Starting phenix.real_space_refine
on Thu Feb 15 10:33:37 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cze_27096/02_2024/8cze_27096.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cze_27096/02_2024/8cze_27096.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cze_27096/02_2024/8cze_27096.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cze_27096/02_2024/8cze_27096.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cze_27096/02_2024/8cze_27096.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cze_27096/02_2024/8cze_27096.pdb"
  }
  resolution = 2.58
  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=  -0.001 sd=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     P     292      5.49       5
     S      12      5.16       5
     C    6646      2.51       5
     N    2258      2.21       5
     O    2821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 12029
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 801
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 3009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3009
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 2977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2977
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
  Time building chain proxies: 6.71, per 1000 atoms: 0.56
  Number of scatterers: 12029
  At special positions: 0
  Unit cell: (79.2, 118.8, 126.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     292     15.00
     O    2821      8.00
     N    2258      7.00
     C    6646      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  - 3.50
        Amino acid           : False - 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: 5.41
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      72.1% alpha, 2.6% beta
      133 base pairs and 267 stacking pairs defined.
    Time for finding SS restraints: 5.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.520A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.845A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 4.352A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.720A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.523A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.378A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.668A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.541A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.568A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.863A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.525A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 121
      removed outlier: 3.859A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA D 121 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.520A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.846A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 4.352A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.719A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.523A  pdb=" N   ILE F  34 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.378A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.668A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.541A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.568A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.862A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.525A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 3.858A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA H 121 " --> pdb=" O   LYS H 117 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.989A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.511A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.717A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.385A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.008A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.557A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.417A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    374 hydrogen bonds defined for protein.
    1098 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      345 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      133 basepair parallelities
      267 stacking parallelities
  Total time for adding SS restraints: 3.95

  Time building geometry restraints manager: 5.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2427
        1.34 -     1.45: 4063
        1.45 -     1.57: 5743
        1.57 -     1.69: 582
        1.69 -     1.81: 22
  Bond restraints: 12837
  Sorted by residual:
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.81e+00
  bond pdb=" C   GLU C  61 "
       pdb=" O   GLU C  61 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.013 1.15e-02 7.56e+03 1.23e+00
  bond pdb=" C   GLU G  61 "
       pdb=" O   GLU G  61 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.012 1.15e-02 7.56e+03 1.15e+00
  bond pdb=" C3'  DC I  30 "
       pdb=" C2'  DC I  30 "
    ideal  model  delta    sigma   weight residual
    1.525  1.546 -0.021 2.00e-02 2.50e+03 1.08e+00
  bond pdb=" C3'  DC J  21 "
       pdb=" C2'  DC J  21 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.00e-02 2.50e+03 1.01e+00
  ... (remaining 12832 not shown)

  Histogram of bond angle deviations from ideal:
       98.90 -   105.64: 1434
      105.64 -   112.39: 7014
      112.39 -   119.14: 3409
      119.14 -   125.88: 5786
      125.88 -   132.63: 952
  Bond angle restraints: 18595
  Sorted by residual:
  angle pdb=" C3'  DC I  52 "
        pdb=" O3'  DC I  52 "
        pdb=" P    DC I  53 "
      ideal   model   delta    sigma   weight residual
     120.20  123.32   -3.12 1.50e+00 4.44e-01 4.32e+00
  angle pdb=" N   LYS B  31 "
        pdb=" CA  LYS B  31 "
