Starting phenix.real_space_refine
on Fri May  9 15:45:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yl7_33903/05_2025/7yl7_33903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yl7_33903/05_2025/7yl7_33903.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/7yl7_33903/05_2025/7yl7_33903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yl7_33903/05_2025/7yl7_33903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yl7_33903/05_2025/7yl7_33903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yl7_33903/05_2025/7yl7_33903.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=   0.002
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      12      5.16       5
     C    1818      2.51       5
     N     558      2.21       5
     O     600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2988
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "F"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "A"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "B"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "K"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 225
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "C"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 225
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "G"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 225
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "L"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 225
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "D"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 225
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "H"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 225
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "J"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "E"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "I"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
  Time building chain proxies: 2.27, per 1000 atoms: 0.76
  Number of scatterers: 2988
  At special positions: 0
  Unit cell: (144.56, 84.24, 42.64, 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      12     16.00
     O     600      8.00
     N     558      7.00
     C    1818      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS F   2 " - pdb=" SG  CYS F   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A   2 " - pdb=" SG  CYS A   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   2 " - pdb=" SG  CYS B   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J   2 " - pdb=" SG  CYS J   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   2 " - pdb=" SG  CYS E   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I   2 " - pdb=" SG  CYS I   7 " 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: 0.82
  Conformation dependent library (CDL) restraints added in 328.1 milliseconds
  

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 32.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10
      removed outlier: 6.541A  pdb=" N   THR F   9 " --> pdb=" O   GLN A  10 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19
      removed outlier: 6.355A  pdb=" N   PHE F  15 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   HIS A  18 " --> pdb=" O   PHE F  15 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL F  17 " --> pdb=" O   HIS A  18 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 31 through 32
      removed outlier: 5.883A  pdb=" N   ASN F  31 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'K' and resid 9 through 22
      removed outlier: 6.230A  pdb=" N   THR C   9 " --> pdb=" O   GLN G  10 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   LEU G  12 " --> pdb=" O   THR C   9 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ARG C  11 " --> pdb=" O   LEU G  12 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   ASN G  14 " --> pdb=" O   ARG C  11 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   ALA C  13 " --> pdb=" O   ASN G  14 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   LEU G  16 " --> pdb=" O   ALA C  13 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE C  15 " --> pdb=" O   LEU G  16 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   HIS G  18 " --> pdb=" O   PHE C  15 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   VAL C  17 " --> pdb=" O   HIS G  18 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   SER G  20 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   SER C  19 " --> pdb=" O   SER G  20 " (cutoff:3.500A)
      removed outlier: 8.368A  pdb=" N   ASN G  22 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ASN C  21 " --> pdb=" O   ASN G  22 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'K' and resid 26 through 28
      removed outlier: 6.073A  pdb=" N   ILE K  26 " --> pdb=" O   LEU G  27 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 22
      removed outlier: 6.822A  pdb=" N   GLN L  10 " --> pdb=" O   ARG H  11 " (cutoff:3.500A)
      removed outlier: 8.277A  pdb=" N   ALA H  13 " --> pdb=" O   GLN L  10 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   LEU L  12 " --> pdb=" O   ALA H  13 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   PHE H  15 " --> pdb=" O   LEU L  12 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ASN L  14 " --> pdb=" O   PHE H  15 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   VAL H  17 " --> pdb=" O   ASN L  14 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LEU L  16 " --> pdb=" O   VAL H  17 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   SER H  19 " --> pdb=" O   LEU L  16 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   HIS L  18 " --> pdb=" O   SER H  19 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   ASN H  21 " --> pdb=" O   HIS L  18 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   SER L  20 " --> pdb=" O   ASN H  21 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   THR D   9 " --> pdb=" O   GLN H  10 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   LEU H  12 " --> pdb=" O   THR D   9 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ARG D  11 " --> pdb=" O   LEU H  12 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   ASN H  14 " --> pdb=" O   ARG D  11 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ALA D  13 " --> pdb=" O   ASN H  14 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   LEU H  16 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   PHE D  15 " --> pdb=" O   LEU H  16 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   HIS H  18 " --> pdb=" O   PHE D  15 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL D  17 " --> pdb=" O   HIS H  18 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   SER H  20 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   SER D  19 " --> pdb=" O   SER H  20 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   ASN H  22 " --> pdb=" O   SER D  19 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ASN D  21 " --> pdb=" O   ASN H  22 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 26 through 28
      removed outlier: 6.074A  pdb=" N   ILE L  26 " --> pdb=" O   LEU H  27 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 9 through 10
      removed outlier: 6.567A  pdb=" N   THR J   9 " --> pdb=" O   GLN E  10 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 14 through 19
      removed outlier: 6.356A  pdb=" N   PHE J  15 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   HIS E  18 " --> pdb=" O   PHE J  15 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL J  17 " --> pdb=" O   HIS E  18 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 31 through 32
      removed outlier: 5.883A  pdb=" N   ASN J  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    29 hydrogen bonds defined for protein.
