Starting phenix.real_space_refine
on Sat Jan 18 14:37:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c4d_45182/01_2025/9c4d_45182.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c4d_45182/01_2025/9c4d_45182.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c4d_45182/01_2025/9c4d_45182.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c4d_45182/01_2025/9c4d_45182.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c4d_45182/01_2025/9c4d_45182.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c4d_45182/01_2025/9c4d_45182.cif"
  }
  resolution = 4.17
  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=   0.012
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
     Mn     16      7.51       5
     P     154      5.49       5
     S      24      5.16       5
     C    7426      2.51       5
     N    2149      2.21       5
     O    2724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12493
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1563
          Classifications: {'DNA': 77}
          Link IDs: {'rna3p': 76}
    Chain: "B"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1594
          Classifications: {'DNA': 77}
          Link IDs: {'rna3p': 76}
    Chain: "C"
      Number of atoms: 1165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1165
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 137}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    D, E, F, G, H, I, J
  Time building chain proxies: 6.92, per 1000 atoms: 0.55
  Number of scatterers: 12493
  At special positions: 0
  Unit cell: (94.8537, 91.5255, 269.584, 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)
     Mn     16     24.99
     S      24     16.00
     P     154     15.00
     O    2724      8.00
     N    2149      7.00
     C    7426      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.89
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 8 sheets defined
      84.4% alpha, 2.9% beta
      74 base pairs and 133 stacking pairs defined.
    Time for finding SS restraints: 4.92
  Creating SS restraints...
    Processing helix  chain 'C' and resid 3 through 21
      removed outlier: 3.662A  pdb=" N   GLU C   7 " --> pdb=" O   THR C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 33
    Processing helix  chain 'C' and resid 35 through 49
    Processing helix  chain 'C' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE C  87 " --> pdb=" O   PHE C  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY C  88 " --> pdb=" O   LEU C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASN C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 122
    Processing helix  chain 'C' and resid 124 through 139
    Processing helix  chain 'C' and resid 140 through 142
      No H-bonds generated for 'chain 'C' and resid 140 through 142'
    Processing helix  chain 'D' and resid 4 through 21
    Processing helix  chain 'D' and resid 24 through 33
    Processing helix  chain 'D' and resid 35 through 49
    Processing helix  chain 'D' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE D  87 " --> pdb=" O   PHE D  83 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY D  88 " --> pdb=" O   LEU D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR D  95 " --> pdb=" O   GLU D  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN D  96 " --> pdb=" O   GLU D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 122
    Processing helix  chain 'D' and resid 124 through 139
    Processing helix  chain 'D' and resid 140 through 142
      No H-bonds generated for 'chain 'D' and resid 140 through 142'
    Processing helix  chain 'E' and resid 4 through 21
    Processing helix  chain 'E' and resid 24 through 33
    Processing helix  chain 'E' and resid 35 through 49
    Processing helix  chain 'E' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE E  87 " --> pdb=" O   PHE E  83 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY E  88 " --> pdb=" O   LEU E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 102
      removed outlier: 4.171A  pdb=" N   TYR E  95 " --> pdb=" O   GLU E  91 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASN E  96 " --> pdb=" O   GLU E  92 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 106 through 122
    Processing helix  chain 'E' and resid 124 through 139
    Processing helix  chain 'E' and resid 140 through 142
      No H-bonds generated for 'chain 'E' and resid 140 through 142'
    Processing helix  chain 'F' and resid 4 through 21
    Processing helix  chain 'F' and resid 24 through 33
    Processing helix  chain 'F' and resid 35 through 49
    Processing helix  chain 'F' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE F  87 " --> pdb=" O   PHE F  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY F  88 " --> pdb=" O   LEU F  84 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 90 through 102