        pdb=" C   LYS B  31 "
      ideal   model   delta    sigma   weight residual
     109.81  114.04   -4.23 2.21e+00 2.05e-01 3.66e+00
  angle pdb=" N   LYS F  31 "
        pdb=" CA  LYS F  31 "
        pdb=" C   LYS F  31 "
      ideal   model   delta    sigma   weight residual
     109.81  114.01   -4.20 2.21e+00 2.05e-01 3.61e+00
  angle pdb=" O4'  DC I -25 "
        pdb=" C1'  DC I -25 "
        pdb=" C2'  DC I -25 "
      ideal   model   delta    sigma   weight residual
     106.40  103.60    2.80 1.50e+00 4.44e-01 3.49e+00
  angle pdb=" C3'  DC I -40 "
        pdb=" C2'  DC I -40 "
        pdb=" C1'  DC I -40 "
      ideal   model   delta    sigma   weight residual
     101.60  104.36   -2.76 1.50e+00 4.44e-01 3.38e+00
  ... (remaining 18590 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.85: 5600
       33.85 -    67.70: 1366
       67.70 -   101.55: 3
      101.55 -   135.40: 0
      135.40 -   169.24: 1
  Dihedral angle restraints: 6970
    sinusoidal: 4755
      harmonic: 2215
  Sorted by residual:
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   50.76  169.24     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.25   14.75     0      5.00e+00 4.00e-02 8.70e+00
  dihedral pdb=" CA  PRO D 100 "
           pdb=" C   PRO D 100 "
           pdb=" N   GLY D 101 "
           pdb=" CA  GLY D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.28   14.72     0      5.00e+00 4.00e-02 8.67e+00
  ... (remaining 6967 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1409
       0.026 -    0.052: 482
       0.052 -    0.079: 164
       0.079 -    0.105: 38
       0.105 -    0.131: 30
  Chirality restraints: 2123
  Sorted by residual:
  chirality pdb=" CA  ILE B  46 "
            pdb=" N   ILE B  46 "
            pdb=" C   ILE B  46 "
            pdb=" CB  ILE B  46 "
    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 G  79 "
            pdb=" N   ILE G  79 "
            pdb=" C   ILE G  79 "
            pdb=" CB  ILE G  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE C  79 "
            pdb=" N   ILE C  79 "
            pdb=" C   ILE C  79 "
            pdb=" CB  ILE C  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 2120 not shown)

  Planarity restraints: 1341
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J -49 "    0.025 2.00e-02 2.50e+03   1.06e-02 3.39e+00
        pdb=" N9   DG J -49 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8   DG J -49 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG J -49 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG J -49 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG J -49 "    0.002 2.00e-02 2.50e+03
        pdb=" O6   DG J -49 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DG J -49 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DG J -49 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2   DG J -49 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DG J -49 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG J -49 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  47 "    0.022 2.00e-02 2.50e+03   9.85e-03 2.67e+00
        pdb=" N9   DA I  47 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DA I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  47 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I  47 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DA I  47 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -35 "   -0.022 2.00e-02 2.50e+03   9.05e-03 2.45e+00
        pdb=" N9   DG I -35 "    0.020 2.00e-02 2.50e+03
        pdb=" C8   DG I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I -35 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I -35 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1   DG I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I -35 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I -35 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1338 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2335
        2.81 -     3.33: 9353
        3.33 -     3.85: 20452
        3.85 -     4.38: 25395
        4.38 -     4.90: 36571
  Nonbonded interactions: 94106
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH2 ARG E 131 "
     model   vdw
     2.285 2.520
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH2 ARG A 131 "
     model   vdw
     2.286 2.520
  nonbonded pdb=" OD1 ASP C  90 "
            pdb=" N   GLU C  91 "
     model   vdw
     2.350 2.520
  nonbonded pdb=" OD1 ASP G  90 "
            pdb=" N   GLU G  91 "
     model   vdw
     2.351 2.520
  nonbonded pdb=" O   THR G  10 "
            pdb=" OG1 THR G  10 "
     model   vdw
     2.381 2.440
  ... (remaining 94101 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 38 through 133 or (resid 134 and (name N or name CA or nam \ 
e C or name O or name CB ))))
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  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:          4.260
  Check model and map are aligned:         0.180
  Set scattering table:                    0.100
  Process input model:                     37.360
  Find NCS groups from input model:        0.450
  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:             0.000
  Load rotamer database and sin/cos tables:12.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
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      :  0.004   0.040  12837  Z= 0.194
  Angle     :  0.553   5.134  18595  Z= 0.339
  Chirality :  0.033   0.131   2123
  Planarity :  0.004   0.033   1341
  Dihedral  : 25.806 169.245   5540
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  4.42 %
    Favored  : 95.26 %