    87 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: 0.55

  Time building geometry restraints manager: 0.96 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: 481
        1.31 -     1.43: 864
        1.43 -     1.56: 1667
        1.56 -     1.68: 0
        1.68 -     1.81: 12
  Bond restraints: 3024
  Sorted by residual:
  bond pdb=" CA  THR B   6 "
       pdb=" C   THR B   6 "
    ideal  model  delta    sigma   weight residual
    1.532  1.475  0.058 9.60e-03 1.09e+04 3.63e+01
  bond pdb=" C   TYC B  37 "
       pdb=" NXT TYC B  37 "
    ideal  model  delta    sigma   weight residual
    1.340  1.451 -0.111 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" C   TYC I  37 "
       pdb=" NXT TYC I  37 "
    ideal  model  delta    sigma   weight residual
    1.340  1.450 -0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" C   TYC F  37 "
       pdb=" NXT TYC F  37 "
    ideal  model  delta    sigma   weight residual
    1.340  1.450 -0.110 2.00e-02 2.50e+03 3.02e+01
  bond pdb=" C   TYC J  37 "
       pdb=" NXT TYC J  37 "
    ideal  model  delta    sigma   weight residual
    1.340  1.450 -0.110 2.00e-02 2.50e+03 3.02e+01
  ... (remaining 3019 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 3962
        2.13 -     4.26: 129
        4.26 -     6.39: 18
        6.39 -     8.52: 0
        8.52 -    10.65: 1
  Bond angle restraints: 4110
  Sorted by residual:
  angle pdb=" C   THR B   6 "
        pdb=" CA  THR B   6 "
        pdb=" CB  THR B   6 "
      ideal   model   delta    sigma   weight residual
     112.27  101.62   10.65 1.75e+00 3.27e-01 3.70e+01
  angle pdb=" C   THR B   6 "
        pdb=" N   CYS B   7 "
        pdb=" CA  CYS B   7 "
      ideal   model   delta    sigma   weight residual
     123.23  117.31    5.92 1.54e+00 4.22e-01 1.48e+01
  angle pdb=" C   ALA B   5 "
        pdb=" N   THR B   6 "
        pdb=" CA  THR B   6 "
      ideal   model   delta    sigma   weight residual
     122.93  117.56    5.37 1.51e+00 4.39e-01 1.27e+01
  angle pdb=" C   ASN F   3 "
        pdb=" N   THR F   4 "
        pdb=" CA  THR F   4 "
      ideal   model   delta    sigma   weight residual
     122.17  116.80    5.37 1.54e+00 4.22e-01 1.21e+01
  angle pdb=" N   ASN F   3 "
        pdb=" CA  ASN F   3 "
        pdb=" C   ASN F   3 "
      ideal   model   delta    sigma   weight residual
     112.89  117.03   -4.14 1.24e+00 6.50e-01 1.12e+01
  ... (remaining 4105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.38: 1511
       11.38 -    22.75: 186
       22.75 -    34.12: 37
       34.12 -    45.50: 48
       45.50 -    56.87: 30
  Dihedral angle restraints: 1812
    sinusoidal: 666
      harmonic: 1146
  Sorted by residual:
  dihedral pdb=" CB  CYS J   2 "
           pdb=" SG  CYS J   2 "
           pdb=" SG  CYS J   7 "
           pdb=" CB  CYS J   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.13   56.87     1      1.00e+01 1.00e-02 4.35e+01
  dihedral pdb=" CB  CYS F   2 "
           pdb=" SG  CYS F   2 "
           pdb=" SG  CYS F   7 "
           pdb=" CB  CYS F   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.37   55.63     1      1.00e+01 1.00e-02 4.18e+01
  dihedral pdb=" CB  CYS E   2 "
           pdb=" SG  CYS E   2 "
           pdb=" SG  CYS E   7 "
           pdb=" CB  CYS E   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.99   54.01     1      1.00e+01 1.00e-02 3.96e+01
  ... (remaining 1809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 312
       0.026 -    0.052: 114
       0.052 -    0.079: 26
       0.079 -    0.105: 26
       0.105 -    0.131: 20
  Chirality restraints: 498
  Sorted by residual:
  chirality pdb=" CA  ILE B  26 "
            pdb=" N   ILE B  26 "
            pdb=" C   ILE B  26 "
            pdb=" CB  ILE B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  ILE I  26 "
            pdb=" N   ILE I  26 "
            pdb=" C   ILE I  26 "
            pdb=" CB  ILE I  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  ILE A  26 "
            pdb=" N   ILE A  26 "
            pdb=" C   ILE A  26 "
            pdb=" CB  ILE A  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 495 not shown)

  Planarity restraints: 540
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA L  13 "   -0.014 2.00e-02 2.50e+03   2.90e-02 8.41e+00
        pdb=" C   ALA L  13 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ALA L  13 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASN L  14 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A   5 "    0.011 2.00e-02 2.50e+03   2.15e-02 4.61e+00
        pdb=" C   ALA A   5 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ALA A   5 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR A   6 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA F   5 "    0.011 2.00e-02 2.50e+03   2.14e-02 4.56e+00
        pdb=" C   ALA F   5 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ALA F   5 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR F   6 "    0.012 2.00e-02 2.50e+03
  ... (remaining 537 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 253
        2.74 -     3.28: 2893
        3.28 -     3.82: 4557
        3.82 -     4.36: 5253
        4.36 -     4.90: 10203
  Nonbonded interactions: 23159
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B   6 "
