.001   PHE a  85 
 TYR   0.012   0.001   TYR M  10 
 ARG   0.008   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
  153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: I    6 MET cc_start: 0.4887 (mtm) cc_final: 0.3873 (ppp)
REVERT: I   57 MET cc_start: 0.8133 (tmm) cc_final: 0.7882 (ttp)
REVERT: J   11 MET cc_start: 0.8125 (tpp) cc_final: 0.7849 (tpt)
REVERT: J   41 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.6835 (ttm-80)
REVERT: N   16 MET cc_start: 0.8243 (ttp) cc_final: 0.7954 (ttp)
REVERT: O   42 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7169 (mm-40)
REVERT: O   57 MET cc_start: 0.8755 (tmm) cc_final: 0.8476 (ttp)
REVERT: P    6 MET cc_start: 0.4836 (ptt) cc_final: 0.4362 (mtp)
REVERT: R   17 MET cc_start: 0.8476 (mmm) cc_final: 0.7929 (mmm)
REVERT: R   57 MET cc_start: 0.8474 (ttp) cc_final: 0.8188 (ttt)
REVERT: X    1 MET cc_start: 0.5695 (mtt) cc_final: 0.5147 (ttm)
REVERT: X   24 TYR cc_start: 0.8223 (m-10) cc_final: 0.7814 (m-10)
REVERT: Y   18 VAL cc_start: 0.8074 (t) cc_final: 0.7795 (t)
REVERT: a    6 MET cc_start: 0.6970 (mmp) cc_final: 0.6735 (mmt)
REVERT: a   40 THR cc_start: 0.7124 (OUTLIER) cc_final: 0.6835 (p)
REVERT: a   46 MET cc_start: 0.7256 (mmm) cc_final: 0.6894 (mtp)
REVERT: a  116 ASN cc_start: 0.8657 (m-40) cc_final: 0.8198 (m110)
REVERT: a  119 ASP cc_start: 0.8295 (t0) cc_final: 0.8065 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 147
  average time/residue: 0.1899
  time to fit residues: 39.2060
Evaluate side-chains
  149 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
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 P residue   44 ASP
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  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  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:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 67 optimal weight:    0.1980
   chunk 103 optimal weight:    0.6980
   chunk 81 optimal weight:    0.3980
   chunk 61 optimal weight:    0.4980
   chunk 73 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0020
   chunk 95 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.3388

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.130403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.110722 restraints weight = 10168.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.09
r_work: 0.3095 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8577  Z= 0.197
  Angle     :  0.593   8.122  11626  Z= 0.293
  Chirality :  0.039   0.314   1415
  Planarity :  0.005   0.048   1434
  Dihedral  :  4.313  53.269   1176
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.28 %
    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:  3.46 (0.24), residues: 1107
  helix:  2.71 (0.15), residues: 958
  sheet:  None (None), residues: 0
  loop : -0.74 (0.47), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP a 231 
 HIS   0.011   0.002   HIS a 245 
 PHE   0.010   0.001   PHE a  85 
 TYR   0.018   0.001   TYR M  10 
 ARG   0.008   0.000   ARG I  41 

*********************** 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
  155 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: I    6 MET cc_start: 0.4914 (mtm) cc_final: 0.3899 (ppp)
REVERT: I   57 MET cc_start: 0.8106 (tmm) cc_final: 0.7848 (ttp)
REVERT: J   11 MET cc_start: 0.8132 (tpp) cc_final: 0.7864 (tpt)
REVERT: O   57 MET cc_start: 0.8725 (tmm) cc_final: 0.8451 (ttp)
REVERT: P    6 MET cc_start: 0.4800 (ptt) cc_final: 0.4255 (mtp)
REVERT: R   57 MET cc_start: 0.8395 (ttp) cc_final: 0.8121 (ttt)
REVERT: X    1 MET cc_start: 0.5654 (mtt) cc_final: 0.5170 (ttm)
REVERT: X   24 TYR cc_start: 0.8176 (m-10) cc_final: 0.7731 (m-10)
REVERT: Y   18 VAL cc_start: 0.8035 (t) cc_final: 0.7762 (t)
REVERT: a   40 THR cc_start: 0.7026 (OUTLIER) cc_final: 0.6729 (p)
REVERT: a   46 MET cc_start: 0.7205 (mmm) cc_final: 0.6872 (mtp)
REVERT: a  116 ASN cc_start: 0.8646 (m-40) cc_final: 0.8162 (m110)
REVERT: a  246 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7979 (mt)
  outliers start: 18
  outliers final: 12
  residues processed: 149
  average time/residue: 0.1929
  time to fit residues: 40.9743
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  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
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:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 11 optimal weight:    0.3980
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.129383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.110694 restraints weight = 10320.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.03
r_work: 0.3097 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8577  Z= 0.252
  Angle     :  0.620   8.219  11626  Z= 0.307
  Chirality :  0.040   0.310   1415
  Planarity :  0.005   0.049   1434
  Dihedral  :  4.320  53.480   1176
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.34 %
    Favored  : 84.77 %
  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 (0.23), residues: 1107
  helix:  2.62 (0.15), residues: 958
  sheet:  None (None), residues: 0
  loop : -0.77 (0.46), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP a 241 
 HIS   0.012   0.002   HIS a  15 
 PHE   0.012   0.001   PHE a  85 
 TYR   0.015   0.001   TYR M  10 
 ARG   0.009   0.000   ARG I  41 

