Starting phenix.real_space_refine
on Wed Mar 12 04:40:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t04_40934/03_2025/8t04_40934.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t04_40934/03_2025/8t04_40934.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t04_40934/03_2025/8t04_40934.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t04_40934/03_2025/8t04_40934.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t04_40934/03_2025/8t04_40934.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t04_40934/03_2025/8t04_40934.cif"
  }
  resolution = 2.98
  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=   0.003 sd=   0.088
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       2      5.49       5
     S      44      5.16       5
     C    4492      2.51       5
     N    1092      2.21       5
     O    1242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6874
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1593
          Classifications: {'peptide': 199}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190}
    Chain: "B"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1593
          Classifications: {'peptide': 199}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190}
    Chain: "C"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 936
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "D"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "E"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 936
          Classifications: {'peptide': 120}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "F"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 76
          Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "B"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 76
          Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
  Time building chain proxies: 4.34, per 1000 atoms: 0.63
  Number of scatterers: 6874
  At special positions: 0
  Unit cell: (72.21, 108.73, 103.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      44     16.00
     P       2     15.00
     O    1242      8.00
     N    1092      7.00
     C    4492      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  59 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  59 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  97 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.55
  Conformation dependent library (CDL) restraints added in 837.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 301 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 180 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 184 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A  48 "
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 184 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 180 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B  48 "


  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 12 sheets defined
      43.1% alpha, 27.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 14
      removed outlier: 3.745A  pdb=" N   LEU A   9 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      Proline residue:  A  11  - end of helix
    Processing helix  chain 'A' and resid 17 through 28
      removed outlier: 4.144A  pdb=" N   THR A  21 " --> pdb=" O   ALA A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 52
    Processing helix  chain 'A' and resid 55 through 59
    Processing helix  chain 'A' and resid 62 through 87
    Processing helix  chain 'A' and resid 91 through 111
    Processing helix  chain 'A' and resid 118 through 141
    Processing helix  chain 'A' and resid 146 through 153
    Processing helix  chain 'A' and resid 153 through 170
    Processing helix  chain 'A' and resid 171 through 174
    Processing helix  chain 'A' and resid 175 through 195
      removed outlier: 3.898A  pdb=" N   SER A 181 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   CYS A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 14
      Proline residue:  B  11  - end of helix
    Processing helix  chain 'B' and resid 17 through 28
      removed outlier: 4.142A  pdb=" N   THR B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 52
    Processing helix  chain 'B' and resid 55 through 59
    Processing helix  chain 'B' and resid 62 through 87
    Processing helix  chain 'B' and resid 91 through 111
      removed outlier: 3.501A  pdb=" N   THR B  95 " --> pdb=" O   PRO B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 141
    Processing helix  chain 'B' and resid 146 through 153
    Processing helix  chain 'B' and resid 153 through 170
    Processing helix  chain 'B' and resid 171 through 174
    Processing helix  chain 'B' and resid 175 through 195
      removed outlier: 3.899A  pdb=" N   SER B 181 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   CYS B 185 " --> pdb=" O   SER B 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 67
      No H-bonds generated for 'chain 'C' and resid 65 through 67'
    Processing helix  chain 'C' and resid 88 through 91
    Processing helix  chain 'D' and resid 79 through 83
    Processing helix  chain 'E' and resid 65 through 67
      No H-bonds generated for 'chain 'E' and resid 65 through 67'
    Processing helix  chain 'E' and resid 88 through 91
    Processing helix  chain 'F' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12
      removed outlier: 7.054A  pdb=" N   VAL C  36 " --> pdb=" O   HIS C  52 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   HIS C  52 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   TRP C  38 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.816A  pdb=" N   TYR C 109 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6
    Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.426A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ILE D  33 " --> pdb=" O   HIS D  49 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   HIS D  49 " --> pdb=" O   ILE D  33 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.426A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12
      removed outlier: 7.050A  pdb=" N   VAL E  36 " --> pdb=" O   HIS E  52 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   HIS E  52 " --> pdb=" O   VAL E  36 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   TRP E  38 " --> pdb=" O   LEU E  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.813A  pdb=" N   TYR E 109 " --> pdb=" O   ARG E  99 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13
      removed outlier: 6.423A  pdb=" N   LEU F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE F  33 " --> pdb=" O   HIS F  49 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   HIS F  49 " --> pdb=" O   ILE F  33 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13
      removed outlier: 6.423A  pdb=" N   LEU F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)

    393 hydrogen bonds defined for protein.