            pdb=" NE  ARG K  11 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OD1 ASN K  35 "
            pdb=" OD1 ASN J  35 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OD1 ASN G  35 "
            pdb=" OD1 ASN I  35 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   LYS J   1 "
            pdb=" O   CYS I   2 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   LYS F   1 "
            pdb=" O   CYS B   2 "
     model   vdw
     2.243 3.040
  ... (remaining 23154 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'L'
}

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:             0.730
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     11.720
  Find NCS groups from input model:        0.110
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
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      :  0.009   0.111   3030  Z= 0.514
  Angle     :  0.870  10.649   4122  Z= 0.501
  Chirality :  0.041   0.131    498
  Planarity :  0.003   0.029    540
  Dihedral  : 14.874  48.315   1038
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 22.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.16 (0.24), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.92 (0.18), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS J  18 
 PHE   0.009   0.002   PHE J  15 
 ARG   0.002   0.001   ARG H  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13800 (   29)
  hydrogen bonds       : angle       8.07466 (   87)
  SS BOND              : bond        0.00227 (    6)
  SS BOND              : angle       0.47448 (   12)
  covalent geometry    : bond        0.00948 ( 3024)
  covalent geometry    : angle       0.87051 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.310 
Fit side-chains
REVERT: B   11 ARG cc_start: 0.6687 (mtt180) cc_final: 0.5959 (mmm160)
REVERT: B   14 ASN cc_start: 0.7951 (m-40) cc_final: 0.7326 (p0)
REVERT: H   11 ARG cc_start: 0.4620 (mtt-85) cc_final: 0.4376 (mtp180)
REVERT: I   11 ARG cc_start: 0.6767 (mtt180) cc_final: 0.5973 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.2180
  time to fit residues: 8.8369
Evaluate side-chains
  21 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 27 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0970
   chunk 32 optimal weight:    0.8980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.100118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.077786 restraints weight = 6361.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 3.20
r_work: 0.3720 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3030  Z= 0.199
  Angle     :  0.536   4.803   4122  Z= 0.295
  Chirality :  0.042   0.132    498
  Planarity :  0.003   0.029    540
  Dihedral  : 11.108  41.145    486
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  :  8.64 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.11 (0.23), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.89 (0.18), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  18 
 PHE   0.011   0.002   PHE C  15 
 ARG   0.002   0.000   ARG K  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02381 (   29)
  hydrogen bonds       : angle       4.43386 (   87)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       1.24749 (   12)
  covalent geometry    : bond        0.00405 ( 3024)
  covalent geometry    : angle       0.53214 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 26
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ILE cc_start: 0.8221 (mt) cc_final: 0.7965 (mt)
REVERT: A   35 ASN cc_start: 0.8182 (m110) cc_final: 0.7962 (m110)
REVERT: B   11 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6349 (mmp-170)
REVERT: I   11 ARG cc_start: 0.6924 (mtt180) cc_final: 0.5995 (mmp-170)
  outliers start: 9
  outliers final: 5
  residues processed: 31
  average time/residue: 0.1774
  time to fit residues: 6.6911
Evaluate side-chains
  30 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain I residue   34 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 3 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0070
   chunk 11 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   overall best weight:    2.9604

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

Flipped N/Q/H residues before XYZ refinement:
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  18 HIS
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  18 HIS
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 HIS
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  18 HIS
** L  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  18 HIS
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  18 HIS
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.095377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.073793 restraints weight = 6690.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 3.16
r_work: 0.3639 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3561 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   3030  Z= 0.337
  Angle     :  0.646   5.653   4122  Z= 0.354
  Chirality :  0.046   0.145    498
  Planarity :  0.003   0.027    540
  Dihedral  : 13.136  48.323    486
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.20 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.09 (0.25), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.87 (0.19), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS E  18 