*********************** 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
  149 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: I    6 MET cc_start: 0.4913 (mtm) cc_final: 0.3931 (ppp)
REVERT: I   57 MET cc_start: 0.8119 (tmm) cc_final: 0.7864 (ttp)
REVERT: J   11 MET cc_start: 0.8207 (tpp) cc_final: 0.7930 (tpt)
REVERT: O   42 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7083 (mm-40)
REVERT: O   57 MET cc_start: 0.8716 (tmm) cc_final: 0.8440 (ttp)
REVERT: P    6 MET cc_start: 0.4791 (ptt) cc_final: 0.4271 (mtp)
REVERT: R   57 MET cc_start: 0.8402 (ttp) cc_final: 0.8136 (ttt)
REVERT: X    1 MET cc_start: 0.5656 (mtt) cc_final: 0.5106 (ttm)
REVERT: X   24 TYR cc_start: 0.8184 (m-10) cc_final: 0.7741 (m-10)
REVERT: Y   18 VAL cc_start: 0.8068 (t) cc_final: 0.7791 (t)
REVERT: a    6 MET cc_start: 0.7137 (mmt) cc_final: 0.6364 (tpt)
REVERT: a   14 HIS cc_start: 0.8065 (m90) cc_final: 0.7771 (t-90)
REVERT: a   40 THR cc_start: 0.7017 (OUTLIER) cc_final: 0.6729 (p)
REVERT: a   46 MET cc_start: 0.7213 (mmm) cc_final: 0.6870 (mtp)
REVERT: a  116 ASN cc_start: 0.8676 (m-40) cc_final: 0.8182 (m110)
  outliers start: 16
  outliers final: 13
  residues processed: 143
  average time/residue: 0.1952
  time to fit residues: 39.2936
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  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
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:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 99 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3408 r_free = 0.3408 target = 0.127814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.107733 restraints weight = 10200.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.14
r_work: 0.3053 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8577  Z= 0.315
  Angle     :  0.652   8.617  11626  Z= 0.321
  Chirality :  0.041   0.313   1415
  Planarity :  0.005   0.050   1434
  Dihedral  :  4.360  51.783   1176
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.70 %
    Favored  : 84.53 %
  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:  3.13 (0.23), residues: 1107
  helix:  2.47 (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   0.007   0.001   TRP a 241 
 HIS   0.012   0.002   HIS a  15 
 PHE   0.014   0.001   PHE a  85 
 TYR   0.014   0.001   TYR a  11 
 ARG   0.010   0.000   ARG I  41 

********************** 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: 15
    poor density    : 135
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: I    6 MET cc_start: 0.5163 (mtm) cc_final: 0.4142 (ppp)
REVERT: I   57 MET cc_start: 0.8155 (tmm) cc_final: 0.7914 (ttp)
REVERT: J   11 MET cc_start: 0.8259 (tpp) cc_final: 0.7970 (tpt)
REVERT: J   41 ARG cc_start: 0.7323 (ttt-90) cc_final: 0.6961 (ttm-80)
REVERT: J   57 MET cc_start: 0.8492 (tmm) cc_final: 0.8060 (ttp)
REVERT: O   42 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7210 (mm-40)
REVERT: O   57 MET cc_start: 0.8742 (tmm) cc_final: 0.8476 (ttp)
REVERT: P    6 MET cc_start: 0.4926 (ptt) cc_final: 0.4319 (mtp)
REVERT: R   17 MET cc_start: 0.8411 (mmm) cc_final: 0.8050 (mtp)
REVERT: R   57 MET cc_start: 0.8474 (ttp) cc_final: 0.8202 (ttt)
REVERT: X    1 MET cc_start: 0.5168 (mtt) cc_final: 0.4744 (ttm)
REVERT: X   24 TYR cc_start: 0.8280 (m-10) cc_final: 0.7888 (m-10)
REVERT: Y   18 VAL cc_start: 0.8111 (t) cc_final: 0.7845 (t)
REVERT: a    6 MET cc_start: 0.7178 (mmt) cc_final: 0.6277 (tpt)
REVERT: a   14 HIS cc_start: 0.8086 (m90) cc_final: 0.7748 (t-90)
REVERT: a   40 THR cc_start: 0.7094 (OUTLIER) cc_final: 0.6793 (p)
REVERT: a   46 MET cc_start: 0.7313 (mmm) cc_final: 0.6935 (mtp)
REVERT: a  116 ASN cc_start: 0.8696 (m-40) cc_final: 0.8229 (m110)
  outliers start: 15
  outliers final: 14
  residues processed: 146
  average time/residue: 0.1938
  time to fit residues: 39.5503
Evaluate side-chains
  149 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LEU
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:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 104 optimal weight:    0.7980
   chunk 99 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3419 r_free = 0.3419 target = 0.128567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.108398 restraints weight = 10367.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.16
r_work: 0.3065 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
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   0.033   8577  Z= 0.276
  Angle     :  0.639   8.776  11626  Z= 0.315
  Chirality :  0.041   0.315   1415
  Planarity :  0.005   0.050   1434
  Dihedral  :  4.349  51.675   1176
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  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:  3.17 (0.23), residues: 1107
  helix:  2.50 (0.15), residues: 959
  sheet:  None (None), residues: 0
  loop : -0.77 (0.46), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP a 241 
 HIS   0.010   0.002   HIS a  15 
 PHE   0.013   0.001   PHE a  85 
 TYR   0.020   0.001   TYR M  10 
 ARG   0.009   0.000   ARG I  41 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4204.47 seconds
wall clock time: 73 minutes 28.10 seconds (4408.10 seconds total)