    1047 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: 1.93

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1024
        1.31 -     1.44: 2033
        1.44 -     1.56: 3921
        1.56 -     1.69: 8
        1.69 -     1.82: 72
  Bond restraints: 7058
  Sorted by residual:
  bond pdb=" C   ARG B  93 "
       pdb=" N   SER B  94 "
    ideal  model  delta    sigma   weight residual
    1.335  1.446 -0.111 1.31e-02 5.83e+03 7.19e+01
  bond pdb=" C25 LBN B 303 "
       pdb=" O5  LBN B 303 "
    ideal  model  delta    sigma   weight residual
    1.326  1.433 -0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" C25 LBN A 303 "
       pdb=" O5  LBN A 303 "
    ideal  model  delta    sigma   weight residual
    1.326  1.432 -0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" C34 LBN A 303 "
       pdb=" O7  LBN A 303 "
    ideal  model  delta    sigma   weight residual
    1.331  1.423 -0.092 2.00e-02 2.50e+03 2.12e+01
  bond pdb=" C34 LBN B 303 "
       pdb=" O7  LBN B 303 "
    ideal  model  delta    sigma   weight residual
    1.331  1.422 -0.091 2.00e-02 2.50e+03 2.08e+01
  ... (remaining 7053 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.36: 8955
        3.36 -     6.73: 584
        6.73 -    10.09: 22
       10.09 -    13.45: 1
       13.45 -    16.82: 2
  Bond angle restraints: 9564
  Sorted by residual:
  angle pdb=" O   ARG A  93 "
        pdb=" C   ARG A  93 "
        pdb=" N   SER A  94 "
      ideal   model   delta    sigma   weight residual
     122.09  129.02   -6.93 1.04e+00 9.25e-01 4.45e+01
  angle pdb=" O1  LBN A 303 "
        pdb=" P1  LBN A 303 "
        pdb=" O2  LBN A 303 "
      ideal   model   delta    sigma   weight residual
      93.45  110.27  -16.82 3.00e+00 1.11e-01 3.14e+01
  angle pdb=" O1  LBN B 303 "
        pdb=" P1  LBN B 303 "
        pdb=" O2  LBN B 303 "
      ideal   model   delta    sigma   weight residual
      93.45  110.19  -16.74 3.00e+00 1.11e-01 3.12e+01
  angle pdb=" N   GLU B  90 "
        pdb=" CA  GLU B  90 "
        pdb=" C   GLU B  90 "
      ideal   model   delta    sigma   weight residual
     110.07  103.09    6.98 1.26e+00 6.30e-01 3.07e+01
  angle pdb=" N   GLU A  90 "
        pdb=" CA  GLU A  90 "
        pdb=" C   GLU A  90 "
      ideal   model   delta    sigma   weight residual
     110.07  103.11    6.96 1.26e+00 6.30e-01 3.06e+01
  ... (remaining 9559 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.41: 4126
       34.41 -    68.82: 103
       68.82 -   103.23: 17
      103.23 -   137.64: 2
      137.64 -   172.05: 2
  Dihedral angle restraints: 4250
    sinusoidal: 1788
      harmonic: 2462
  Sorted by residual:
  dihedral pdb=" CA  HIS F  49 "
           pdb=" C   HIS F  49 "
           pdb=" N   TYR F  50 "
           pdb=" CA  TYR F  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.96  -29.04     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  HIS D  49 "
           pdb=" C   HIS D  49 "
           pdb=" N   TYR D  50 "
           pdb=" CA  TYR D  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.08  -28.92     0      5.00e+00 4.00e-02 3.34e+01
  dihedral pdb=" CA  GLU A  90 "
           pdb=" C   GLU A  90 "
           pdb=" N   PRO A  91 "
           pdb=" CA  PRO A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   26.21  -26.21     0      5.00e+00 4.00e-02 2.75e+01
  ... (remaining 4247 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.983: 1052
       0.983 -    1.966: 0
       1.966 -    2.949: 0
       2.949 -    3.932: 0
       3.932 -    4.915: 2
  Chirality restraints: 1054
  Sorted by residual:
  chirality pdb=" C2  LBN B 303 "
            pdb=" C1  LBN B 303 "
            pdb=" C3  LBN B 303 "
            pdb=" O7  LBN B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.55   -4.91 2.00e-01 2.50e+01 6.04e+02
  chirality pdb=" C2  LBN A 303 "
            pdb=" C1  LBN A 303 "
            pdb=" C3  LBN A 303 "