      removed outlier: 4.173A  pdb=" N   TYR F  95 " --> pdb=" O   GLU F  91 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASN F  96 " --> pdb=" O   GLU F  92 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 106 through 122
    Processing helix  chain 'F' and resid 124 through 139
    Processing helix  chain 'F' and resid 140 through 142
      No H-bonds generated for 'chain 'F' and resid 140 through 142'
    Processing helix  chain 'G' and resid 4 through 21
    Processing helix  chain 'G' and resid 24 through 33
    Processing helix  chain 'G' and resid 35 through 49
    Processing helix  chain 'G' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE G  87 " --> pdb=" O   PHE G  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY G  88 " --> pdb=" O   LEU G  84 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 106 through 122
    Processing helix  chain 'G' and resid 124 through 139
    Processing helix  chain 'G' and resid 140 through 142
      No H-bonds generated for 'chain 'G' and resid 140 through 142'
    Processing helix  chain 'H' and resid 4 through 21
    Processing helix  chain 'H' and resid 24 through 33
    Processing helix  chain 'H' and resid 35 through 49
    Processing helix  chain 'H' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE H  87 " --> pdb=" O   PHE H  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY H  88 " --> pdb=" O   LEU H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR H  95 " --> pdb=" O   GLU H  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN H  96 " --> pdb=" O   GLU H  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 106 through 122
    Processing helix  chain 'H' and resid 124 through 139
    Processing helix  chain 'H' and resid 140 through 142
      No H-bonds generated for 'chain 'H' and resid 140 through 142'
    Processing helix  chain 'I' and resid 4 through 21
    Processing helix  chain 'I' and resid 24 through 33
    Processing helix  chain 'I' and resid 35 through 49
    Processing helix  chain 'I' and resid 63 through 88
      removed outlier: 3.568A  pdb=" N   ILE I  87 " --> pdb=" O   PHE I  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY I  88 " --> pdb=" O   LEU I  84 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR I  95 " --> pdb=" O   GLU I  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN I  96 " --> pdb=" O   GLU I  92 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 106 through 122
    Processing helix  chain 'I' and resid 124 through 139
    Processing helix  chain 'I' and resid 140 through 142
      No H-bonds generated for 'chain 'I' and resid 140 through 142'
    Processing helix  chain 'J' and resid 4 through 21
    Processing helix  chain 'J' and resid 24 through 33
    Processing helix  chain 'J' and resid 35 through 49
    Processing helix  chain 'J' and resid 63 through 88
      removed outlier: 3.566A  pdb=" N   ILE J  87 " --> pdb=" O   PHE J  83 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY J  88 " --> pdb=" O   LEU J  84 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR J  95 " --> pdb=" O   GLU J  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN J  96 " --> pdb=" O   GLU J  92 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 106 through 122
    Processing helix  chain 'J' and resid 124 through 139
    Processing helix  chain 'J' and resid 140 through 142
      No H-bonds generated for 'chain 'J' and resid 140 through 142'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 54
    Processing sheet with id=AA2, first strand: chain 'D' and resid 52 through 54
    Processing sheet with id=AA3, first strand: chain 'E' and resid 52 through 54
    Processing sheet with id=AA4, first strand: chain 'F' and resid 52 through 54
    Processing sheet with id=AA5, first strand: chain 'G' and resid 52 through 54
    Processing sheet with id=AA6, first strand: chain 'H' and resid 52 through 54
    Processing sheet with id=AA7, first strand: chain 'I' and resid 52 through 54
    Processing sheet with id=AA8, first strand: chain 'J' and resid 52 through 54

    680 hydrogen bonds defined for protein.
    2040 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      172 hydrogen bonds
      344 hydrogen bond angles
      0 basepair planarities
      74 basepair parallelities
      133 stacking parallelities
  Total time for adding SS restraints: 4.65

  Time building geometry restraints manager: 3.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2516
        1.33 -     1.45: 3529
        1.45 -     1.57: 6621
        1.57 -     1.69: 306
        1.69 -     1.80: 48
  Bond restraints: 13020
  Sorted by residual:
  bond pdb=" C3'  DA B -44 "
       pdb=" O3'  DA B -44 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.71e+00
  bond pdb=" C3'  DA B -28 "
       pdb=" O3'  DA B -28 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.65e+00
  bond pdb=" C3'  DA B -25 "