 PHE   0.017   0.004   PHE F  15 
 ARG   0.003   0.001   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01778 (   29)
  hydrogen bonds       : angle       3.97864 (   87)
  SS BOND              : bond        0.00323 (    6)
  SS BOND              : angle       0.57121 (   12)
  covalent geometry    : bond        0.00671 ( 3024)
  covalent geometry    : angle       0.64571 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 21
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A   26 ILE cc_start: 0.8404 (mt) cc_final: 0.8193 (mt)
REVERT: B   11 ARG cc_start: 0.6843 (mtt180) cc_final: 0.6523 (mmp-170)
REVERT: L   34 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8058 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 26
  average time/residue: 0.1617
  time to fit residues: 5.3228
Evaluate side-chains
  26 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain H residue   26 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain I residue   34 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 34 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** B  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.097320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.075575 restraints weight = 6752.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 3.19
r_work: 0.3680 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3030  Z= 0.229
  Angle     :  0.560   5.341   4122  Z= 0.304
  Chirality :  0.042   0.144    498
  Planarity :  0.002   0.018    540
  Dihedral  : 11.409  45.424    486
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.59 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.19 (0.25), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.95 (0.19), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E  18 
 PHE   0.011   0.002   PHE C  15 
 ARG   0.002   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01414 (   29)
  hydrogen bonds       : angle       3.83481 (   87)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       0.82324 (   12)
  covalent geometry    : bond        0.00457 ( 3024)
  covalent geometry    : angle       0.55917 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   26 ILE cc_start: 0.8319 (mt) cc_final: 0.8118 (mt)
REVERT: A   35 ASN cc_start: 0.8292 (m110) cc_final: 0.8016 (m-40)
REVERT: B   11 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6523 (mmp-170)
REVERT: K   11 ARG cc_start: 0.6144 (mtt-85) cc_final: 0.5743 (pmt-80)
REVERT: L   34 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.8121 (m)
  outliers start: 6
  outliers final: 4
  residues processed: 27
  average time/residue: 0.1929
  time to fit residues: 6.3619
Evaluate side-chains
  26 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain H residue   26 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.2980
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** B  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  35 ASN
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.098481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.076483 restraints weight = 6612.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 3.18
r_work: 0.3698 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3030  Z= 0.171
  Angle     :  0.509   6.237   4122  Z= 0.272
  Chirality :  0.041   0.141    498
  Planarity :  0.002   0.012    540
  Dihedral  :  8.317  30.223    486
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.90 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.22 (0.25), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.97 (0.19), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  18 
 PHE   0.009   0.002   PHE F  15 
 ARG   0.002   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01172 (   29)
  hydrogen bonds       : angle       3.67587 (   87)
  SS BOND              : bond        0.00310 (    6)
  SS BOND              : angle       0.82249 (   12)
  covalent geometry    : bond        0.00344 ( 3024)
  covalent geometry    : angle       0.50825 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   26 ILE cc_start: 0.8186 (mt) cc_final: 0.7984 (mt)
REVERT: B   11 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6551 (mmp-170)
REVERT: K   11 ARG cc_start: 0.5781 (mtt-85) cc_final: 0.5531 (pmt-80)
REVERT: L   34 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8079 (m)
REVERT: H   11 ARG cc_start: 0.4982 (mtt-85) cc_final: 0.3938 (mtp180)
REVERT: E   27 LEU cc_start: 0.8310 (tt) cc_final: 0.7799 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 34
  average time/residue: 0.1888
  time to fit residues: 7.6692
Evaluate side-chains
  34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain H residue   26 ILE
Chi-restraints excluded: chain J residue   12 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:   30.0000
   chunk 29 optimal weight:    0.2980
   chunk 28 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    0.1980
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.097095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.075324 restraints weight = 6769.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 3.16
r_work: 0.3813 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3030  Z= 0.222
  Angle     :  0.536   5.428   4122  Z= 0.289
  Chirality :  0.042   0.145    498
  Planarity :  0.002   0.014    540
  Dihedral  :  9.312  34.532    486