            pdb=" O7  LBN A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.55   -4.91 2.00e-01 2.50e+01 6.03e+02
  chirality pdb=" CA  ILE D  21 "
            pdb=" N   ILE D  21 "
            pdb=" C   ILE D  21 "
            pdb=" CB  ILE D  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 1051 not shown)

  Planarity restraints: 1156
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 110 "    0.021 2.00e-02 2.50e+03   1.19e-02 3.55e+00
        pdb=" CG  TRP C 110 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 110 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 110 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 110 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 110 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 110 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 110 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 110 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 110 "   -0.021 2.00e-02 2.50e+03   1.18e-02 3.46e+00
        pdb=" CG  TRP E 110 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 110 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 110 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 110 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 110 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 110 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 110 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 110 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  93 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.74e+00
        pdb=" C   ARG B  93 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ARG B  93 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER B  94 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1153 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1240
        2.84 -     3.35: 6694
        3.35 -     3.87: 10820
        3.87 -     4.38: 14301
        4.38 -     4.90: 23575
  Nonbonded interactions: 56630
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG D  61 "
            pdb=" OD2 ASP D  82 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NH1 ARG F  61 "
            pdb=" OD2 ASP F  82 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NH2 ARG D  61 "
            pdb=" OE2 GLU D  81 "
     model   vdw
     2.479 3.120
  nonbonded pdb=" NH2 ARG F  61 "
            pdb=" OE2 GLU F  81 "
     model   vdw
     2.479 3.120
  nonbonded pdb=" N   GLY B 116 "
            pdb=" O4  LBN B 303 "
     model   vdw
     2.483 3.120
  ... (remaining 56625 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.100
  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:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.710
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:10.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6556
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      :  0.014   0.111   7058  Z= 0.933
  Angle     :  1.828  16.817   9564  Z= 1.300
  Chirality :  0.230   4.915   1054
  Planarity :  0.004   0.027   1156
  Dihedral  : 16.387 172.049   2666
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.81 %
    Favored  : 92.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.29), residues: 840
  helix: -1.11 (0.26), residues: 278
  sheet:  0.01 (0.40), residues: 166
  loop : -0.57 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP C 110 
 HIS   0.007   0.002   HIS C  52 
 PHE   0.021   0.002   PHE B  69 
 TYR   0.028   0.003   TYR D  91 
 ARG   0.006   0.001   ARG A  62 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.6311 (mt) cc_final: 0.6099 (mp)
REVERT: A   29 ARG cc_start: 0.6564 (mmm160) cc_final: 0.6358 (mtp180)
REVERT: A   61 MET cc_start: 0.6262 (mtm) cc_final: 0.6026 (mtp)
REVERT: A   87 ASP cc_start: 0.6284 (t70) cc_final: 0.6065 (t70)
REVERT: A   94 SER cc_start: 0.6510 (m) cc_final: 0.6075 (p)
REVERT: A  137 MET cc_start: 0.5787 (mtm) cc_final: 0.5572 (mtm)
REVERT: A  170 PHE cc_start: 0.6461 (t80) cc_final: 0.6152 (t80)