       pdb=" O3'  DA B -25 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.60e+00
  bond pdb=" C3'  DC B -66 "
       pdb=" O3'  DC B -66 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.56e+00
  bond pdb=" C3'  DA B -24 "
       pdb=" O3'  DA B -24 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.47e+00
  ... (remaining 13015 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 17709
        1.30 -     2.59: 412
        2.59 -     3.89: 50
        3.89 -     5.18: 8
        5.18 -     6.48: 8
  Bond angle restraints: 18187
  Sorted by residual:
  angle pdb=" C3'  DT A  22 "
        pdb=" C2'  DT A  22 "
        pdb=" C1'  DT A  22 "
      ideal   model   delta    sigma   weight residual
     101.60   98.17    3.43 1.50e+00 4.44e-01 5.23e+00
  angle pdb=" C4'  DA A  60 "
        pdb=" C3'  DA A  60 "
        pdb=" C2'  DA A  60 "
      ideal   model   delta    sigma   weight residual
     102.40  105.68   -3.28 1.50e+00 4.44e-01 4.78e+00
  angle pdb=" C3'  DA B -25 "
        pdb=" O3'  DA B -25 "
        pdb=" P    DA B -24 "
      ideal   model   delta    sigma   weight residual
     120.20  123.45   -3.25 1.50e+00 4.44e-01 4.70e+00
  angle pdb=" C4'  DA B -24 "
        pdb=" C3'  DA B -24 "
        pdb=" C2'  DA B -24 "
      ideal   model   delta    sigma   weight residual
     102.40  105.60   -3.20 1.50e+00 4.44e-01 4.55e+00
  angle pdb=" C3'  DA B -44 "
        pdb=" O3'  DA B -44 "
        pdb=" P    DT B -43 "
      ideal   model   delta    sigma   weight residual
     120.20  123.36   -3.16 1.50e+00 4.44e-01 4.44e+00
  ... (remaining 18182 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.90: 6882
       35.90 -    71.80: 669
       71.80 -   107.70: 0
      107.70 -   143.60: 1
      143.60 -   179.50: 10
  Dihedral angle restraints: 7562
    sinusoidal: 4250
      harmonic: 3312
  Sorted by residual:
  dihedral pdb=" CA  GLU H  55 "
           pdb=" C   GLU H  55 "
           pdb=" N   LYS H  56 "
           pdb=" CA  LYS H  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.40  -21.60     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  GLU I  55 "
           pdb=" C   GLU I  55 "
           pdb=" N   LYS I  56 "
           pdb=" CA  LYS I  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.41  -21.59     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  GLU F  55 "
           pdb=" C   GLU F  55 "
           pdb=" N   LYS F  56 "
           pdb=" CA  LYS F  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.41  -21.59     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 7559 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1311
       0.026 -    0.051: 458
       0.051 -    0.077: 158
       0.077 -    0.102: 53
       0.102 -    0.128: 12
  Chirality restraints: 1992
  Sorted by residual:
  chirality pdb=" P    DT B -46 "
            pdb=" OP1  DT B -46 "
            pdb=" OP2  DT B -46 "
            pdb=" O5'  DT B -46 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.47   -0.13 2.00e-01 2.50e+01 4.09e-01
  chirality pdb=" CA  PRO G  36 "
            pdb=" N   PRO G  36 "
            pdb=" C   PRO G  36 "
            pdb=" CB  PRO G  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.08e-01
  chirality pdb=" CA  PRO I  36 "
            pdb=" N   PRO I  36 "
            pdb=" C   PRO I  36 "
            pdb=" CB  PRO I  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.02e-01
  ... (remaining 1989 not shown)

  Planarity restraints: 1778
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT A  24 "    0.023 2.00e-02 2.50e+03   1.13e-02 3.17e+00
        pdb=" N1   DT A  24 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2   DT A  24 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2   DT A  24 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT A  24 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT A  24 "    0.005 2.00e-02 2.50e+03
        pdb=" O4   DT A  24 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DT A  24 "    0.001 2.00e-02 2.50e+03
        pdb=" C7   DT A  24 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DT A  24 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C  55 "    0.006 2.00e-02 2.50e+03   1.13e-02 1.27e+00
        pdb=" C   GLU C  55 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   GLU C  55 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LYS C  56 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU I  55 "    0.005 2.00e-02 2.50e+03   1.12e-02 1.25e+00
        pdb=" C   GLU I  55 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   GLU I  55 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LYS I  56 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1775 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 248
        2.65 -     3.21: 11050
        3.21 -     3.77: 22212
        3.77 -     4.34: 27150
        4.34 -     4.90: 41222
  Nonbonded interactions: 101882
  Sorted by model distance:
  nonbonded pdb=" OP1  DT B -20 "
            pdb=" OH  TYR D  54 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" OP1  DT A  27 "
            pdb=" NZ  LYS E  56 "
     model   vdw
     2.114 3.120
  nonbonded pdb=" OE1 GLU H 102 "
            pdb="MN    MN H 201 "
     model   vdw
     2.123 2.320
  nonbonded pdb=" OE1 GLU E 102 "
            pdb="MN    MN E 201 "
     model   vdw
     2.124 2.320
  nonbonded pdb=" OE1 GLU J 102 "
            pdb="MN    MN J 201 "
     model   vdw
     2.124 2.320
  ... (remaining 101877 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.290
  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:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     31.590
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
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      :  0.002   0.039  13020  Z= 0.130
  Angle     :  0.480   6.477  18187  Z= 0.281
  Chirality :  0.032   0.128   1992
  Planarity :  0.002   0.014   1778
  Dihedral  : 22.140 179.502   5434
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  3.91 %
    Favored  : 93.75 %
  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:  4.02 (0.26), residues: 1104
  helix:  3.09 (0.18), residues: 880
  sheet:  None (None), residues: 0
  loop :  0.86 (0.45), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 107 
 HIS   0.002   0.001   HIS J 139 
 PHE   0.003   0.001   PHE I 120 
 TYR   0.005   0.001   TYR D  75 
 ARG   0.001   0.000   ARG I 126 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   42 MET cc_start: 0.8849 (tpp) cc_final: 0.7901 (tpp)
REVERT: E  112 ARG cc_start: 0.8147 (mmp80) cc_final: 0.7903 (mmp80)
REVERT: F   14 TYR cc_start: 0.7095 (t80) cc_final: 0.6876 (t80)
REVERT: F   51 TYR cc_start: 0.8041 (m-80) cc_final: 0.7619 (m-80)
REVERT: F   80 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8414 (tp)
REVERT: F   83 PHE cc_start: 0.8905 (t80) cc_final: 0.8607 (t80)
REVERT: H   15 MET cc_start: 0.9108 (ttp) cc_final: 0.8853 (ttm)
REVERT: H   42 MET cc_start: 0.8371 (tpp) cc_final: 0.8047 (tpp)
REVERT: I   51 TYR cc_start: 0.7619 (m-80) cc_final: 0.7234 (m-10)
REVERT: I  107 TRP cc_start: 0.5520 (m100) cc_final: 0.5280 (m100)
REVERT: J  107 TRP cc_start: 0.6915 (m100) cc_final: 0.6474 (t-100)
  outliers start: 24
  outliers final: 8
  residues processed: 179
  average time/residue: 0.2719
  time to fit residues: 67.8906
Evaluate side-chains
  84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.0970
   chunk 95 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0270
   chunk 51 optimal weight:    0.6980
   chunk 98 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 114 optimal weight:    6.9990
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 HIS
E 139 HIS
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 GLN
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 139 HIS
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.091167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.070894 restraints weight = 82027.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.070585 restraints weight = 57491.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.071048 restraints weight = 45509.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13020  Z= 0.169
  Angle     :  0.527   7.167  18187  Z= 0.301
  Chirality :  0.034   0.131   1992
  Planarity :  0.003   0.043   1778
  Dihedral  : 27.793 179.468   2986
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.66 %
    Favored  : 98.14 %
  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:  3.31 (0.26), residues: 1104
  helix:  2.66 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop :  0.17 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 107 
 HIS   0.005   0.001   HIS F  77 
 PHE   0.010   0.001   PHE F 120 
 TYR   0.012   0.001   TYR I 119 
 ARG   0.008   0.001   ARG I  76 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 MET cc_start: 0.8635 (mmp) cc_final: 0.8303 (tpp)
REVERT: D   42 MET cc_start: 0.8493 (tpp) cc_final: 0.8039 (tpp)
REVERT: E  121 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8481 (pp20)
REVERT: F   42 MET cc_start: 0.8013 (tpt) cc_final: 0.7752 (tpp)
REVERT: F   51 TYR cc_start: 0.8232 (m-80) cc_final: 0.7913 (m-80)
REVERT: F  112 ARG cc_start: 0.8878 (mmp80) cc_final: 0.8612 (mmp80)
REVERT: F  134 GLN cc_start: 0.8435 (pt0) cc_final: 0.7956 (mt0)
REVERT: G  137 THR cc_start: 0.8032 (p) cc_final: 0.7574 (t)
REVERT: H   15 MET cc_start: 0.8959 (ttp) cc_final: 0.7961 (ttm)
REVERT: H   42 MET cc_start: 0.8356 (tpp) cc_final: 0.8074 (tpp)
REVERT: I   51 TYR cc_start: 0.7970 (m-80) cc_final: 0.7444 (m-10)
REVERT: J  107 TRP cc_start: 0.7399 (m100) cc_final: 0.6486 (t-100)
  outliers start: 2
  outliers final: 0
  residues processed: 102
  average time/residue: 0.3053
  time to fit residues: 43.0552
Evaluate side-chains