  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:  2.43 (0.31), residues: 747
  helix:  2.98 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -1.74 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.009   0.001   TYR C  50 
 ARG   0.003   0.000   ARG F  39 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.991 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7113 (t0)
REVERT: C   75 LYS cc_start: 0.8483 (mmtp) cc_final: 0.8183 (mmtp)
REVERT: C   99 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7910 (mtp85)
REVERT: D   31 LYS cc_start: 0.8645 (mttm) cc_final: 0.8353 (mtmm)
REVERT: D   59 MET cc_start: 0.9122 (mmp) cc_final: 0.8880 (mmm)
REVERT: D   65 ASP cc_start: 0.9239 (t0) cc_final: 0.8871 (t0)
REVERT: D   73 GLU cc_start: 0.9108 (tp30) cc_final: 0.8683 (tp30)
REVERT: E  105 GLU cc_start: 0.8015 (tt0) cc_final: 0.7738 (mt-10)
REVERT: F   74 GLU cc_start: 0.8251 (tt0) cc_final: 0.8015 (tt0)
REVERT: G   73 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.6892 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 119
  average time/residue: 1.9778
  time to fit residues: 248.0321
Evaluate side-chains
  101 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain G residue   73 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    2.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.0903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12837  Z= 0.285
  Angle     :  0.574   5.465  18595  Z= 0.352
  Chirality :  0.036   0.135   2123
  Planarity :  0.005   0.038   1341
  Dihedral  : 29.007 168.859   4046
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  9.32 %
    Favored  : 89.10 %
  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:  2.49 (0.31), residues: 747
  helix:  3.01 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.80 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  31 
 PHE   0.015   0.002   PHE F  61 
 TYR   0.011   0.002   TYR G  50 
 ARG   0.004   0.001   ARG A  49 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.997 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8880 (mtt) cc_final: 0.8597 (mtm)
REVERT: C   73 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7055 (t0)
REVERT: C   99 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7929 (mtp85)
REVERT: D   59 MET cc_start: 0.9161 (mmp) cc_final: 0.8910 (mmm)
REVERT: D   65 ASP cc_start: 0.9275 (t0) cc_final: 0.8803 (t0)
REVERT: D   73 GLU cc_start: 0.9047 (tp30) cc_final: 0.8507 (tp30)
REVERT: F   74 GLU cc_start: 0.8337 (tt0) cc_final: 0.8102 (tt0)
REVERT: G   73 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6820 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 111
  average time/residue: 2.0083
  time to fit residues: 235.0412
Evaluate side-chains
  109 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 90 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.0913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12837  Z= 0.238
  Angle     :  0.565   7.312  18595  Z= 0.346
  Chirality :  0.034   0.132   2123
  Planarity :  0.004   0.038   1341
  Dihedral  : 29.006 168.887   4046
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.11 %
    Favored  : 88.31 %
  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:  2.46 (0.31), residues: 747
  helix:  2.99 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.82 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H 106 
 PHE   0.012   0.002   PHE F  61 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.002   0.000   ARG E 131 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8853 (mtt) cc_final: 0.8555 (mtm)
REVERT: C   73 ASN cc_start: 0.7625 (t0) cc_final: 0.6996 (t0)
REVERT: C   99 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7903 (mtp85)
REVERT: D   31 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8440 (mtmm)
REVERT: D   65 ASP cc_start: 0.9271 (t0) cc_final: 0.8806 (t0)
REVERT: D   73 GLU cc_start: 0.9050 (tp30) cc_final: 0.8508 (tp30)
REVERT: F   74 GLU cc_start: 0.8324 (tt0) cc_final: 0.8074 (tt0)
REVERT: G   73 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.6760 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 108
  average time/residue: 1.9615
  time to fit residues: 223.0579
Evaluate side-chains
  111 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 91 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 86 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    2.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12837  Z= 0.284
  Angle     :  0.574   5.417  18595  Z= 0.352
  Chirality :  0.036   0.136   2123
  Planarity :  0.005   0.039   1341
  Dihedral  : 28.999 169.083   4044
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  9.95 %
    Favored  : 87.99 %
  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 (0.31), residues: 747
  helix:  2.94 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.89 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  31 
 PHE   0.013   0.002   PHE F  61 
 TYR   0.010   0.002   TYR G  50 
 ARG   0.007   0.001   ARG H  30 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.998 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8896 (mtt) cc_final: 0.8586 (mtm)
REVERT: B   59 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8818 (tppt)
REVERT: B   84 MET cc_start: 0.9053 (mmp) cc_final: 0.8259 (mmp)
REVERT: C   73 ASN cc_start: 0.7597 (t0) cc_final: 0.7031 (t0)
REVERT: C   99 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7871 (mtp85)
REVERT: D   65 ASP cc_start: 0.9269 (t0) cc_final: 0.8801 (t0)
REVERT: D   73 GLU cc_start: 0.9042 (tp30) cc_final: 0.8510 (tp30)
REVERT: D   82 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8977 (mtpt)