REVERT: B    9 LEU cc_start: 0.7564 (mt) cc_final: 0.7242 (mp)
REVERT: B   83 MET cc_start: 0.8086 (mmp) cc_final: 0.7550 (mmp)
REVERT: B  137 MET cc_start: 0.7561 (mtm) cc_final: 0.7157 (mtm)
REVERT: B  170 PHE cc_start: 0.7342 (t80) cc_final: 0.7119 (t80)
REVERT: B  189 MET cc_start: 0.7518 (tpt) cc_final: 0.7299 (mmm)
REVERT: C   61 TYR cc_start: 0.7574 (m-80) cc_final: 0.7330 (m-80)
REVERT: C   83 MET cc_start: 0.5581 (mmt) cc_final: 0.5237 (mmt)
REVERT: C  112 GLN cc_start: 0.7255 (mt0) cc_final: 0.6928 (mm110)
REVERT: D   63 SER cc_start: 0.6740 (m) cc_final: 0.6539 (p)
REVERT: E   83 MET cc_start: 0.6846 (mmt) cc_final: 0.6255 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 115
  average time/residue: 0.8730
  time to fit residues: 107.7282
Evaluate side-chains
  84 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.174925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.123969 restraints weight = 6983.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.35
r_work: 0.3295 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7058  Z= 0.246
  Angle     :  0.607   6.250   9564  Z= 0.318
  Chirality :  0.045   0.161   1054
  Planarity :  0.005   0.035   1156
  Dihedral  : 12.411 138.993   1136
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 11.17 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.30), residues: 840
  helix:  1.16 (0.28), residues: 288
  sheet:  0.05 (0.36), residues: 230
  loop : -0.10 (0.40), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 110 
 HIS   0.006   0.002   HIS E  52 
 PHE   0.021   0.002   PHE A  42 
 TYR   0.010   0.001   TYR D  91 
 ARG   0.002   0.000   ARG B  93 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7607 (ttmt) cc_final: 0.6704 (mptt)
REVERT: A   61 MET cc_start: 0.7767 (mtm) cc_final: 0.7563 (mtp)
REVERT: A  138 LYS cc_start: 0.6577 (mttt) cc_final: 0.6144 (mppt)
REVERT: B   27 LYS cc_start: 0.7614 (ttmt) cc_final: 0.6725 (mptt)
REVERT: B  138 LYS cc_start: 0.6595 (mttt) cc_final: 0.6127 (mppt)
REVERT: C   83 MET cc_start: 0.7289 (mmt) cc_final: 0.6748 (mmt)
REVERT: C  107 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8730 (pmm)
REVERT: D   63 SER cc_start: 0.8468 (m) cc_final: 0.8160 (p)
REVERT: D   65 SER cc_start: 0.8308 (m) cc_final: 0.8018 (p)
REVERT: E   83 MET cc_start: 0.7317 (mmt) cc_final: 0.6775 (mmt)
REVERT: F    4 MET cc_start: 0.7381 (mmm) cc_final: 0.6902 (mmm)
REVERT: F   65 SER cc_start: 0.8277 (m) cc_final: 0.8059 (p)
  outliers start: 23
  outliers final: 9
  residues processed: 117
  average time/residue: 1.1983
  time to fit residues: 147.7785
Evaluate side-chains
  101 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 13 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.177818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.127539 restraints weight = 7033.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.32
r_work: 0.3339 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7058  Z= 0.162
  Angle     :  0.518   6.093   9564  Z= 0.272
  Chirality :  0.042   0.145   1054
  Planarity :  0.004   0.035   1156
  Dihedral  : 11.066 134.250   1136
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.44 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.31), residues: 840
  helix:  1.80 (0.28), residues: 296
  sheet:  0.37 (0.37), residues: 230
  loop :  0.05 (0.40), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 110 
 HIS   0.005   0.001   HIS E  52 
 PHE   0.015   0.001   PHE A  39 
 TYR   0.008   0.001   TYR D  91 
 ARG   0.003   0.000   ARG A 168 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.7988 (mt) cc_final: 0.7735 (mp)
REVERT: A   27 LYS cc_start: 0.7608 (ttmt) cc_final: 0.6788 (mptt)
REVERT: A  138 LYS cc_start: 0.6757 (mttt) cc_final: 0.6328 (tppt)
REVERT: B   27 LYS cc_start: 0.7638 (ttmt) cc_final: 0.6809 (mptt)
REVERT: B  138 LYS cc_start: 0.6714 (mttt) cc_final: 0.6299 (tppt)