  67 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 124 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0980
   chunk 95 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
E  77 HIS
E 134 GLN
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  12 GLN
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.089105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.068429 restraints weight = 82842.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.068316 restraints weight = 65264.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.069077 restraints weight = 48402.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13020  Z= 0.199
  Angle     :  0.538   8.274  18187  Z= 0.311
  Chirality :  0.035   0.309   1992
  Planarity :  0.003   0.058   1778
  Dihedral  : 27.677 179.909   2986
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.64 %
    Favored  : 97.07 %
  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:  2.93 (0.26), residues: 1104
  helix:  2.45 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.29 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 107 
 HIS   0.005   0.001   HIS F  35 
 PHE   0.022   0.002   PHE J  83 
 TYR   0.011   0.001   TYR E  22 
 ARG   0.012   0.001   ARG E 126 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 1.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   42 MET cc_start: 0.8625 (tpp) cc_final: 0.8142 (tpp)
REVERT: E    6 MET cc_start: 0.8191 (tmm) cc_final: 0.7786 (tmm)
REVERT: E  121 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8587 (pt0)
REVERT: F   42 MET cc_start: 0.8190 (tpt) cc_final: 0.7767 (tpp)
REVERT: F   51 TYR cc_start: 0.8170 (m-80) cc_final: 0.7900 (m-80)
REVERT: F  134 GLN cc_start: 0.8538 (pt0) cc_final: 0.7827 (mt0)
REVERT: H   42 MET cc_start: 0.8691 (tpp) cc_final: 0.8223 (tpp)
  outliers start: 3
  outliers final: 1
  residues processed: 93
  average time/residue: 0.2522
  time to fit residues: 34.4519
Evaluate side-chains
  60 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 123 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D 134 GLN
** F  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 134 GLN
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  12 GLN
J  77 HIS
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.087966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.066734 restraints weight = 81991.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.066559 restraints weight = 57936.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.066890 restraints weight = 44689.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13020  Z= 0.208
  Angle     :  0.569   9.461  18187  Z= 0.322
  Chirality :  0.035   0.171   1992
  Planarity :  0.003   0.042   1778
  Dihedral  : 27.711 179.928   2986
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  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:  2.59 (0.26), residues: 1104
  helix:  2.26 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.60 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 107 
 HIS   0.005   0.001   HIS F  35 
 PHE   0.008   0.001   PHE J  83 
 TYR   0.013   0.001   TYR E  14 
 ARG   0.009   0.001   ARG E 126 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   15 MET cc_start: 0.8646 (ppp) cc_final: 0.8421 (ppp)
REVERT: D    6 MET cc_start: 0.8149 (mmp) cc_final: 0.7897 (mmt)
REVERT: D   42 MET cc_start: 0.8941 (tpp) cc_final: 0.8496 (tpp)
REVERT: E    6 MET cc_start: 0.8242 (tmm) cc_final: 0.7998 (tmm)
REVERT: E   49 ASP cc_start: 0.8810 (t0) cc_final: 0.8600 (t70)
REVERT: E  121 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8661 (pt0)
REVERT: F   42 MET cc_start: 0.8325 (tpt) cc_final: 0.7877 (tpp)
REVERT: F   51 TYR cc_start: 0.8285 (m-80) cc_final: 0.7911 (m-80)
REVERT: F  134 GLN cc_start: 0.8528 (pt0) cc_final: 0.8269 (pt0)
REVERT: G  142 GLN cc_start: 0.6858 (mt0) cc_final: 0.6442 (mp10)
REVERT: H   42 MET cc_start: 0.8763 (tpp) cc_final: 0.8269 (tpp)
REVERT: I   42 MET cc_start: 0.8105 (tmm) cc_final: 0.7904 (tmm)
REVERT: I  136 LYS cc_start: 0.7945 (mptt) cc_final: 0.7599 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2345
  time to fit residues: 27.6850
Evaluate side-chains
  62 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 123 optimal weight:    7.9990
   chunk 104 optimal weight:    0.0000
   chunk 84 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 120 optimal weight:    6.9990
   chunk 94 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.4562

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

Flipped N/Q/H residues before XYZ refinement:
C 134 GLN
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 140 HIS
F  12 GLN
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 103 HIS
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.088661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.067042 restraints weight = 79443.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.066403 restraints weight = 55911.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.066775 restraints weight = 42899.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.4398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13020  Z= 0.159