REVERT: F   74 GLU cc_start: 0.8349 (tt0) cc_final: 0.8110 (tt0)
REVERT: G   73 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6970 (t0)
  outliers start: 13
  outliers final: 7
  residues processed: 116
  average time/residue: 1.8985
  time to fit residues: 232.2277
Evaluate side-chains
  112 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 66 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12837  Z= 0.216
  Angle     :  0.570   7.249  18595  Z= 0.348
  Chirality :  0.034   0.126   2123
  Planarity :  0.004   0.037   1341
  Dihedral  : 29.001 169.068   4044
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.01 %
    Favored  : 86.26 %
  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:  2.41 (0.31), residues: 747
  helix:  2.97 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.89 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS D  46 
 PHE   0.010   0.002   PHE F  61 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.002   0.000   ARG B  39 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8855 (mtt) cc_final: 0.8547 (mtm)
REVERT: B   59 LYS cc_start: 0.9024 (ttmm) cc_final: 0.8809 (tppt)
REVERT: C   73 ASN cc_start: 0.7546 (t0) cc_final: 0.6987 (t0)
REVERT: C   99 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7852 (mtp85)
REVERT: D   65 ASP cc_start: 0.9262 (t0) cc_final: 0.8804 (t0)
REVERT: D   73 GLU cc_start: 0.9038 (tp30) cc_final: 0.8486 (tp30)
REVERT: D   82 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8976 (mtpt)
REVERT: F   74 GLU cc_start: 0.8326 (tt0) cc_final: 0.8093 (tt0)
REVERT: G   73 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6897 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 108
  average time/residue: 1.9623
  time to fit residues: 223.1682
Evaluate side-chains
  112 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 96 optimal weight:    6.9990
   chunk 80 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.1782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12837  Z= 0.198
  Angle     :  0.547   5.189  18595  Z= 0.337
  Chirality :  0.033   0.123   2123
  Planarity :  0.004   0.038   1341
  Dihedral  : 28.983 169.422   4044
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.48 %
    Favored  : 85.62 %
  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:  2.55 (0.31), residues: 747
  helix:  3.08 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.84 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 106 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.008   0.001   TYR G  50 
 ARG   0.008   0.000   ARG H  30 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8816 (mtt) cc_final: 0.8500 (mtm)
REVERT: B   59 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8801 (tppt)
REVERT: B   84 MET cc_start: 0.8990 (mmp) cc_final: 0.8292 (mmp)
REVERT: C   73 ASN cc_start: 0.7499 (t0) cc_final: 0.6925 (t0)
REVERT: C   99 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7849 (mtp85)
REVERT: D   65 ASP cc_start: 0.9264 (t0) cc_final: 0.8814 (t0)
REVERT: D   73 GLU cc_start: 0.9039 (tp30) cc_final: 0.8503 (tp30)
REVERT: D   82 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8968 (mtpt)
REVERT: D  109 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8584 (m)
REVERT: F   74 GLU cc_start: 0.8287 (tt0) cc_final: 0.8050 (tt0)
REVERT: G   73 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6743 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 110
  average time/residue: 1.8471
  time to fit residues: 214.5667
Evaluate side-chains
  112 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   chunk 60 optimal weight:    0.0980
   chunk 58 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12837  Z= 0.172
  Angle     :  0.534   5.884  18595  Z= 0.329
  Chirality :  0.032   0.124   2123
  Planarity :  0.004   0.039   1341
  Dihedral  : 28.972 169.333   4044
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.74 %
    Favored  : 84.52 %
  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:  2.70 (0.31), residues: 747
  helix:  3.19 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.77 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS D 106 
 PHE   0.008   0.001   PHE B  61 
 TYR   0.007   0.001   TYR G  50 
 ARG   0.009   0.000   ARG B  23 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.847 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8720 (mtt) cc_final: 0.8396 (mtm)
REVERT: B   84 MET cc_start: 0.8986 (mmp) cc_final: 0.8300 (mmp)
REVERT: C   73 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6784 (t0)
REVERT: C   99 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7839 (mtp85)
REVERT: D   65 ASP cc_start: 0.9191 (t0) cc_final: 0.8716 (t0)
REVERT: D   73 GLU cc_start: 0.9040 (tp30) cc_final: 0.8536 (tp30)
REVERT: D   82 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8937 (mtpt)
REVERT: D  109 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8576 (m)
REVERT: F   74 GLU cc_start: 0.8222 (tt0) cc_final: 0.7999 (tt0)
REVERT: G   73 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6699 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 107
  average time/residue: 1.8768
  time to fit residues: 211.7758
Evaluate side-chains
  111 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   chunk 87 optimal weight:    8.9990
   chunk 92 optimal weight:    5.9990
   chunk 84 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    2.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12837  Z= 0.291
  Angle     :  0.575   5.658  18595  Z= 0.350
  Chirality :  0.036   0.139   2123
  Planarity :  0.005   0.039   1341
  Dihedral  : 28.991 168.697   4044