REVERT: C   83 MET cc_start: 0.7357 (mmt) cc_final: 0.7094 (mmm)
REVERT: D   61 ARG cc_start: 0.7142 (ptp-170) cc_final: 0.6936 (ptp-170)
REVERT: D   65 SER cc_start: 0.8079 (m) cc_final: 0.7793 (p)
REVERT: E   83 MET cc_start: 0.7344 (mmt) cc_final: 0.7066 (mmm)
REVERT: F   61 ARG cc_start: 0.7197 (ptp-170) cc_final: 0.6978 (ptp-170)
  outliers start: 17
  outliers final: 5
  residues processed: 112
  average time/residue: 1.1938
  time to fit residues: 141.7817
Evaluate side-chains
  99 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 46 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4043 r_free = 0.4043 target = 0.175646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.124511 restraints weight = 7111.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.38
r_work: 0.3308 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7058  Z= 0.183
  Angle     :  0.515   6.119   9564  Z= 0.268
  Chirality :  0.042   0.141   1054
  Planarity :  0.004   0.032   1156
  Dihedral  : 10.941 133.777   1136
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.90 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.31), residues: 840
  helix:  2.02 (0.28), residues: 296
  sheet:  0.55 (0.38), residues: 220
  loop : -0.16 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 110 
 HIS   0.004   0.001   HIS C  52 
 PHE   0.016   0.002   PHE A  39 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.003   0.000   ARG B 168 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 1.106 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7740 (ttmt) cc_final: 0.6818 (mptt)
REVERT: A   29 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7784 (mtp85)
REVERT: A  138 LYS cc_start: 0.6733 (mttt) cc_final: 0.6323 (tppt)
REVERT: A  200 LYS cc_start: 0.8138 (mttt) cc_final: 0.7926 (mttt)
REVERT: B   27 LYS cc_start: 0.7715 (ttmt) cc_final: 0.6813 (mptt)
REVERT: B   29 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7883 (mtp85)
REVERT: B  138 LYS cc_start: 0.6735 (mttt) cc_final: 0.6326 (tppt)
REVERT: C   83 MET cc_start: 0.7382 (mmt) cc_final: 0.7137 (mmm)
REVERT: D   61 ARG cc_start: 0.7273 (ptp-170) cc_final: 0.7049 (ptp-170)
REVERT: E   83 MET cc_start: 0.7376 (mmt) cc_final: 0.7127 (mmm)
REVERT: F   61 ARG cc_start: 0.7386 (ptp-170) cc_final: 0.7175 (ptp-170)
  outliers start: 18
  outliers final: 8
  residues processed: 105
  average time/residue: 1.1813
  time to fit residues: 131.4694
Evaluate side-chains
  97 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 20 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.4049 r_free = 0.4049 target = 0.175681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.125236 restraints weight = 6983.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.34
r_work: 0.3296 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7058  Z= 0.212
  Angle     :  0.528   6.131   9564  Z= 0.274
  Chirality :  0.042   0.141   1054
  Planarity :  0.004   0.032   1156
  Dihedral  : 10.626 137.603   1136
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.44 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.30), residues: 840
  helix:  2.04 (0.28), residues: 296
  sheet:  0.60 (0.37), residues: 220
  loop : -0.32 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 110 
 HIS   0.004   0.001   HIS F  49 
 PHE   0.023   0.002   PHE B  42 
 TYR   0.010   0.001   TYR D  91 
 ARG   0.002   0.000   ARG B 168 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7694 (ttmt) cc_final: 0.6780 (mptt)
REVERT: A  138 LYS cc_start: 0.6755 (mttt) cc_final: 0.6315 (tppt)
REVERT: A  200 LYS cc_start: 0.8153 (mttt) cc_final: 0.7914 (mtpt)
REVERT: B   27 LYS cc_start: 0.7661 (ttmt) cc_final: 0.6791 (mptt)
REVERT: B   29 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7889 (mtp85)
REVERT: B  138 LYS cc_start: 0.6737 (mttt) cc_final: 0.6327 (tppt)
REVERT: C   83 MET cc_start: 0.7458 (mmt) cc_final: 0.7145 (mmm)
REVERT: C  107 MET cc_start: 0.8986 (ptp) cc_final: 0.8763 (pmm)