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.83 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.21 (0.26), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.97 (0.20), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E  18 
 PHE   0.011   0.002   PHE G  15 
 ARG   0.002   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01154 (   29)
  hydrogen bonds       : angle       3.68449 (   87)
  SS BOND              : bond        0.00297 (    6)
  SS BOND              : angle       0.64883 (   12)
  covalent geometry    : bond        0.00444 ( 3024)
  covalent geometry    : angle       0.53519 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B   11 ARG cc_start: 0.7158 (mtt180) cc_final: 0.6573 (mmp-170)
REVERT: K   11 ARG cc_start: 0.5756 (mtt-85) cc_final: 0.5441 (pmt-80)
REVERT: E   27 LEU cc_start: 0.8329 (tt) cc_final: 0.7881 (mp)
REVERT: I   27 LEU cc_start: 0.7917 (tt) cc_final: 0.7426 (mp)
  outliers start: 7
  outliers final: 7
  residues processed: 29
  average time/residue: 0.2116
  time to fit residues: 7.2928
Evaluate side-chains
  32 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain H residue   26 ILE
Chi-restraints excluded: chain J residue   12 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 5 optimal weight:    0.1980
   chunk 27 optimal weight:   20.0000
   chunk 30 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.100468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.078368 restraints weight = 6492.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 3.24
r_work: 0.3919 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3030  Z= 0.105
  Angle     :  0.458   6.867   4122  Z= 0.240
  Chirality :  0.041   0.140    498
  Planarity :  0.001   0.008    540
  Dihedral  :  5.916  20.074    486
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.52 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.19 (0.26), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.95 (0.20), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS J  18 
 PHE   0.006   0.001   PHE K  15 
 ARG   0.001   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.00969 (   29)
  hydrogen bonds       : angle       3.52833 (   87)
  SS BOND              : bond        0.00259 (    6)
  SS BOND              : angle       0.85940 (   12)
  covalent geometry    : bond        0.00210 ( 3024)
  covalent geometry    : angle       0.45662 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.351 
Fit side-chains
REVERT: B   11 ARG cc_start: 0.7085 (mtt180) cc_final: 0.6666 (mmp-170)
REVERT: K   11 ARG cc_start: 0.5714 (mtt-85) cc_final: 0.5397 (pmt-80)
REVERT: E   27 LEU cc_start: 0.8408 (tt) cc_final: 0.7923 (mp)
REVERT: I   27 LEU cc_start: 0.7981 (tt) cc_final: 0.7566 (mp)
  outliers start: 9
  outliers final: 7
  residues processed: 34
  average time/residue: 0.1940
  time to fit residues: 7.8951
Evaluate side-chains
  33 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain H residue   26 ILE
Chi-restraints excluded: chain J residue   12 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 32 optimal weight:    0.0040
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 12 optimal weight:    0.2980
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.100275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.078200 restraints weight = 6456.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.4008 rms_B_bonded: 3.21
r_work: 0.3911 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3030  Z= 0.107
  Angle     :  0.448   6.371   4122  Z= 0.234
  Chirality :  0.040   0.139    498
  Planarity :  0.001   0.007    540
  Dihedral  :  5.850  18.678    486
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.21 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.10 (0.27), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.88 (0.21), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E  18 
 PHE   0.006   0.001   PHE E  15 
 ARG   0.001   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.00951 (   29)
  hydrogen bonds       : angle       3.38573 (   87)
  SS BOND              : bond        0.00235 (    6)
  SS BOND              : angle       0.73521 (   12)
  covalent geometry    : bond        0.00214 ( 3024)
  covalent geometry    : angle       0.44708 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A    6 THR cc_start: 0.5304 (OUTLIER) cc_final: 0.5054 (p)
REVERT: B   11 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6663 (mmp-170)
REVERT: K   11 ARG cc_start: 0.5755 (mtt-85) cc_final: 0.5403 (pmt-80)
REVERT: K   34 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7693 (m)
REVERT: E   27 LEU cc_start: 0.8388 (tt) cc_final: 0.7931 (mp)
REVERT: I   27 LEU cc_start: 0.8006 (tt) cc_final: 0.7571 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 30
  average time/residue: 0.2186
  time to fit residues: 7.9175
Evaluate side-chains
  35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain H residue   26 ILE
Chi-restraints excluded: chain J residue   12 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   chunk 10 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
B  14 ASN
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.098558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.076685 restraints weight = 6654.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 3.17