  Angle     :  0.524   8.235  18187  Z= 0.300
  Chirality :  0.034   0.146   1992
  Planarity :  0.003   0.025   1778
  Dihedral  : 27.668 179.588   2986
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.46 %
    Favored  : 98.34 %
  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:  2.82 (0.26), residues: 1104
  helix:  2.43 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.60 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 107 
 HIS   0.014   0.001   HIS E 139 
 PHE   0.008   0.001   PHE J  83 
 TYR   0.010   0.001   TYR E  14 
 ARG   0.009   0.000   ARG E 126 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   42 MET cc_start: 0.8876 (tpp) cc_final: 0.8408 (tpp)
REVERT: E   49 ASP cc_start: 0.8888 (t0) cc_final: 0.8631 (t70)
REVERT: E  121 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8663 (pt0)
REVERT: E  140 HIS cc_start: 0.6716 (OUTLIER) cc_final: 0.6199 (p90)
REVERT: F  134 GLN cc_start: 0.8599 (pt0) cc_final: 0.8163 (mt0)
REVERT: H   42 MET cc_start: 0.8865 (tpp) cc_final: 0.8228 (tpp)
REVERT: H   43 VAL cc_start: 0.9430 (t) cc_final: 0.9180 (p)
REVERT: I  136 LYS cc_start: 0.7968 (mptt) cc_final: 0.7671 (mttt)
  outliers start: 2
  outliers final: 0
  residues processed: 84
  average time/residue: 0.2336
  time to fit residues: 29.4136
Evaluate side-chains
  63 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 105 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  12 GLN
E 140 HIS
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  77 HIS
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.086243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.064409 restraints weight = 81632.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.064747 restraints weight = 55267.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.064459 restraints weight = 45748.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.5185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13020  Z= 0.259
  Angle     :  0.599   8.200  18187  Z= 0.342
  Chirality :  0.036   0.143   1992
  Planarity :  0.003   0.028   1778
  Dihedral  : 27.780 179.721   2986
  Min Nonbonded Distance : 1.256

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.37 %
    Favored  : 98.44 %
  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:  2.37 (0.26), residues: 1104
  helix:  2.15 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.93 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 107 
 HIS   0.007   0.001   HIS E 139 
 PHE   0.008   0.002   PHE J  83 
 TYR   0.020   0.002   TYR F   9 
 ARG   0.010   0.001   ARG E 126 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 1.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   42 MET cc_start: 0.8498 (tpp) cc_final: 0.8297 (tpp)
REVERT: E    6 MET cc_start: 0.8407 (tmm) cc_final: 0.8189 (tmm)
REVERT: E   49 ASP cc_start: 0.9154 (t0) cc_final: 0.8755 (t0)
REVERT: E  121 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8715 (pt0)
REVERT: F   71 LYS cc_start: 0.9049 (tttt) cc_final: 0.8710 (pttm)
REVERT: F  134 GLN cc_start: 0.8574 (pt0) cc_final: 0.8307 (pt0)
REVERT: H   42 MET cc_start: 0.8790 (tpp) cc_final: 0.8384 (tpp)
REVERT: H   43 VAL cc_start: 0.9460 (t) cc_final: 0.9245 (p)
REVERT: I  136 LYS cc_start: 0.7982 (mptt) cc_final: 0.7739 (mttt)
REVERT: J   47 ASP cc_start: 0.6190 (t70) cc_final: 0.5894 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 92
  average time/residue: 0.2110
  time to fit residues: 30.1700
Evaluate side-chains
  64 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 87 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 102 optimal weight:    6.9990
   chunk 116 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 140 HIS
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.086054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.063994 restraints weight = 80059.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.063780 restraints weight = 53790.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.063730 restraints weight = 44345.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.5636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13020  Z= 0.249
  Angle     :  0.593   8.054  18187  Z= 0.339
  Chirality :  0.037   0.131   1992
  Planarity :  0.003   0.025   1778
  Dihedral  : 27.784 179.914   2986
  Min Nonbonded Distance : 1.402

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.46 %
    Favored  : 98.44 %
  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:  2.15 (0.26), residues: 1104
  helix:  2.04 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -1.19 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 107 
 HIS   0.006   0.001   HIS E 103 