REVERT: D   61 ARG cc_start: 0.7382 (ptp-170) cc_final: 0.7173 (ptp-170)
REVERT: E   83 MET cc_start: 0.7462 (mmt) cc_final: 0.7139 (mmm)
REVERT: F   61 ARG cc_start: 0.7404 (ptp-170) cc_final: 0.7200 (ptp-170)
  outliers start: 20
  outliers final: 17
  residues processed: 107
  average time/residue: 1.6444
  time to fit residues: 186.4534
Evaluate side-chains
  107 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   21 ILE
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0970
   chunk 10 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4058 r_free = 0.4058 target = 0.176700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.126455 restraints weight = 6995.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.33
r_work: 0.3311 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7058  Z= 0.183
  Angle     :  0.507   6.030   9564  Z= 0.264
  Chirality :  0.042   0.140   1054
  Planarity :  0.004   0.031   1156
  Dihedral  : 10.300 133.873   1136
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.85 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.30), residues: 840
  helix:  2.17 (0.28), residues: 296
  sheet:  0.64 (0.37), residues: 220
  loop : -0.36 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  55 
 HIS   0.004   0.001   HIS C  52 
 PHE   0.018   0.002   PHE A  42 
 TYR   0.009   0.001   TYR F  91 
 ARG   0.003   0.000   ARG A 168 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 1.767 
Fit side-chains
REVERT: A   29 ARG cc_start: 0.8102 (mtp180) cc_final: 0.7848 (mtp85)
REVERT: A  138 LYS cc_start: 0.6683 (mttt) cc_final: 0.6287 (tppt)
REVERT: B   27 LYS cc_start: 0.7660 (ttmt) cc_final: 0.6780 (mptt)
REVERT: B   29 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7877 (mtp85)
REVERT: B  138 LYS cc_start: 0.6681 (mttt) cc_final: 0.6284 (tppt)
REVERT: C   83 MET cc_start: 0.7459 (mmt) cc_final: 0.7146 (mmm)
REVERT: C  107 MET cc_start: 0.8988 (ptp) cc_final: 0.8751 (pmm)
REVERT: D    4 MET cc_start: 0.7513 (mmm) cc_final: 0.7272 (tpp)
REVERT: E   83 MET cc_start: 0.7462 (mmt) cc_final: 0.7136 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 111
  average time/residue: 1.3389
  time to fit residues: 158.0787
Evaluate side-chains
  109 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 50 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0770
   chunk 36 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.177099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.126529 restraints weight = 6970.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.35
r_work: 0.3333 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7058  Z= 0.158
  Angle     :  0.495   5.996   9564  Z= 0.258
  Chirality :  0.041   0.141   1054
  Planarity :  0.004   0.031   1156
  Dihedral  :  9.929 127.691   1136
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.80 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.30), residues: 840
  helix:  2.35 (0.28), residues: 296
  sheet:  0.70 (0.37), residues: 220
  loop : -0.38 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C  55 
 HIS   0.003   0.001   HIS C  52 
 PHE   0.015   0.001   PHE A  39 
 TYR   0.008   0.001   TYR F  91 
 ARG   0.002   0.000   ARG B 168 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7718 (mtpt) cc_final: 0.6724 (mptt)
REVERT: A   29 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7905 (mtp85)
REVERT: A  138 LYS cc_start: 0.6710 (mttt) cc_final: 0.6337 (tppt)
REVERT: B   27 LYS cc_start: 0.7638 (ttmt) cc_final: 0.6813 (mptt)
REVERT: B  138 LYS cc_start: 0.6725 (mttt) cc_final: 0.6348 (tppt)
REVERT: C   83 MET cc_start: 0.7455 (mmt) cc_final: 0.7128 (mmm)
REVERT: D   61 ARG cc_start: 0.7240 (ptp-170) cc_final: 0.7015 (ttp-170)
REVERT: E   83 MET cc_start: 0.7451 (mmt) cc_final: 0.7117 (mmm)
REVERT: F   61 ARG cc_start: 0.7244 (ptp-170) cc_final: 0.7000 (ttp-170)
  outliers start: 20
  outliers final: 12
  residues processed: 112