r_work: 0.3871 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3787 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3030  Z= 0.153
  Angle     :  0.471   6.772   4122  Z= 0.247
  Chirality :  0.040   0.140    498
  Planarity :  0.002   0.010    540
  Dihedral  :  7.012  22.592    486
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.83 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.02 (0.28), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.22), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  18 
 PHE   0.008   0.002   PHE F  15 
 ARG   0.001   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01007 (   29)
  hydrogen bonds       : angle       3.37938 (   87)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       0.58527 (   12)
  covalent geometry    : bond        0.00306 ( 3024)
  covalent geometry    : angle       0.47071 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A    6 THR cc_start: 0.5161 (OUTLIER) cc_final: 0.4895 (p)
REVERT: B   11 ARG cc_start: 0.7137 (mtt180) cc_final: 0.6633 (mmp-170)
REVERT: K   11 ARG cc_start: 0.5617 (mtt-85) cc_final: 0.5413 (pmt-80)
REVERT: K   34 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7822 (m)
REVERT: E   27 LEU cc_start: 0.8406 (tt) cc_final: 0.7937 (mp)
REVERT: I   27 LEU cc_start: 0.8009 (tt) cc_final: 0.7588 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 31
  average time/residue: 0.2241
  time to fit residues: 8.3483
Evaluate side-chains
  35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain H residue   26 ILE
Chi-restraints excluded: chain J residue   12 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 17 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0170
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.0222

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

Flipped N/Q/H residues before XYZ refinement:
B  14 ASN
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.099594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.077689 restraints weight = 6492.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 3.17
r_work: 0.3898 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3813 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3030  Z= 0.127
  Angle     :  0.454   6.694   4122  Z= 0.235
  Chirality :  0.040   0.139    498
  Planarity :  0.001   0.009    540
  Dihedral  :  6.241  19.368    486
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.14 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.03 (0.28), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.21), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E  18 
 PHE   0.007   0.001   PHE F  15 
 ARG   0.001   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.00927 (   29)
  hydrogen bonds       : angle       3.35292 (   87)
  SS BOND              : bond        0.00232 (    6)
  SS BOND              : angle       0.70985 (   12)
  covalent geometry    : bond        0.00253 ( 3024)
  covalent geometry    : angle       0.45300 ( 4110)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.318 
Fit side-chains
REVERT: F   27 LEU cc_start: 0.8044 (tt) cc_final: 0.7705 (mp)
REVERT: A    6 THR cc_start: 0.5320 (OUTLIER) cc_final: 0.5070 (p)
REVERT: B   11 ARG cc_start: 0.7140 (mtt180) cc_final: 0.6636 (mmp-170)
REVERT: K   11 ARG cc_start: 0.5501 (mtt-85) cc_final: 0.5289 (pmt-80)
REVERT: K   34 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7841 (m)
REVERT: E   27 LEU cc_start: 0.8408 (tt) cc_final: 0.7961 (mp)
REVERT: I   27 LEU cc_start: 0.7997 (tt) cc_final: 0.7668 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 32
  average time/residue: 0.2034
  time to fit residues: 7.7895
Evaluate side-chains
  36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain B residue   12 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain H residue   26 ILE
Chi-restraints excluded: chain J residue   12 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0570
   chunk 8 optimal weight:    0.0020
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.0112

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

Flipped N/Q/H residues before XYZ refinement:
B  14 ASN
** K  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.099532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.077500 restraints weight = 6537.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 3.18
r_work: 0.3900 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3809 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3030  Z= 0.125
  Angle     :  0.450   6.683   4122  Z= 0.232
  Chirality :  0.040   0.140    498
  Planarity :  0.001   0.009    540
  Dihedral  :  6.170  19.357    486
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.83 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.06 (0.28), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.22), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E  18 
 PHE   0.007   0.001   PHE F  15 
 ARG   0.001   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.00904 (   29)
  hydrogen bonds       : angle       3.35693 (   87)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       0.65879 (   12)
  covalent geometry    : bond        0.00251 ( 3024)
  covalent geometry    : angle       0.44946 ( 4110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2024.85 seconds
wall clock time: 35 minutes 47.48 seconds (2147.48 seconds total)