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.90 %
    Favored  : 84.20 %
  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:  2.50 (0.31), residues: 747
  helix:  3.05 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.89 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 106 
 PHE   0.013   0.002   PHE F  61 
 TYR   0.009   0.002   TYR G  50 
 ARG   0.009   0.000   ARG H  30 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8897 (mtt) cc_final: 0.8579 (mtm)
REVERT: B   84 MET cc_start: 0.9062 (mmp) cc_final: 0.8335 (mmp)
REVERT: C   73 ASN cc_start: 0.7492 (t0) cc_final: 0.6851 (t0)
REVERT: C   99 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7870 (mtp85)
REVERT: D   65 ASP cc_start: 0.9281 (t0) cc_final: 0.8828 (t0)
REVERT: D   73 GLU cc_start: 0.9037 (tp30) cc_final: 0.8493 (tp30)
REVERT: D   82 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8963 (mtpt)
REVERT: D  109 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8620 (m)
REVERT: F   74 GLU cc_start: 0.8347 (tt0) cc_final: 0.8118 (tt0)
REVERT: G   73 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.6950 (t0)
REVERT: G  118 LYS cc_start: 0.8230 (tppt) cc_final: 0.7943 (tppt)
  outliers start: 12
  outliers final: 6
  residues processed: 111
  average time/residue: 1.9945
  time to fit residues: 232.9988
Evaluate side-chains
  114 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 84 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    2.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12837  Z= 0.308
  Angle     :  0.596   6.724  18595  Z= 0.362
  Chirality :  0.036   0.141   2123
  Planarity :  0.005   0.039   1341
  Dihedral  : 28.989 169.188   4044
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.06 %
    Favored  : 83.89 %
  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:  2.32 (0.31), residues: 747
  helix:  2.91 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.95 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  46 
 PHE   0.013   0.002   PHE F  61 
 TYR   0.009   0.002   TYR E  54 
 ARG   0.006   0.000   ARG H  30 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8921 (mtt) cc_final: 0.8626 (mtm)
REVERT: C   73 ASN cc_start: 0.7671 (t0) cc_final: 0.7032 (t0)
REVERT: C   99 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7769 (mtp85)
REVERT: D   65 ASP cc_start: 0.9297 (t0) cc_final: 0.8991 (t0)
REVERT: D   73 GLU cc_start: 0.9029 (tp30) cc_final: 0.8484 (tp30)
REVERT: D   82 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8989 (mtpt)
REVERT: D  109 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8632 (m)
REVERT: F   74 GLU cc_start: 0.8372 (tt0) cc_final: 0.8132 (tt0)
REVERT: G   73 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7018 (t0)
REVERT: G  118 LYS cc_start: 0.8204 (tppt) cc_final: 0.7934 (tppt)
  outliers start: 13
  outliers final: 8
  residues processed: 109
  average time/residue: 1.9546
  time to fit residues: 224.1394
Evaluate side-chains
  114 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 1.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 66 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12837  Z= 0.195
  Angle     :  0.568   6.991  18595  Z= 0.347
  Chirality :  0.034   0.127   2123
  Planarity :  0.004   0.039   1341
  Dihedral  : 28.984 169.512   4044
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.53 %
    Favored  : 84.04 %
  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:  2.41 (0.31), residues: 747
  helix:  2.99 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.92 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS D 106 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.009   0.001   TYR B  51 
 ARG   0.007   0.000   ARG H  30 

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.988 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8851 (mtt) cc_final: 0.8548 (mtm)
REVERT: C   73 ASN cc_start: 0.7591 (t0) cc_final: 0.7018 (t0)
REVERT: C   99 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7763 (mtp85)
REVERT: D   65 ASP cc_start: 0.9282 (t0) cc_final: 0.8833 (t0)
REVERT: D   73 GLU cc_start: 0.9031 (tp30) cc_final: 0.8468 (tp30)
REVERT: D   82 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8987 (mtpt)
REVERT: F   74 GLU cc_start: 0.8323 (tt0) cc_final: 0.8083 (tt0)
REVERT: G   73 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.6967 (t0)
REVERT: G  118 LYS cc_start: 0.8192 (tppt) cc_final: 0.7926 (tppt)
  outliers start: 9
  outliers final: 7
  residues processed: 107
  average time/residue: 2.0077
  time to fit residues: 226.1508
Evaluate side-chains
  110 residues out of total 635 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.9180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.088610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.066541 restraints weight = 20901.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.59
r_work: 0.2771 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12837  Z= 0.192
  Angle     :  0.567   7.107  18595  Z= 0.346
  Chirality :  0.033   0.126   2123
  Planarity :  0.004   0.039   1341
  Dihedral  : 28.982 169.539   4044
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.38 %
    Favored  : 84.04 %
  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:  2.44 (0.31), residues: 747
  helix:  3.00 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.91 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS D 106 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.009   0.001   TYR B  51 
 ARG   0.006   0.000   ARG H  30 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3966.38 seconds
wall clock time: 70 minutes 54.25 seconds (4254.25 seconds total)