  average time/residue: 1.1274
  time to fit residues: 133.6117
Evaluate side-chains
  104 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 50 optimal weight:    0.4980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4018 r_free = 0.4018 target = 0.173272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.122810 restraints weight = 7078.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.38
r_work: 0.3298 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7058  Z= 0.207
  Angle     :  0.519   6.056   9564  Z= 0.270
  Chirality :  0.042   0.143   1054
  Planarity :  0.004   0.030   1156
  Dihedral  :  9.992 125.905   1136
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.89 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.30), residues: 840
  helix:  2.13 (0.28), residues: 308
  sheet:  0.74 (0.37), residues: 220
  loop : -0.45 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E  55 
 HIS   0.004   0.001   HIS D  49 
 PHE   0.021   0.002   PHE B  42 
 TYR   0.011   0.001   TYR D  91 
 ARG   0.002   0.000   ARG A 168 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7708 (mtpt) cc_final: 0.6721 (mptt)
REVERT: A   29 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7902 (mtp85)
REVERT: A  138 LYS cc_start: 0.6695 (mttt) cc_final: 0.6285 (tppt)
REVERT: B   29 ARG cc_start: 0.8139 (mtp180) cc_final: 0.7916 (mtp85)
REVERT: B  138 LYS cc_start: 0.6688 (mttt) cc_final: 0.6287 (tppt)
REVERT: C   66 LYS cc_start: 0.7629 (ttmm) cc_final: 0.6816 (ttmm)
REVERT: C   83 MET cc_start: 0.7474 (mmt) cc_final: 0.7168 (mmm)
REVERT: D   61 ARG cc_start: 0.7347 (ptp-170) cc_final: 0.7086 (ttp-170)
REVERT: E   66 LYS cc_start: 0.7626 (ttmm) cc_final: 0.6814 (ttmm)
REVERT: E   83 MET cc_start: 0.7485 (mmt) cc_final: 0.7173 (mmm)
REVERT: F   61 ARG cc_start: 0.7348 (ptp-170) cc_final: 0.7093 (ttp-170)
  outliers start: 20
  outliers final: 17
  residues processed: 112
  average time/residue: 1.6730
  time to fit residues: 199.9305
Evaluate side-chains
  109 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   12 SER
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   89 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 54 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0270
   chunk 2 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.175247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.124645 restraints weight = 7046.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.39
r_work: 0.3329 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7058  Z= 0.162
  Angle     :  0.498   5.967   9564  Z= 0.260
  Chirality :  0.041   0.140   1054
  Planarity :  0.004   0.031   1156
  Dihedral  :  9.771 123.370   1136
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.30 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.30), residues: 840
  helix:  2.26 (0.28), residues: 308
  sheet:  0.91 (0.37), residues: 220
  loop : -0.50 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP E  55 
 HIS   0.002   0.001   HIS D  49 
 PHE   0.017   0.001   PHE B 170 
 TYR   0.008   0.001   TYR D  91 
 ARG   0.002   0.000   ARG A 168 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 1.641 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7779 (mtpt) cc_final: 0.6750 (mptt)
REVERT: A   29 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7883 (mtp85)
REVERT: A  138 LYS cc_start: 0.6729 (mttt) cc_final: 0.6346 (tppt)
REVERT: B   23 SER cc_start: 0.7871 (p) cc_final: 0.7662 (m)
REVERT: B   27 LYS cc_start: 0.7734 (mtpt) cc_final: 0.6730 (mptt)
REVERT: B   29 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7865 (mtp85)
REVERT: B   83 MET cc_start: 0.8343 (mmp) cc_final: 0.7964 (mmp)
REVERT: B  138 LYS cc_start: 0.6718 (mttt) cc_final: 0.6341 (tppt)
REVERT: C   83 MET cc_start: 0.7505 (mmt) cc_final: 0.7191 (mmm)
REVERT: D   61 ARG cc_start: 0.7307 (ptp-170) cc_final: 0.7099 (ttp-170)
REVERT: E   83 MET cc_start: 0.7481 (mmt) cc_final: 0.7168 (mmm)