 PHE   0.036   0.002   PHE F 120 
 TYR   0.023   0.002   TYR F   9 
 ARG   0.008   0.001   ARG E 126 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 MET cc_start: 0.7344 (tpp) cc_final: 0.6791 (tpp)
REVERT: D   42 MET cc_start: 0.8544 (tpp) cc_final: 0.8252 (tpp)
REVERT: E  121 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8737 (pt0)
REVERT: E  140 HIS cc_start: 0.6902 (OUTLIER) cc_final: 0.6345 (p90)
REVERT: F  134 GLN cc_start: 0.8457 (pt0) cc_final: 0.7887 (mt0)
REVERT: H   42 MET cc_start: 0.8703 (tpp) cc_final: 0.8033 (tpp)
REVERT: H   43 VAL cc_start: 0.9440 (t) cc_final: 0.9212 (p)
REVERT: I   43 VAL cc_start: 0.9422 (t) cc_final: 0.9188 (t)
REVERT: I  136 LYS cc_start: 0.8000 (mptt) cc_final: 0.7795 (mttt)
REVERT: J   42 MET cc_start: 0.7292 (mmp) cc_final: 0.7064 (mmm)
REVERT: J   47 ASP cc_start: 0.6416 (t70) cc_final: 0.6143 (t0)
REVERT: J  107 TRP cc_start: 0.6775 (t-100) cc_final: 0.6439 (m100)
REVERT: J  111 ASP cc_start: 0.5736 (m-30) cc_final: 0.4908 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 78
  average time/residue: 0.2085
  time to fit residues: 25.2832
Evaluate side-chains
  68 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 114 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 109 optimal weight:    7.9990
   chunk 83 optimal weight:    0.7980
   chunk 120 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 104 HIS
** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 103 HIS
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 118 GLN
I  12 GLN
J  77 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.086342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.064285 restraints weight = 80387.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.064697 restraints weight = 53745.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.064611 restraints weight = 40477.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.5798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13020  Z= 0.199
  Angle     :  0.571   8.004  18187  Z= 0.324
  Chirality :  0.036   0.130   1992
  Planarity :  0.003   0.024   1778
  Dihedral  : 27.782 179.777   2986
  Min Nonbonded Distance : 1.411

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.59 %
    Favored  : 99.32 %
  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:  2.30 (0.26), residues: 1104
  helix:  2.15 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -1.21 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 107 
 HIS   0.006   0.001   HIS E 139 
 PHE   0.017   0.001   PHE F 120 
 TYR   0.024   0.001   TYR F   9 
 ARG   0.007   0.000   ARG E 126 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 MET cc_start: 0.7382 (tpp) cc_final: 0.6741 (tpp)
REVERT: D   42 MET cc_start: 0.8740 (tpp) cc_final: 0.8321 (tpp)
REVERT: E   42 MET cc_start: 0.8238 (tpp) cc_final: 0.8027 (tpt)
REVERT: E  121 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8667 (pt0)
REVERT: F  134 GLN cc_start: 0.8433 (pt0) cc_final: 0.7774 (mt0)
REVERT: G   82 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8670 (tm-30)
REVERT: G  142 GLN cc_start: 0.7195 (mt0) cc_final: 0.6653 (mp10)
REVERT: H   42 MET cc_start: 0.8630 (tpp) cc_final: 0.8166 (tpp)
REVERT: I  136 LYS cc_start: 0.7994 (mptt) cc_final: 0.7789 (mttt)
REVERT: J   47 ASP cc_start: 0.6133 (t70) cc_final: 0.5855 (t0)
REVERT: J  107 TRP cc_start: 0.6766 (t-100) cc_final: 0.6452 (m100)
REVERT: J  111 ASP cc_start: 0.5738 (m-30) cc_final: 0.4917 (m-30)
REVERT: J  124 ASP cc_start: 0.6940 (m-30) cc_final: 0.5810 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2184
  time to fit residues: 27.2850
Evaluate side-chains
  65 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 106 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0570
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.9502

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 140 HIS
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.086991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.066500 restraints weight = 82562.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.066947 restraints weight = 54124.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.067144 restraints weight = 45215.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.6212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13020  Z= 0.241
  Angle     :  0.601   7.862  18187  Z= 0.341
  Chirality :  0.036   0.141   1992
  Planarity :  0.003   0.043   1778
  Dihedral  : 27.827 179.209   2986
  Min Nonbonded Distance : 1.369

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.68 %
    Favored  : 99.22 %
  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:  2.05 (0.26), residues: 1104
  helix:  1.94 (0.18), residues: 896
  sheet:  None (None), residues: 0
  loop : -1.23 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 107 
 HIS   0.006   0.001   HIS F  35 
 PHE   0.007   0.001   PHE I  83 
 TYR   0.026   0.002   TYR F   9 