  outliers start: 20
  outliers final: 16
  residues processed: 112
  average time/residue: 1.5314
  time to fit residues: 180.3458
Evaluate side-chains
  106 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue    5 THR
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 11 optimal weight:    0.0970
   chunk 34 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0060
   chunk 52 optimal weight:    9.9990
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    0.4980
   chunk 80 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.4394

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.176623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.125758 restraints weight = 7094.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.42
r_work: 0.3346 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7058  Z= 0.145
  Angle     :  0.494   5.939   9564  Z= 0.257
  Chirality :  0.041   0.140   1054
  Planarity :  0.004   0.031   1156
  Dihedral  :  9.546 119.784   1136
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.98 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.30), residues: 840
  helix:  2.36 (0.28), residues: 308
  sheet:  1.02 (0.38), residues: 220
  loop : -0.50 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E  55 
 HIS   0.002   0.001   HIS C  52 
 PHE   0.023   0.002   PHE A  42 
 TYR   0.008   0.001   TYR F  71 
 ARG   0.002   0.000   ARG A 168 

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

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

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1680 Ramachandran restraints generated.
    840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.7771 (mtpt) cc_final: 0.6762 (mptt)
REVERT: A   29 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7893 (mtp85)
REVERT: A  138 LYS cc_start: 0.6722 (mttt) cc_final: 0.6344 (tppt)
REVERT: B   27 LYS cc_start: 0.7747 (mtpt) cc_final: 0.6695 (mptt)
REVERT: B   29 ARG cc_start: 0.8084 (mtp180) cc_final: 0.7857 (mtp85)
REVERT: B   83 MET cc_start: 0.8341 (mmp) cc_final: 0.7984 (mmp)
REVERT: B  138 LYS cc_start: 0.6713 (mttt) cc_final: 0.6348 (tppt)
REVERT: C   66 LYS cc_start: 0.7594 (ttmm) cc_final: 0.6856 (ttmm)
REVERT: C   83 MET cc_start: 0.7502 (mmt) cc_final: 0.7182 (mmm)
REVERT: E   83 MET cc_start: 0.7481 (mmt) cc_final: 0.7161 (mmm)
  outliers start: 16
  outliers final: 14
  residues processed: 113
  average time/residue: 1.0860
  time to fit residues: 129.9526
Evaluate side-chains
  114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   52 HIS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   52 SER
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain D residue   72 SER
Chi-restraints excluded: chain D residue   89 LEU
Chi-restraints excluded: chain E residue   52 HIS
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain F residue   52 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 10 optimal weight:    0.4980
   chunk 80 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.175100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.124389 restraints weight = 7053.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.41
r_work: 0.3331 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7058  Z= 0.175
  Angle     :  0.510   6.044   9564  Z= 0.265
  Chirality :  0.041   0.148   1054
  Planarity :  0.004   0.031   1156
  Dihedral  :  9.553 118.187   1136
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.26 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.30), residues: 840
  helix:  2.26 (0.28), residues: 308
  sheet:  1.08 (0.37), residues: 220
  loop : -0.55 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP E  55 
 HIS   0.003   0.001   HIS F  49 
 PHE   0.022   0.001   PHE B 170 
 TYR   0.009   0.001   TYR D  71 
 ARG   0.002   0.000   ARG A 168 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4881.52 seconds
wall clock time: 87 minutes 51.28 seconds (5271.28 seconds total)