 ARG   0.007   0.001   ARG E 126 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 MET cc_start: 0.7311 (tpp) cc_final: 0.6570 (tpp)
REVERT: D   42 MET cc_start: 0.8632 (tpp) cc_final: 0.8423 (tpp)
REVERT: E   42 MET cc_start: 0.8240 (tpp) cc_final: 0.8037 (tpt)
REVERT: E  140 HIS cc_start: 0.6792 (OUTLIER) cc_final: 0.6272 (p90)
REVERT: F  134 GLN cc_start: 0.8448 (pt0) cc_final: 0.7885 (mt0)
REVERT: G   42 MET cc_start: 0.7981 (tpt) cc_final: 0.7534 (tpp)
REVERT: H   42 MET cc_start: 0.8650 (tpp) cc_final: 0.8161 (tpp)
REVERT: H   43 VAL cc_start: 0.9431 (t) cc_final: 0.9215 (p)
REVERT: I  136 LYS cc_start: 0.7988 (mptt) cc_final: 0.7788 (mttt)
REVERT: J   42 MET cc_start: 0.7318 (mmp) cc_final: 0.7081 (tpt)
REVERT: J   47 ASP cc_start: 0.6400 (t70) cc_final: 0.6141 (t0)
REVERT: J  107 TRP cc_start: 0.6772 (t-100) cc_final: 0.6459 (m100)
REVERT: J  111 ASP cc_start: 0.6048 (m-30) cc_final: 0.5478 (m-30)
REVERT: J  124 ASP cc_start: 0.7394 (m-30) cc_final: 0.6297 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 73
  average time/residue: 0.2064
  time to fit residues: 24.0784
Evaluate side-chains
  61 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 99 optimal weight:    0.0980
   chunk 59 optimal weight:    0.2980
   chunk 102 optimal weight:    0.5980
   chunk 107 optimal weight:    9.9990
   chunk 45 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 120 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 134 GLN
** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.086662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.065386 restraints weight = 79538.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.064079 restraints weight = 56512.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.064183 restraints weight = 47340.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.6227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13020  Z= 0.170
  Angle     :  0.557   7.598  18187  Z= 0.315
  Chirality :  0.035   0.134   1992
  Planarity :  0.003   0.025   1778
  Dihedral  : 27.790 179.731   2986
  Min Nonbonded Distance : 1.406

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.20 %
    Favored  : 99.71 %
  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:  2.34 (0.26), residues: 1104
  helix:  2.13 (0.18), residues: 896
  sheet:  None (None), residues: 0
  loop : -1.08 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 107 
 HIS   0.007   0.001   HIS H 140 
 PHE   0.020   0.002   PHE C 120 
 TYR   0.027   0.001   TYR F   9 
 ARG   0.007   0.000   ARG E 126 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 MET cc_start: 0.7490 (tpp) cc_final: 0.6709 (tpp)
REVERT: D   42 MET cc_start: 0.8848 (tpp) cc_final: 0.8309 (tpp)
REVERT: D  134 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7973 (mm-40)
REVERT: F   42 MET cc_start: 0.8830 (ttt) cc_final: 0.8372 (tpp)
REVERT: F  134 GLN cc_start: 0.8438 (pt0) cc_final: 0.7900 (mt0)
REVERT: G   42 MET cc_start: 0.8056 (tpt) cc_final: 0.7597 (tpp)
REVERT: G  142 GLN cc_start: 0.7350 (mt0) cc_final: 0.6786 (mp10)
REVERT: H   42 MET cc_start: 0.8757 (tpp) cc_final: 0.8179 (tpp)
REVERT: J   42 MET cc_start: 0.7492 (mmp) cc_final: 0.7188 (tpp)
REVERT: J   47 ASP cc_start: 0.6102 (t70) cc_final: 0.5866 (t0)
REVERT: J  107 TRP cc_start: 0.6833 (t-100) cc_final: 0.6510 (m100)
REVERT: J  111 ASP cc_start: 0.6316 (m-30) cc_final: 0.5747 (m-30)
REVERT: J  124 ASP cc_start: 0.7421 (m-30) cc_final: 0.6379 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 74
  average time/residue: 0.2133
  time to fit residues: 24.7201
Evaluate side-chains
  64 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 29 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 84 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.086242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.064282 restraints weight = 79953.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.064715 restraints weight = 50862.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.064641 restraints weight = 41567.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.6401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13020  Z= 0.193
  Angle     :  0.573   8.953  18187  Z= 0.326
  Chirality :  0.035   0.137   1992
  Planarity :  0.003   0.023   1778
  Dihedral  : 27.746 179.663   2986
  Min Nonbonded Distance : 1.395

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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:  2.30 (0.26), residues: 1104
  helix:  2.10 (0.18), residues: 896
  sheet:  None (None), residues: 0
  loop : -1.08 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 107 
 HIS   0.005   0.001   HIS E 139 
 PHE   0.044   0.002   PHE J  83 
 TYR   0.028   0.001   TYR F   9 
 ARG   0.006   0.000   ARG E 126 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3680.77 seconds
wall clock time: 67 minutes 28.99 seconds (4048.99 seconds total)